In the last 22 years since I have been in the genomics space, my teams (Mapmygenome, Ocimum Biosolutions, Genelogic ) have published in journals like Nature , JAMA , PLOS and more. What is also very exciting is the thousands of publications that refer our products and services. As a science based organization, one of the key differentiators is that not only do we need to do high quality science but we need to communicate our science to the end consumers of this technology. If we understand the science well, we can communicate it well too. For that purpose we have a blog on the mapmygenome page mapmygenome.in/blog

The first section shows a select 21 recent publications from the team.

Select Publications by Mapmygenome Team

Patents ( Mapmygenome)

Sequencing Services

BioExpress Publications

Ascenta

Genchek/ Genowiz/OptGene/Irnacheck

Spoligotyping

Toxexpress

LIMS – Biotracker

 

Select Publications by Mapmygenome Team 

1. [HTML] A Review on the Challenges in Indian Genomics Research for Variant Identification and Interpretation

SK Pemmasani, R Raman, R Mohapatra… – Frontiers in …, 2020 – frontiersin.org

Today, genomic data holds great potential to improve healthcare strategies across various
dimensions – be it disease prevention, enhanced diagnosis or optimized treatment. The

2. Prevalence of SARS-CoV-2 in Karnataka, India

M Mohanan, A Malani, K Krishnan, A Acharya – Jama, 2021 – jamanetwork.com Methods| This study was approved by the Indian government and institutional review boards at participating institutions. Written informed consent was obtained from all participants (…

3 [HTML] WIP1 phosphatase as a potential therapeutic target in neuroblastoma

…, T Dayaram, AG Gilmartin, G Ganji, SK Pemmasani… – PloS one, 2015 – journals.plos.org

The wild-type p53-induced phosphatase 1 (WIP1) is a serine/threonine phosphatase that
negatively regulates multiple proteins involved in DNA damage response including p53, CHK

4. Prevalence rates of ADIPOQ polymorphisms in Indian population and a comparison with other populations
Year
: 2018  |  Volume : 22  |  Issue : 1  |  Page : 36-40

Sandhya Kiran Pemmasani1, Rasika Raman2, Anuradha Acharya31 Genetics Department, Mapmygenome India Limited; Bioinformatics Department, Ocimum Biosolutions Limited, Hyderabad, Telangana, India2 Genetics Department, Mapmygenome India Limited, Hyderabad, Telangana, India3 Bioinformatics Department, Ocimum Biosolutions Limited, Hyderabad, Telangana, India

5. Comprehensive analysis of WGS and RNA-seq data to identify genetic variations in a patient with clear cell renal carcinoma

SK Pemmasani, N Chitturi, A Acharya – Molecular Genetics and Metabolism, 2021 – Elsevier

6. [HTML] Infectivity and progression of COVID-19 based on selected host candidate gene variants

GR Iyer, S Samajder, S Zubeda, V Mali, SK Pv… – Frontiers in …, 2020 – frontiersin.org

Introduction: Severe Acute Respiratory Syndrome Corona Virus- 2 (SARS-CoV-2) has spread
around the globe. Susceptibility has been associated with age, biological sex and other …

7. EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations.

Nature(2012)

8. Genome Wide Expression Analysis Suggests Perturbation of Vascular Homeostasis during High Altitude Pulmonary Edema

9. Polymorphism in RD1 locus and its effect  on downstream genes among South Indian clinical isolates of M.Tuberculosis

10. Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease. Nidhi Rawat,Sandhya P. Kiran,Dongliang Du,Fred G. GmitterJr andZhanao DengBMC Plant Biology201515:184 

11 Data Integration and Analysis: P.falciparum Microarray Data as a Case Study 

Rekha Rao Bioinformatics Scientist Ocimum Biosolutions Ltd. Ashwin Sivakumar Head-Research outreach Ocimum Biosolutions Ltd. Govind Rao Bioinformatics Product manager Ocimum Biosolutions Ltd. Hyderabad, (A.P.),

12 Differentially expressed genes in tumors of prostate cancer in American patients with European and African origin

K.Venkatesh, D.Lajwanti, Sandhya.P.Kiran, D.V.Raje, AnurajNayarisseri Journal of Pharmacy Research (2013).

13 Identification of cis-regulatory elements associated with salinity and drought stress tolerance in rice from co-expressed gene interaction networks

Pragya Mishra,Nisha Singh, Ajay Jain, Neha Jain, Vagish Mishra, Pushplatha G, Kiran P. Sandhya, Nagendra Kumar Singh and Vandna Rai Bioinformation. 2018; 14(3): 123–131doi: 10.6026/97320630014123

14. Impact of Human Exome Sequencing on Clinical Research
A Acharya, S Kannan, B Kumar… – … Ethics and Training: …, 2017 – books.google.com
247 Chapter 12 Impact of Human Exome Sequencing on Clinical Research Anu Acharya
Mapmygenome India, India Shibichakravarthy Kannan Ocimum Biosolutions, India Brajendra
Kumar Ocimum Biosolutions, India Jasmine Khurana Mapmygenome India, India Sushma

15. [BOOK] Pharmaceutical Outsourcing: Discovery and Preclinical Services
WC Stevens Jr, M Lim-Wilby – 2011 – books.google.com
Page 9. Contract Research Organizations 9. Turning Cells Into Reagents 167 Oliver
Klotzsche – CCS Cell Culture Service 10. Research as a Service (Raas) – Creating
a New Trend 182 Anu Acharya – Ocimum Biosolutions 11.

 16 Establishment and Characterization of Brain Cancer Primary Cell Cultures From Patients to Enable Phenotypic Screening for New Drugs

M dePadua, P Kulothungan, R Lath… – Frontiers in …, 2022 – ncbi.nlm.nih.govAim: Desmoplastic infantile ganglioglioma (DIG), is a rare tumor arising mainly during the first 2 years of life. Molecular characterization of these benign yet rapidly proliferating tumors

17 Current Perspective Of Pharmacogenomics In Clinical Practice In India

SR Nittu, K Ruchika, SM Ch, D Divya… – Annals of the …, 2021 – annalsofrscb.ro Pharmacogenomics is a new field of study that investigates how genetic characteristics influence a person’s drug response. Pharmacogenetics investigates” monogenetic variants” that 

18 Prevalence of COVID-19 in rural versus urban areas in a low-income country: findings from a State-Wide study in Karnataka, India M Mohanan, A Malani, K Krishnan… – University of Chicago …, 2021 – papers.ssrn.com

… The VTM we used was the CovisafeTM kit (manufactured by Mapmygenome) for collectingoropharyngeal swabs that make it possible to transport the swabs at ambient temperature

19 COVID-19 and Indian population: a comparative genetic analysis

S Patil, SK Pemmasani, N Chitturi, I Bhatnagar… – medRxiv, 2021 – medrxiv.org

Genotype data of these polymorphisms were either sourced from the GenomegaDB

database of Mapmygenome India Ltd. (sample size = 3054; Indian origin) or were imputed.

20 The influence of polymorphisms of fat mass and obesity (FTO, rs9939609) and vitamin D receptor (VDR, BsmI, TaqI, ApaI, FokI) genes on weight loss by diet and …

S Gulati, A Misra, R Tiwari, M Sharma… – European Journal of …, 2020 – nature.com Objective The aim of the present study was to evaluate polymorphisms of fat mass and obesity (FTO; rs9939609) and vitamin D receptor (VDR, FokI (rs2228570), BsmI (rs1544410), …

21 [PDF] PREVALENCE OF KRAS CODON 12 MUTATION IN PATIENTS WITH ORAL SQUAMOUS CELL CARCINOMA (OSCC) FROM SOUTH INDIAN POPULATION

S Gadde, S Poda, S Veeravalli, L Addala – academia.edu

Background: The RAS gene family is the most studied and best characterized of the known
cancer-related genes KRAS is the most frequently altered gene, with mutations occurring in …

22.  Detection of katG Ser315Thr substitution in Mycobacterium tuberculosis infected patients using PCR -RFLP method for screening Isoniazid-Resistance

SK Jadhav, SR Mote – Journal of HIV for Clinical and …, 2019 – peertechzpublications.com

Materials and Methods A total of ten Sputum samples which are TB Confirmed positive
samples were collected from primary health care centers Hyderabad. The patients are already …

23 Lack of the BRAF V600E Mutation in Oral Squamous Cell Carcinoma

S Gadde, S Poda, S Veeravilli, L Addala – 216.10.240.19

The aim of this study was to estimate the frequency of BRAF (V600E) mutation in oral squamous
cell carcinoma (OSCC) in the south Indian population. In the present study we analyzed 



 

Patents ( Mapmygenome) 

Mapymygenome Patent Published in the Official Journal of Patents, Dated: 18/11/2016

Patent Application no. 201641028519 A: 

Title : System and Method for Analysing an Individual’s Genomic Profile

Abstract: A method for analyzing an individual genomic profile to detect genetic predisposition to several diseases, traits and drug responses is disclosed. The biological sample is collected from an individual, DNA is extracted and hybridized onto a custom made microarray to generate SNP genotype calls. The genetic risks for selected set of conditions are calculated using algorithms that consider genotypes of all associated SNP’s. A genetic report is compiled,evaluated thoroughly by a genetic expert and then stored in the computer implemented laboratory information management system, called Biotracker.  The personalized report is then delivered to the client through BiotrackerTMs email facility and a counselling is conducted to every person by an in-house genetic counsellor to help understand and interpret the report correctly and a guidance is given with a Secondary Recommendation Report.

Sequencing Services 

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2012 

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Molecular characterisation of high-strength polycyclic aromatic hydrocarbon (PAH)-degrading and phenol-tolerant bacteria obtained from thermal power plant …

S Dalal, DP Panigrahi, GS Randhawa, RC Dubey – 2012 – Taylor & Francis

The amplified products were analysed using 2% w/v agarose gel. The desired band was cut and eluted. The products were sequenced through the sequencing service provided by Ocimum Biosolutions, Hyderabad, India.

Cited by 1Related articles

Enzymatic degradation of textile dye Reactive Orange 13 by newly isolated bacterial strain< i> Alcaligenes faecalis</i> PMS-1

PD Shah, SR Dave, MS Rao – International Biodeterioration & …, 2012 – Elsevier

photolytic activity etc. and based on these results the isolate was identified as Alcaligenes species. 16S rDNA sequencing of isolated bacteria was carried out at Ocimum Biosolutions, Hyderabad, India. The nucleotide sequence Cited by 1 [PDF] from jneuroinflammation.com

[PDF] Sphingosine 1-phosphate receptor 5 mediates the immune quiescence of the human brain endothelial barrier

R van Doorn, MAL Pinheiro, G Kooij… – Journal of …, 2012 – jneuroinflammation.com

All oligonucleotides were synthesized by Ocimum Biosolutions (Ocimum Biosolutions, Ijsselstein, The Netherlands) (Table 2), RNA was isolated using the qPCR reactions were performed in an ABI7900HT sequence detection system with the SYBR Green method (Applied View as HTML [HTML] from isrn.com

[HTML] Cloning, Sequencing and In Silico Analysis of Omp C of Salmonella Typhimurium

R Jha, A Kumar, A Saxena, S Tamuly… – ISRN Veterinary Science, 2012 – isrn.com

The recombinant clones were screened to obtain insert of desired size verified by  colony PCR amplification. The cloned product was sequenced by Ocimum Biosolutions Ltd., Hyderabad. The sequence was submitted to NCBI. 

Related articlesCachedAll 3 versions

[CITATION] Quantitative competitive PCR for the detection and quantification of genetically modified cotton event MON-531

D Narra, V Srivatsava – 2012

Simultaneous adsorption and bioaccumulation: A study on continuous mass transfer in column reactor

V Mishra, C Balomajumder… – … Progress & Sustainable …, 2012 – Wiley Online Library

The same was sent to Ocimum biosolutions, Hyderabad, India for sequencing. The nucleotide sequence similarity searches were conducted using BLAST program of NCBI and the phylogenetic analysis was carried out using the MEGA package version 4. Carrier Preparation.[PDF] from academicjournals.org

[PDF] In vitro characterization of Saccharomyces cerevisiae HM535662 obtained from an indigenous fermented food “Bhaturu” of Western Himalayas

A Sourabh, SS Kanwar… – African Journal of …, 2012 – academicjournals.org

3730xl automated sequencer) by using same upstream and downstream primers (Life Technologies India,Pvt. Ltd), by a commercial sequencing facility (Ocimum biosolutions, Pvt. Ltd. Hyderabad, India). View as HTML

Optimization of physical parameters for batch mode Zn (II) ion removal from liquid phase: A potential biosorption study

V Mishra, S Dalal, C Balomajumder – Environmental Progress & … – Wiley Online Library

Amplification was confirmed by running the PCR products on 1% agarose gel. A desired length was cut from the gel and purified using Bangalore Genei PCR purification kit, and after elution the product was sent to Ocimum biosolutions for sequencing. Related articles [PDF] from jcbsc.org

[PDF] Journal of Chemical, Biological and Physical Sciences

JA Johnson, T Citarasu, PAM Helen – jcbsc.org

Fr. Prem Kumar, Correspondent and Secretary, Malankara Catholic College, Mariagiri for his constant encouragement and support. We are also grateful to CEPC Laboratory, Kollam for the GC-MS analysis and Ocimum Biosolutions, Hyderabad for Sequencing work. View as HTML

[PDF] Differential Gene Expression Profile in Essential Hypertension

P Yang – cdn.intechopen.com

(47) SHR and BNR for the control Kidney Affymetrix U34A-C microarrays, validation by RT-PCR, DNA sequencing and RFLP analyses. Affymetrix Scanner 428, Imagene and Genowiz softwares by Ocimum Biosolutions (India) and subjected to arsinh transformation View as HTML

Cold-active extracellular α-amylase production from novel bacteria< i> Microbacterium foliorum</i> GA2 and< i> Bacillus cereus</i> GA6 isolated from Gangotri …

M Kuddus, IZ Ahmad – Journal of Genetic Engineering and Biotechnology, 2012 – Elsevier

processed for sequencing. Sequencing was carried out using the same set of primers in both directions to check the validity of the sequence. Sequencing was done by Ocimum Biosolutions, India. [PDF] from tubitak.gov.tr

[PDF] Full length cDNA synthesis of differentially displayed ESTs during lactation in the Indian buffalo (Bubalus bubalis)

AK TRIPATHI, KM SINGH, MN VAZE… – Turk. J. Vet. Anim …, 2012 – journals.tubitak.gov.tr

 Sequence analysis Analysis of the 5′ RACE amplified products of the respective ESTs was carried  out using Megablast. Seven sense primers were designed and commercially synthesized (OCIMUM BIOSOLUTIONS, Hyderabad) Related articlesView as HTML [PDF] from ias.ac.in

[PDF] Transcription of gD and gI gene in BHV-1 infected cells

S Chowdhury, B Sharma – ias.ac.in

RLM product was cloned into Pgemt easy TA vector and was sequenced through vendors (Ocimum Biosolutions, Hyderabad). The sequence was aligned with BHV-1 sequence and theTSS identified from the aligned sequence. Results: Computational analysis: View as HTML

Fingolimod attenuates ceramide-induced blood–brain barrier dysfunction in multiple sclerosis by targeting reactive astrocytes

R van Doorn, PG Nijland, N Dekker, ME Witte… – Acta …, 2012 – Springer

Oligonucleotides were synthesized by Ocimum Biosolutions (Ocimum Biosolutions, IJsselstein, The Netherlands). Quantitative PCR (qPCR) reactions were performed in an ABI7900HT sequence detection system using the SYBR Green method (Applied Biosys- tems, New York Cited by 1

Differential expression of silent polyketide biosynthesis gene clusters in chemostat cultures of< i> Aspergillus nidulans</i>

A Sarkar, AN Funk, K Scherlach, F Horn… – Journal of …, 2012 – Elsevier

Mining the A. nidulans full genome sequence revealed the existence of nearly 50 gene loci encoding polyketide synthases (PKSs) or nonribosomal peptide synthetases Custom made A.nidulans full genome microarrays (Ocimum Biosolutions) were used in these studies. .Related articlesAll 2 versions

Superparamagnetic Nanoparticles Based Immunomagnetic SeparationMultiplex Polymerase Chain Reaction Assay for Detection of Salmonella

B Padmavathy, A Patel, RV Kumar… – Science of Advanced …, 2012 – ingentaconnect.com

Four pairs of oligonucleotide primers based on the sequence of invA, prt, fliC, viaB genes are used for detec- tion of the presence of Salmonella Typhi and Salmonella All the oligonucleotide primers were custom synthesized from Ocimum Biosolutions Pvt Ltd., Netherlands.

Identification and distribution of putative virulence genes in clinical strains of Yersinia enterocolitica biovar 1A by suppression subtractive hybridization

P Kumar, JS Virdi – Journal of Applied Microbiology, 2012 – Wiley Online Library

sequenced directly using appropriate primers in either one or both directions. The commercial facilities provided by M/s Link Biotech (Ocimum Biosolutions, Delhi) and M/S Lab India (Gurgaon, India) were used for sequencing of the samples. The sequences obtained were [PDF] from virologyj.com

[PDF] Non structural protein of avian influenza A (H11N1) virus is a weaker suppressor of immune responses but capable of inducing apoptosis in host cells

S Mukherjee, S Majumdar, VC Vipat, AC Mishra… – Virology …, 2012 – virologyj.com

Amplicons cloned into pcDNA 3.0(-) expression vector (Invitrogen, Carlsbad, CA) were screened by sequencing. Data was analyzed using GENOWIZ Microarray and Pathway analysis tool (Ocimum Biosolutions, Hyderabad, India). View as HTML

Polymorphism in RD1 locus and its effect on down stream genes among South Indian clinical isolates of M. tuberculosis

AK Refaya, SS Kumar, S Balaji… – Journal of Medical …, 2012 – Soc General Microbiol

earlier (Baess 1974). Spoligotyping was performed with a commercially available kit 111 (Ocimum biosolutions, Hyderabad, India) according to the instructions of the 112 manufacturer. 134 135 Automated DNA sequencing 136

A novel mechanism of gall midge resistance in the rice variety Kavya revealed by microarray analysis

N Rawat, N Chiruvuri Naga… – Functional & integrative …, 2012 – Springer

RNA, target hybridization, as well as washing, staining, and scanning of the arrays were carried out by Ocimum Biosolutions (Hyderabad, India The data were analyzed using the 7500 Sequence Detection Software (Applied Biosystems, USA) with default baseline and threshold. Cited by 2 [PDF] from ias.ac.in

[PDF] Inhibition of HIV-1 Integrase gene expression by 10-23 DNAzyme

N Singh, A Ranjan, S Sur, R Chandra, V Tandon – Journal of biosciences, 2012 – ias.ac.in

The sequence GGCTAGCTACAACGA was a specific catalytic domain of 10-23 DNAzyme molecule, which was flanked by two substrate recognition arm of seven to nine deoxynucleotides. All the DNAzymes were synthesized by Ocimum Biosolutions, Hyderabad, India. Cited by 1View as HTML

GenoType MTBDRsl performance on clinical samples with diverse genetic background

P Miotto, AM Cabibbe, P Mantegani… – European …, 2012 – Eur Respiratory Soc

Sequencing. Genomic regions harbouring drug-resistance mutations were amplified and The amplified direct repeat locus of clinical isolates was investigated using the Spoligotyping kit (Ocimum Biosolutions, Hyderabad, India) following the manufacturer’s instructions. Cited by 1Related articlesAll 2 versions

A promising strain of Streptomyces sp. with agricultural traits for growth promotion and disease management

M Alam, S Dharni, SKS Abdul-Khaliq… – Indian Journal of …, 2012 – nopr.niscair.res.in

Primers were procured from Ocimum Biosolutions, India. The recombinants were selected byblue/white screening and recombinant plasmid DNA was isolated for further restriction analysis and sequencing of the insert on a 3130XL Genetic analyzer (Applied Biosystems, USA

Rapid and Sensitive Detection of Major Uropathogens in a Single-Pot Multiplex PCR Assay

B Padmavathy, R Vinoth Kumar, A Patel… – Current …, 2012 – Springer

Comparison with closely related species was found to predict no homology or less homology with the primer sequence used in the mPCR assay. All the primers were synthesized on custom-order from Ocimum Biosolutions, Netherlands. Optimization of Uniplex and mPCR

Performance comparison of multiple microarray platforms for gene expression profiling.

F Liu, WP Kuo, TK Jenssen, E Hovig – Methods in molecular biology ( …, 2012 – Springer

Following recent studies (17–19), we used probe sequence information to map probes both on levels of genes and Biosystems (ABI), Amersham (now GE Healthcare), Compugen (now Sigma-Genosys), Mergen, MWG BioTech (now Ocimum Biosolutions), Operon, “academic All 2 versions [PDF] from tjpr.org

Detection of Salmonella enterica serovars in shrimps in eight hours by multiplex PCR assay

G Jeyasekaran, KT Raj, RJ Shakila, AJ Thangarani… – Annals of …, 2012 – Springer 1992), while fimA, coding for the fimbrial gene, demonstrates a high degree of sequence conservation among Salmonella serovars (Cohen et al. 1996; Townsend et al. 2001). All primer sequences were synthe- sized by Ocimum Biosolutions (Indianapolis, IN). Related articlesAll 2 versions

Antagonism of microRNA Function in Zebrafish Embryos by Using Locked Nucleic Acid Enzymes (LNAzymes)

H Suryawanshi, MK Lalwani, S Ramasamy… – …, 2012 – Wiley Online Library

was exactly as previously described.18 All DNA and LNA oligonucleotides used in this study were purchased from Ocimum Biosolutions (Hyderabad, India RT products were then used for real-time PCR with mature miRNA sequence as the forward primer and the universal Cited by 1Related articlesAll 3 versions

Demonstration of sequential adaptation strategy for developing salt tolerance in bacteria for wastewater treatment: A study using< i> Escherichia coli</i> as model

S Puranik, S Shaligram, V Paliwal, DV Raje… – Bioresource …, 2012 – Elsevier The expression data for each sample was obtained on OciChip E.coli K-12 gene chip (M/s Ocimum Biosolutions, Hyderabad); the gene probe details with chip have been described in Supplementary Table 1. The Term and GO ID, Primer Sequence(5′-3′), Product length (bp).

Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae

MK Yadav, SK Kwon, CG Cho, SW Park… – Microbiology and …, 2012 – Wiley Online Library

Microarray data analysis was carried out by Genowiz 4.0TM (Ocimum Biosolutions, Hyderabad, India). Global lowess was used for data analysis with normalization. Primers were designed by standard procedures from nucleotide sequence of S. pneumoniae R6 strain

New insight into the molecular characterization of isoniazid and rifampicin resistant< i> Gene Expression Profiling of Escherichia coli in Response to Interactions with the Lettuce Rhizosphere

Z Hou, RC Fink, E Black, M Sugawara… – Journal of Applied …, 2012 – Wiley Online Library

2007). 2.4 Microarray expression analysis. Triplicate E. coli O157 microarrays (6 slides) (OciChip™,Ocimum Biosolutions Inc., Indianapolis, IN) were used in this study. primers listed in Table 2, using an ABI 7500 real-time PCR system with sequence detection [PDF] from mdpi.com

The Effect of Secretory Factors of Adipose-Derived Stem Cells on Human Keratinocytes

KM Moon, YH Park, JS Lee, YB Chae, MM Kim… – International journal of …, 2012 – mdpi.com

Trypsin spot Protein name Accession # Protein score Pep. count Position Sequence coverage 303 Type VI collagen, alpha-2, isoform 2C2a’ NP_478055 86 9 96–393 12% Trypsin spot Protein name Accession # Protein score Pep. count Position Sequence coverage Cited by 2Related articlesAll 5 versions

[PDF] Yersiniosis and Food Safety

K Isshiki, RC Ray, D Montet – downloads.hindawi.com

1, no. 4, pp. 323– 333, 1999. [7] X. Wang, Y. Li, H. Jing et al., “Complete genome sequence of a Yersinia enterocolitica “old world” (3/O:9) strain and comparison with the “new world” (1B/O:8) strain,” Journal of Clinical Microbiology, vol. 49, no. 4, pp. 2.1.1. Sequence Retrieval. View as HTML

 [HTML] Functional Genomic Analysis of Candida glabrata-Macrophage Interaction: Role of Chromatin Remodeling in Virulence

MN Rai, S Balusu, N Gorityala, L Dandu, R Kaur – PLoS Pathogens, 2012 – dx.plos.org

the screen. Tn7 insertion in the identified mutants was mapped, by transposon rescue and sequencing analyses, to 56 C. glabrata ORFs and 20 intergenic regions (http://www.genolevures.org) (Tables S1 and S2). Using the

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Molecular cloning, overexpression, purification, crystallization and preliminary X-ray diffraction studies of histidinol phosphate aminotransferase (HisC2) from …

N Nasir, R Vyas, C Chugh… – … Section F: Structural …, 2011 – scripts.iucr.org

positive clones using the same restriction enzymes. The sequence and the directionality of the clone were confirmed by DNA sequencing (Ocimum Biosolutions, India). A construct with the following expression sequence, consisting Related articlesAll 3 versions

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[PDF] Potential of Alkaline Protease Isolated from Thermoactinomyces sp. RM4 as an Alternative to Conventional Chemicals in Leather Industry Dehairing Process

[PDF] from ndpublisher.in

A Verma, HS Pal, R Singh… – International Journal of …, 2011 – ndpublisher.in

Bergey’s manual (Pillai and Archana, 2008). Approximately 1,500- bp-sequence information of amplified fragment was obtained through the sequencing services provided by Ocimum Biosolutions Pvt. Ltd., Hyderabad, India. Cited by 1Related articlesView as HTMLAll 5 versions

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Roohi, M. Kuddus, IZ Ahmad and JM Arif

[HTML] from scialert.net

ISI Thomson – Asian Journal of Biotechnology, 2011 – scialert.net

The PCR amplicon for the partial 16S rRNA gene was further processed for sequencing. Sequencing was carried out using the same set of primers in both the directions to check the validity of the sequence. Sequencing was done by Ocimum Biosolutions, India. Related articlesCached

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[PDF] Production of Cold-active Extracellular a-Amylase by Newly Isolated Microbacterium foliorum GA2 from Gangotri glacier, Western Himalaya, India

[PDF] from docsdrive.com

MK Roohi, IZ Ahmad… – Asian Journal of Biotechnology, 2011 – docsdrive.com Sequencing was done by Ocimum Biosolutions, lndia. Antibiotic susceptibility and plasmid curing: The antibiotic susceptibility of the isolate was studied on Muller-Hinton agar media by disc diffusion methods (Bauer elf al., 1966). Cited by 2Related articlesAll 2 versions

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HisB from Mycobacterium tuberculosis: cloning, overexpression in Mycobacterium smegmatis, purification, crystallization and preliminary X-ray crystallographic …

MS Ahangar, Y Khandokar, N Nasir… – … Section F: Structural …, 2011 – scripts.iucr.org using T4 DNA ligase. Successful integration of the insert into the expression vector and its directionality were confirmed by DNA sequencing (Ocimum Biosolutions,Hyderabad, India). Table 1 Primers used for PCR amplification. Cited by 1Related articlesAll 3 versions

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Genome sequence of Avery’s virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6

[HTML] from nih.gov

JA Lanie, WL Ng, KM Kazmierczak… – Journal of …, 2007 – Am Soc Microbiol As was done previously (48), we inserted a placeholder sequence containing the five repeats reported previously for R6 into this region of the D39 genome sequence (see the text). (now available from Ocimum Biosolutions). Cited by 106Related articlesBL DirectAll 11 versions

BioExpress Publications

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To know more about  BioExpress® System please see

http://www.ocimumbio.com/bioexpress-system/

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[PDF] Identification of fat storage-inducing transmembrane proteins 1 and 2 as putative therapeutic targets for heart failure by integrated analysis of proteome and …

N Nishihama, Y Abe, K Kubota… – J Proteom …, 2018 – pdfs.semanticscholar.org

… The expression of all target genes in the heart was assessed by using the BioExpress database (GeneLogic, USA). Total RNA isolation and microarray analysis For the MI model, LV of three sham mice and four MI mice were used …

  Cited by 1 Related articles 

Klotho beta

L Desnoyers – US Patent App. 15/701,243, 2018 – Google Patents

… Whisker-box plots showing KLβ ( FIG. 4A ) and FGFR4 ( FIG. 4B ) expression in human tissues, as determined by mRNA analysis of the BioExpress database. The center line indicates the median; the box represents the inter-quartile range between the first and third quartiles …  All 2 versions PDF] googleapis.com

Compositions and methods for treating and diagnosing cancer

AL Gurney, A Sato – US Patent App. 15/631,259, 2018 – Google Patents

The present invention relates to compositions and methods for characterizing, diagnosing and treating cancer. In particular, the present invention identifies LGR5 as a protein over-expressed in solid tumor stem cell. The present invention further identifies an interaction between …  All 2 versions 

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2017

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Compositions and methods for treating and diagnosing cancer

AL Gurney, AK Sato – US Patent 9,717,794, 2017 – Google Patents

US9717794B2 – Compositions and methods for treating and diagnosing cancer – Google Patents. Compositions and methods for treating and diagnosing cancer. Download PDF Info. Publication number US9717794B2. US9717794B2 …  Related articles All 4 versions 

Compositions and Methods for Treating and Diagnosing Cancer

AL Gurney – US Patent App. 15/441,700, 2017 – Google Patents

The present invention relates to compositions and methods for characterizing, diagnosing and treating cancer. In particular, the present invention identifies LGR5 as a protein over-expressed in solid tumor stem cells. The present invention further identifies an interaction between …  All 2 versions 

Rspo binding agents and uses thereof

AL Gurney, FT Axelrod, TC Hoey… – US Patent App. 15 …, 2017 – Google Patents

US20170298143A1 – Rspo binding agents and uses thereof – Google Patents. Rspo binding agents and uses thereof. Download PDF Info. Publication number US20170298143A1. US20170298143A1 US15/480,081 US201715480081A …  All 2 versions 

Anti-RSPO2 antibodies and uses thereof

AL Gurney, FT Axelrod, TC Hoey… – US Patent …, 2017 – Google Patents

US9644034B2 – Anti-RSPO2 antibodies and uses thereof – Google Patents. Anti-RSPO2 antibodies and uses thereof. Download PDF Info. Publication number US9644034B2. US9644034B2 US14/795,811 US201514795811A …  Related articles All 2 versions 

RSPO3 binding agents and uses thereof

AL Gurney, CJ Bond – US Patent 9,598,497, 2017 – Google Patents

US9598497B2 – RSPO3 binding agents and uses thereof – Google Patents. RSPO3 binding agents and uses thereof. Download PDF Info. Publication number US9598497B2. US9598497B2 US14/870,145 US201514870145A …  Cited by 2 Related articles All 4 versions 

RSPO3 Binding Agents and Uses Thereof

AL Gurney, CJ Bond – US Patent App. 15/439,288, 2017 – Google Patents

The present invention relates to RSPO-binding agents, particularly RSPO3-binding agents and methods of using the agents for treating diseases such as cancer. The present invention provides antibodies that specifically bind human RSPO3 proteins and modulate β-catenin activity …  All 2 versions 

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Bruton tyrosine kinase–dependent immune cell cross-talk drives pancreas cancer

AJ Gunderson, MM Kaneda, T Tsujikawa, AV Nguyen… – Cancer discovery, 2016 – AACR

 Cited by 181 Related articles All 8 versions

[HTML] sciencedirect.com

[HTML] Bone health nutraceuticals alter microarray mRNA gene expression: A randomized, parallel, open-label clinical study

Y Lin, V Kazlova, S Ramakrishnan, MA Murray, D Fast… – Phytomedicine, 2016 – Elsevier

… using Feature Extraction software, version 9.5.3. Functionally annotated genes (those linked to any metabolic processes) were further analyzed for their relationship to bone health by comparison with the Gene Logic BioExpress ® gene expression database (Markowitz and …  Cited by 11 Related articles All 9 versions

Method to improve expression and other biological analysis

R Lehrer – US Patent App. 14/776,621, 2016 – Google Patents

… on a large number of biological samples. For example, Gene Logic’s BioExpress system is a database of 22,000 human tissue samples with data generated on the Aggy HU133 2+platform. The data may be selected as those …

  Related articles All 2 versions 

Anti-fgfr4 antibodies and methods of use

M Dennis, L Desnoyers, D French – US Patent App. 14/995,111, 2016 – Google Patents

… antibody). FIGS. 6A-6C : FGFR4 expression is deregulated in cancer. A, Whisker-box plots show FGFR4 expression in human tumors and normal tissues as determined by mRNA analysis of the BioExpress database. The center …  Cited by 1 Related articles All 2 versions 

Rspo binding agents and uses thereof

AL Gurney, FT Axelrod, TC Hoey… – US Patent App. 14 …, 2016 – Google Patents

US20160002344A1 – Rspo binding agents and uses thereof – Google Patents. 

Rspobinding agents and uses thereof. Download PDF Info. Publication number US20160002344A1. US20160002344A1 US14/795,811 US201514795811A …  All 2 versions 

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2014

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[HTML] Systematic evaluation of connectivity map for disease indications

J Cheng, L Yang, V Kumar… – Genome …, 2014 – genomemedicine.biomedcentral

 …… normal) across 124 human tissues were retrieved from the Gene Logic BioExpress™ system [20 … The BioExpress System provides gene expression data and associated clinical and pathological … For each study conducted at Genelogic, the research protocol was approved by one …  Cited by 43 Related articles All 12 versions 

IQGAP1 selectively interacts with K-Ras but not with H-Ras and modulates K-Ras function

H Matsunaga, K Kubota, T Inoue, F Isono… – … and biophysical research …, 2014 – Elsevier

… Expression data of IQGAP1 gene in normal pancreatic tissues (n = 28) and pancreatic adenocarcinomas (n = 44) were retrieved from BioExpress System (Gene Logic Division, Ocimum Biosolutions, Inc.), gene expression database containing human gene expression profiles …  Cited by 17 Related articles All 7 versions [HTML] sciencedirect.com

[HTML] B cells regulate macrophage phenotype and response to chemotherapy in squamous carcinomas

NI Affara, B Ruffell, TR Medler, AJ Gunderson… – Cancer cell, 2014 – Elsevier

… To address this, we queried cDNA microarray data on a panel of human tumors from the BioExpress System and assessed CD20 (MS4A1) and Ig (IGHG1, IGHG2, IGHV4-31, IGHM) mRNA expression relative to corresponding normal tissue …[PDF] googleapis.com

Organ-specific gene, method for identifying the same and use thereof

S Miyamoto, K Takami, A Horinouchi – US Patent App. 13/951,897, 2014 – Google Patents

… Example 1 Materials and Methods; [0111]. 1. Database Used and Method of Data Extraction. [0112]. Gene expression data on male C57BL/6 mice were extracted from BioExpress of GENE LOGIC™ on Apr. 21, 2006. The parameters [HTML] pharmaceuticalintelligence.com

[HTML] Archive for January, 2015

NS Abul-Husn, AO Obeng… – …, 2014 – pharmaceuticalintelligence.com

… pairs. The disease signatures were generated using Gene Logic BioExpress system and the compound profiles were derived from the Connectivity Map database (CMAP, build 02, http://www.broadinstitute.org/CMAP/). Results … 

Combining bioinformatics and MS-based proteomics: clinical implications

AE Acosta-Martin, L Lane – Expert review of proteomics, 2014 – Taylor & Francis
..Page 1. Combining bioinformatics and MS-based proteomics: clinical implications Expert Rev. Proteomics 11(3), 269–284 (2014) Adelina Elena Acosta-Martin*1,2 and Lydie Lane*1,3 1Department of Human Protein Sciences …

  Cited by 5 Related articles All 7 versions

Compositions and methods for treating and diagnosing cancer

A Gurney, AK Sato – US Patent 8,628,774, 2014 – Google Patents

US8628774B2 – Compositions and methods for treating and diagnosing cancer – Google Patents. Compositions and methods for treating and diagnosing cancer. Download PDF Info. Publication number US8628774B2. US8628774B2  Cited by 21 Related articles All 4 versions 

Compositions and methods for treating and diagnosing cancer

A Gurney – US Patent 8,883,736, 2014 – Google Patents

..The present invention relates to compositions and methods for characterizing, diagnosing and treating cancer. In particular, the present invention identifies LGR5 as a protein over-expressed in solid tumor stem cells. The present invention further identifies an interaction between …  Cited by 12 Related articles All 4 versions 

Anti-RSPO1 antibodies

AL Gurney, FT Axelrod, TC Hoey… – US Patent …, 2014 – Google Patents

..US8802097B2 – Anti-RSPO1 antibodies – Google Patents. Anti-RSPO1 antibodies. Publication number US8802097B2. US8802097B2 US13/549,050US201213549050A US8802097B2 US 8802097 B2 US8802097 …  Cited by 11 Related articles All 2 versions 

[PDF] Effect of novel glass-lonomer cements on human osteoblasts

J Sangsuwan – 2014 – kb.psu.ac.th

..Page 1. Effect of Novel Glass- Ionomer Cements on Human Osteoblasts Jiraporn Sangsuwan A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science in Molecular Biology and Bioinformatics Prince of Songkla University 2014 …

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2013

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[HTML] Major vault protein supports glioblastoma survival and migration by upregulating the EGFR/PI3K signalling axis

D Lötsch, E Steiner, K Holzmann, S Spiegl-Kreinecker… – Oncotarget, 2013 – ncbi.nlm.nih.gov

… A. MVP mRNA expression data in normal (green) and malignant (red) brain tissues as well as tumour cell cultures (yellow), determined by gene expression array analyses,were extracted from the BioExpress database (GeneLogic) …  Cited by 44 Related articles All 12 versions

Ocimum Biosolutions: Genomics Outsourcing in India

A Knauer – Women Entrepreneurs, 2013 – content.taylorfrancis.com

… Ocimum’s database, purchased in the Gene Logic acquisition, is con – sidered the largest and most comprehensive in the industry. There are a number of public databases available that lack the ease of use and reliability of information of BioExpress[PDF] googleapis.com

Organ-specific gene, method for identifying the same and use thereof

S Miyamoto, K Takami, A Horinouchi – US Patent 8,535,880, 2013 – Google Patents

… Gene expression data on male C57BL/6 mice were extracted from BioExpress of GENE LOGIC™ on Apr. 21, 2006 … [Results]. 1. Data Used. The data used were extracted from the gene expression database BioExpress, introduced from GENE LOGIC™ …  Related articles All 4 versions [PDF] googleapis.com

Antibody molecules specific for fibroblast activation protein and immunoconjugates containing them

G Adolf, E Ostermann, M Kalat, KH Heider – US Patent 8,568,727, 2013 – Google Patents

..Anti-FAP-antibodies and immunoconjugates, pharmaceutical compositions containing such conjugates, and their use in cancer therapy.  Cited by 16 Related articles All 4 versions [HTML] nih.gov

Gene expression in the human brain: the current state of the study of specificity and spatiotemporal dynamics

OY Naumova, M Lee, SY Rychkov… – Child …, 2013 – Wiley Online Library Skip to Main Content …  Cited by 32 Related articles All 9 versions

Compositions and methods for treating and diagnosing cancer

A Gurney – US Patent 8,540,989, 2013 – Google Patents

US8540989B2 – Compositions and methods for treating and diagnosing cancer – Google Patents. Compositions and methods for treating and diagnosing cancer. Download PDF Info. Publication number US8540989B2. US8540989B2 … Cited by 22 Related articles All 4 versions 

RSPO Binding Agents and Uses Thereof

AL Gurney, FT Axelrod, TC Hoey… – US Patent App. 13 …, 2013 – Google Patents

US20130095116A1 – RSPO Binding Agents and Uses Thereof – Google Patents. RSPO Binding Agents and Uses Thereof. Download PDF Info. Publication number US20130095116A1. US20130095116A1 US13/549,050 US201213549050A …  Cited by 18 Related articles All 2 versions 

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2012

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Applications of Connectivity Map in drug discovery and development

XA Qu, DK Rajpal – Drug discovery today, 2012 – Elsevier

…of marketed drugs and compounds. BioExpress™, http://www.genelogic.com/knowledge-suites/bioexpress-system, Commercial database for human disease-centric gene expression data. Library of Integrated Network-based …  Cited by 139 Related articles All 4 versions [HTML] plos.org

[HTML] Targeting FGFR4 inhibits hepatocellular carcinoma in preclinical mouse models

DM French, BC Lin, M Wang, C Adams, T Shek… – PloS one, 2012 – journals.plos.org

 ..The fibroblast growth factor (FGF)-FGF receptor (FGFR) signaling system plays critical roles in a variety of normal developmental and physiological processes. It is also well documented that dysregulation of FGF-FGFR signaling may have important roles in tumor development and …  Cited by 132 Related articles All 14 versions [PDF] aacrjournals.org  Free from Publisher

Expression of g protein-coupled receptor 19 in human lung cancer cells is triggered by entry into s-phase and supports g2–m cell-cycle progression

S Kastner, T Voss, S Keuerleber, C Glöckel… – Molecular Cancer …, 2012 – AACR  Cited by 18 Related articles All 9 versions

Bioinformatics advances for clinical biomarker development

KPH Pritzker, LB Pritzker – Expert opinion on medical diagnostics, 2012 – Taylor & Francis

… features BioExpress System GeneLogic http://www.genelogic.com Whole genomeGene expression database with histopathology, clinical chemistry, hematology, treatment, follow-up and other clinical details Thomson Reuters …  Cited by 6 Related articles All 3 versions [PDF] googleapis.com

Tetrahydrofolate synthetase gene

T Sugiura – US Patent 8,168,392, 2012 – Google Patents

… The gene whose expression is elevated in the cancer cell in comparison with the normal cell was identified making use of the microarray data base of Bioexpress (Genelogic). Expression profile data in respective cells of 117 …  Related articles All 4 versions  [PDF] googleapis.com

Method for treatment of pancreatitis

LA Tartaglia, TM Barnes, RM Coopersmith… – US Patent App. 13 …, 2012 – Google Patents

US20120009183A1 – Method for treatment of pancreatitis – Google Patents. Method for treatment of pancreatitis. Download PDF Info. Publication number US20120009183A1. US20120009183A1 US13/171,058 US201113171058A …  All 2 versions

Treatment of breast cancer with iodonitrobenzamides in combination with anti-tumor agents

BM Sherman, C Bradley… – US Patent App. 13/430,475, 2012 – Google Patents

US20120269861A1 – Treatment of breast cancer with iodonitrobenzamides in combination with anti-tumor agents – Google Patents. Treatment of breast cancer with iodonitrobenzamides in combination with anti-tumor agents. Download PDF Info …  All 2 versions  

[PDF] Investigation into the role of novel interferon lambdas in the treatment of viral disease, primarily hepatitis C

RM Lowe – 2012 – core.ac.uk… 124 5.3 Gene Logic human tissue microarray screen ….. 127 … Figure 5.2 A: Gene Logic graph showing IFNAR1 expression in a range of human cell types and tissues ….. 128 …  Related articles All 3 versions [PDF] unsw.edu.au

[PDF] CHARACTERISING THE ROLE OF TRIM16 IN DIFFERENTIATION, PROLIFERATION AND TUMOUR DEVELOPMENT IN NEUROBLASTOMA

JL Bell – unsworks.unsw.edu.au

Page 1. CHARACTERISING THE ROLE OF TRIM16 IN DIFFERENTIATION, PROLIFERATION AND TUMOUR DEVELOPMENT IN NEUROBLASTOMA By Jessica Lilian Bell This thesis is submitted in fulfilment of the requirements for the degree …

Compositions and methods for treating and diagnosing cancer

A Gurney – US Patent 8,158,758, 2012 – Google Patents

US8158758B2 – Compositions and methods for treating and diagnosing cancer – Google Patents. Compositions and methods for treating and diagnosing cancer. Download PDF Info. Publication number US8158758B2. US8158758B2 …

Compositions and methods for treating and diagnosing cancer

AL Gurney, AK Sato – US Patent 8,158,757, 2012 – Google Patents

US8158757B2 – Compositions and methods for treating and diagnosing cancer – Google Patents. Compositions and methods for treating and diagnosing cancer. Download PDF Info. Publication number US8158757B2. US8158757B2 

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2011

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Siglec-15, a member of the sialic acid-binding lectin, is a novel regulator for osteoclast differentiation

Y Hiruma, T Hirai, E Tsuda – Biochemical and biophysical research …, 2011 – Elsevier

… The human gene expression database, BioExpress System (Gene Logic Division, OcimumBiosolutions, Inc.), containing Affymetrix U133 GeneChip expression profiles of numerous human samples from > 60 normal and diseased tissue types, was analyzed to identify genes… Cited by 4 Related articles All 3 versions Cite

Knowledge-Driven, Data-Assisted Integrative Pathway Analytics

PS Reddy, S Murray, W Liu – Handbook of Research on …, 2011 – books.google.com

… mechanisms. Examples include ICONIX’s Drug Matrix (Ganter, Snyder, Halbert, & Lee, 2006) and Gene Logic’s BioExpress (http://www. genelogic. com/knowledge-suites/bioexpress-system)(Katz, 231 Page 266. Knowledge… 

Related articles All 3 versions Cite [HTML] from europepmc.org

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2010

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[HTML] Molecular biomarker analyses using circulating tumor cells

EA Punnoose, SK Atwal, JM Spoerke, H Savage… – PloS one, 2010 – journals.plos.org

… 32], [33]. To examine the expression of marker genes in primary tumors, gene expression profiles were extracted from the commercially available database BioExpress (GeneLogic, Gaithersburg MD). Cell surface expression …

  Cited by 297 Related articles All 17 versions  [PDF] sagepub.com  Full View

Upregulation of poly (ADP-ribose) polymerase-1 (PARP1) in triple-negative breast cancer and other primary human tumor types

V Ossovskaya, IC Koo, EP Kaldjian… – Genes & …, 2010 – journals.sagepub.com

Poly (ADP-ribose) polymerase-1 (PARP1) is a key facilitator of DNA repair and is implicated in pathways of tumorigenesis. PARP inhibitors have gained recent att…  Cited by 160 Related articles All 5 versions [PDF] wiley.com Full View

TMPRSS13, a type II transmembrane serine protease, is inhibited by hepatocyte growth factor activator inhibitor type 1 and activates pro‐hepatocyte growth factor

T Hashimoto, M Kato, T Shimomura… – The FEBS …, 2010 – Wiley Online Library

… members of the TTSP family. These proteases have been shown to be co‐expressed with HAI‐1 in various tissues (database of BioExpress System, Gene Logic Inc.,Gaithersburg, MD, USA). Then, the putative activation cleavage …  Cited by 63 Related articles All 8 versions

EGFL6 is increasingly expressed in human obesity and promotes proliferation of adipose tissue-derived stromal vascular cells

R Oberauer, W Rist, MC Lenter, BS Hamilton… – Molecular and cellular …, 2010 – Springer

… Affymetrix GeneChip analysis in a wide range of human normal tissues (BioExpress ® database,Gene Logic) showed high expression of EGFL6 in placenta, lung, and fat, whereas most other tissues displayed weak or no expression indicating that EGFL6 expression is rather …  Cited by 31 Related articles All 10 versions

Information technology solutions for integration of biomolecular and clinical data in the identification of new cancer biomarkers and targets for therapy

H Hackl, G Stocker, P Charoentong, B Mlecnik… – Pharmacology & …, 2010 – Elsevier

Skip to main content Skip to article …  Cited by 10 Related articles All 6 versions [PDF] amegroups.com

Mutated genes in pancreatic cancer

S He, D Li – Chinese Journal of Cancer Research, 2010 – Springer

… Cao D et al utilized the Gene Logic Inc. BioExpress™ platform and Affymetrix U133 GeneChip® set to determine the changes in gene expression associated with SMAD4 gene inactivation in a series of well-characterized pancreatic cancer cell lines to define the downstream …  Cited by 2 Related articles All 7 versions 

Diagnoses and therapeutics for cancer

DR Wonsey, MT Follettie – US Patent 7,655,402, 2010 – Google Patents

US7655402B2 – Diagnoses and therapeutics for cancer – Google Patents. Diagnoses and therapeutics for cancer. Download PDF Info. Publication number US7655402B2. US7655402B2 US11051679 US5167905A US7655402B2 …

  Cited by 17 Related articles All 4 versions 

Treatment of breast cancer with a PARP inhibitor alone or in combination with anti-tumor agents

BM Sherman, C Bradley – US Patent 7,732,491, 2010 – Google Patents

In one aspect, the present invention provides a method of treating breast cancer that is negative for at least one of ER, PR, or HER2, comprising administering to a subject at least one PARP inhibitor. In another aspect, the present invention provides a method of treating breast cancer …  Cited by 36 Related articles All 4 versions 

Method for treating inflammatory diseases of the digestive tract

LA Tartaglia, TM Barnes, RM Coopersmith… – US Patent …, 2010 – Google Patents

US7842709B2 – Method for treating inflammatory diseases of the digestive tract – GooglePatents. Method for treating inflammatory diseases of the digestive tract. Download PDF Info. Publication number US7842709B2. US7842709B2 …  Cited by 16 Related articles All 4 versions 

Treatment of breast cancer with a parp inhibitor alone or in combination with anti-tumor agents

BM Sherman, C Bradley – US Patent App. 12/496,593, 2010 – Google Patents

US20100003192A1 – Treatment of breast cancer with a parp inhibitor alone or in combination with anti-tumor agents – Google Patents. Treatment of breast cancer with a parp inhibitor alone or in combination with anti-tumor agents. Download PDF Info …  Cited by 6 Related articles All 2 versions 

Method for reducing gastrointestinal adverse effects of cytotoxic agents

SR Donahue, JJ Byrnes – US Patent App. 12/704,286, 2010 – Google Patents

A method for moderating a gastrointestinal adverse effect induced by at least one cytotoxic agent, for example ionizing radiation and/or at least one chemotherapeutic agent, in a subject comprises administering to the subject a therapeutically effective amount of an ACE2 inhibitor …  All 2 versions 

Treatment of uterine cancer and ovarian cancer with a parp inhibitor alone or in conbination with anti-tumor agents

BM Sherman, C Bradley – US Patent App. 12/502,943, 2010 – Google Patents

US20100009930A1 – Treatment of uterine cancer and ovarian cancer with a parp inhibitor alone or in conbination with anti-tumor agents – Google Patents. Treatment of uterine cancer and ovarian cancer with a parp inhibitor …

  Cited by 6 Related article

Methods for breast cancer screening and treatment

D White, S Jin, RM Coopersmith… – US Patent App. 12 …, 2010 – Google Patents

US20100029734A1 – Methods for breast cancer screening and treatment – Google Patents. Methods for breast cancer screening and treatment. Download PDF Info. Publication number US20100029734A1. US20100029734A1 …

  Cited by 6 Related articles All 2 versions 

Method For Identification of Compound Having Anti-Anxiety Effect

D Okajima, H Yokota, O Ohara, T Nagase… – US Patent App. 12 …, 2010 – Google Patents

There are provided a method for identifying a compound having an anti-anxiety effect, an inhibitor of a function of a protein having a function as a G-protein coupled receptor, characterized by finding the protein and a gene encoding the protein and using at least one of a DNA represented …

  Related articles All 2 versions 

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2009

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Functional characterisation of calcium-activated chloride channel 2 (CLCA2) in human tumour cells

DS Kozina – 2009 – othes.univie.ac.at

Page 1. DISSERTATION Titel der Dissertation Functional Characterisation of Calcium-Activated Chloride Channel 2 (CLCA2) in Human Tumour Cells angestrebter akademischer Grad Doktorinder Naturwissenschaften (Dr. rer.nat.) Verfasserin / Verfasser: Mag. Daniela Kozina …

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Similar compounds searching system by using the gene expression microarray database

H Toyoshiba, H Sawada, I Naeshiro, A Horinouchi – Toxicology letters, 2009 – Elsevier

… Tong et al., 2003), ArrayExpress at the EBI (Parkinson et al., 2007), the Toxicogenomics Project (TGP) (Takashima et al., 2006), Iconix DrugMatrix, the GeneLogic ToxExpress and BioExpress, and the NCBI microarray data repository Gene Expression Omnibus (GEO) (www.ncbi …  Cited by 16 Related articles All 5 versions

Tetrahydrofolate synthetase gene

T Sugiura – US Patent 7,534,562, 2009 – Google Patents

US7534562B2 – Tetrahydrofolate synthetase gene – Google Patents. Tetrahydrofolate synthetase gene. Download PDF Info. Publication number US7534562B2. US7534562B2 US10/573,969 US57396904A US7534562B2 US …

  Cited by 1 Related articles All 4 versions 

Method for treatment of pancreatitis

LA Tartaglia, TM Barnes, RM Coopersmith… – US Patent App. 12 …, 2009 – Google Patents

A method for treating acute or chronic pancreatitis in a subject comprises administering to the subject a therapeutically effective amount of an ACE2 inhibitor…  Related articles All 2 versions 

Inhibition of urokinase-type plasminogen activator (uPA) activity

JF Bazan, P Kirk – US Patent App. 12/290,013, 2009 – Google Patents

The invention concerns methods for inhibiting the binding of urokinase-type plasminogen activator (uPA) to its receptor uPAR and/or inhibiting uPA biological activity. The invention further concerns methods for inhibiting tumor formation or metastasis, angiogenesis, such as tumor …  All 2 versions 

Molecular cardiotoxicology modeling

DL Mendrick, KR Johnson – US Patent App. 12/064,933, 2009 – Google Patents

… WO 02/095659, published Nov. 23, 2002, and US Pat. No. 5,953,727, which are herein incorporated by reference in their entirety. In a preferred embodiment, the database is a ToxExpress® or BioExpress database marketed by Gene Logic Inc., Gaithersburg, Md …  Related articles All 2 versions 

Treatment of uterine cancer and ovarian cancer with a parp inhibitor alone or in combination with anti-tumor agents

BM Sherman, C Bradley… – US Patent App. 12/269,833, 2009 – Google Patents

US20090123419A1 – Treatment of uterine cancer and ovarian cancer with a parp inhibitor alone or in combination with anti-tumor agents – Google Patents. Treatment of uterine cancer and ovarian cancer with a parp inhibitor …

  Cited by 23 Related articles All 2 versions 

Method for treating er+ breast cancer

RM Coopersmith, DW White, S Jin… – US Patent App. 12 …, 2009 – Google Patents

US20090012052A1 – Method for treating er+ breast cancer – Google Patents. Method for treating er+ breast cancer. Download PDF Info. Publication number US20090012052A1. US20090012052A1 US12/100,053 US10005308A …

  Cited by 7 Related articles All 2 versions 

Assay employing a g-protein coupled receptor that is activated by CCK-8S

O Ohara, T Nagase, M Ohishi, D Okajima… – US Patent …, 2009 – Google Patents

US7527937B2 – Assay employing a g-protein coupled receptor that is activated byCCK-8S – Google Patents. Assay employing a g-protein coupled receptor that is activated by CCK-8S. Download PDF Info. Publication number …

  Cited by 2 Related articles All 2 versions 

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2008

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[HTML] Molecular analysis of the vaginal response to estrogens in the ovariectomized rat and postmenopausal woman

SA Jelinsky, SE Choe… – BMC medical …, 2008 – bmcmedgenomics.biomedcentral …

… First, all qualifiers were annotated with unigene accession numbers through BioExpress (GeneLogic) … In order to do this, probe set annotations and ortholog assignments were obtainedfrom BioExpress 2.0 (GeneLogic) and NCBI Homologene, respectively …  Cited by 9 Related articles All 12 versions 

Protein phosphatase 1H, overexpressed in colon adenocarcinoma, is associated with CSE1L

T Sugiura, Y Noguchi, K Sakurai… – Cancer biology & …, 2008 – Taylor & Francis

… Data mining of the BioExpress database. We identified the genes upregulated in human colon adenocarcinomas using the BioExpress database (Gene Logic Inc., Gaithersburg, MA, USA) comprising the Affymetrix U133 GeneChip expression profiles as described previously …  Cited by 24 Related articles All 3 versions

Preventive and/or Therapeutic Agent for Cancer

T Yoshikawa, W Watanabe… – US Patent App. 11/547,334, 2008 – Google Patents

… For example, 69 kinds of genes highly expressed in pancreatic cancer were tried to be identifiedusing BioExpress (Gene Logic Co., Ltd.) in … of SEQ ID NOS: 1 to 4 were selected by the followingprocedures using an expression profile database, BioExpress (GeneLogic Co., Ltd …  Related articles All 2 versions 

Characterization of TRIM31, upregulated in gastric adenocarcinoma, as a novel RBCC protein

T Sugiura, K Miyamoto – Journal of cellular biochemistry, 2008 – Wiley Online Library

… MATERIALS AND METHODS. Data Mining of the BioExpress Database. We identified the genes upregulated in human stomach adenocarcinoma by using the BioExpress database (Gene Logic Inc., Gaithersburg, MA) as described previously [Sugiura et al., 2004, 2007b] …

A cancer-associated RING finger protein, RNF43, is a ubiquitin ligase that interacts with a nuclear protein, HAP95

T Sugiura, A Yamaguchi, K Miyamoto – Experimental cell research, 2008 – Elsevier

… Materials and methods. Identification of RNF43 upregulated in colon cancers. Expression profiles of RNF43 in various normal and diseased tissues were analyzed by virtue of the BioExpress database (Gene Logic Inc., Gaithersburg, MA) as described previously [10], [11] …  Cited by 49 Related articles All 9 versions

[HTML] Differential expression of multiple genes in association with MADH4/DPC4/SMAD4 inactivation in pancreatic cancer

D Cao, R Ashfaq, MG Goggins, RH Hruban… – … journal of clinical and …, 2008 – ncbi.nlm.nih.gov

… in other tumor types [4, 5]. Considering the high rate of MADH4 inactivation in pancreatic cancers, it is attractive to consider the genes differentially expressed in accord with MADH4 status in anunbiased survey [6–9]. We utilized the Gene Logic Inc. BioExpress(tm) platform and …  Cited by 15 Related articles All 8 versions

Evolution of closely linked gene pairs in vertebrate genomes

E Franck, T Hulsen, MA Huynen… – Molecular biology …, 2008 – academic.oup.com

… Gene Expression. An expression data set consisting of a subset of normal human and mouse tissue samples from the Gene Logic BioExpress Database product (http://www.genelogic.com/genomics/bioexpress/) was used. The …

  Cited by 15 Related articles All 13 versions

From pharmacogenomics to translational biomarkers

DL Mendrick – Essential Concepts in Toxicogenomics, 2008 – Springer

… renal cell carcinoma was recently described (21). Examination of Kim-1 in human renal diseases was performed using the BioExpress® database at Gene Logic (Gaithersburg,MD). The expression of Kim-1 mRNA was significantly 

  Cited by 1 Related articles All 5 versions

[HTML] Alpha-CaMKII deficiency causes immature dentate gyrus, a novel candidate endophenotype of psychiatric disorders

N Yamasaki, M Maekawa… – Molecular …, 2008 – molecularbrain.biomedcentral.com

Elucidating the neural and genetic factors underlying psychiatric illness is hampered by current methods of clinical diagnosis. The identification and investigation of clinical endophenotypes may be one solution, but represents a considerable challenge in human subjects. Here we …  Cited by 206 Related articles All 19 versions 

Methods For Molecular Toxicology Modeling

JC Diggans, M Elashoff – US Patent App. 10/580,423, 2008 – Google Patents

… WO 02/095659, published Nov. 23, 2002, and US Pat. No. 5,953,727, which are herein incorporated by reference in their entirety. In a preferred embodiment, the database is a ToxExpress® or BioExpress® database marketed by Gene Logic Inc., Gaithersburg, Md …  Related articles All 2 versions 

Method for reducing or alleviating inflammation in the digestive tract

LA Tartaglia, TM Barnes, RM Coopersmith… – US Patent App. 11 …, 2008 – Google Patents

US20080234345A1 – Method for reducing or alleviating inflammation in the digestive tract – Google Patents. Method for reducing or alleviating inflammation in the digestive tract. Download PDF Info. Publication number US20080234345A1 …  Cited by 1 Related articles All 2 versions

Toxicogenomic predictive modeling: emerging opportunities for more efficient drug discovery and development

A Amir-Aslani – Technological Forecasting and Social Change, 2008 – Elsevier

Skip to main content …  Cited by 12 Related articles All 3 versions

Breast cancer screening and treatment methods

RM Coopersmith, DW White, S Jin… – US Patent App. 11 …, 2008 – Google Patents

US20080132474A1 – Breast cancer screening and treatment methods – Google Patents. Breast cancer screening and treatment methods. Download PDF Info.Publication number US20080132474A1. US20080132474A1 US11 …

  Cited by 2 Related articles All 2 versions 

hGPR87 contributes to viability of human tumor cells

S Glatt, D Halbauer, S Heindl… – … journal of cancer, 2008 – Wiley Online Library

… One hundred divided by the trimmed mean gives the scaling factor, where 100 is the standard value used by GeneLogic … The human sample collection has been described by the originator of the BioExpress database.17 Numbers in brackets indicate the sample numbers …Cited by 45 Related articles All 6 versions

Gene Encoding a Guanine Nucleotide Exchange Factor Binding to Rhoa

O Ohara, T Nagase, M Ohishi, H Yokota… – US Patent App. 11 …, 2008 – Google Patents

A gene encoding a novel protein that binds to a Rho family protein being one group of small GTP binding proteins and is capable of exhibiting a GEF activity, namely, a polynucleotide shown by the nucleotide sequence set forth in SEQ ID NO: 1, or SEQ ID NO: 3, or the complementary …

  Cited by 1 Related articles All 2 versions 

Gene Encoding a Guanine Nucleotide Exchange Factor and Its Gene Product

O Ohara, T Nagase, M Ohishi, H Yokota… – US Patent App. 11 …, 2008 – Google Patents

US20080274954A1 – Gene Encoding a Guanine Nucleotide Exchange Factor and Its Gene Product – Google Patents. Gene Encoding a Guanine Nucleotide Exchange Factor and Its Gene Product. Download PDF Info. Publication …

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2007

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[PDF] DDX39, upregulated in lung squamous cell cancer, displays RNA helicase activities and promotes cancer cell growth

T Sugiura, Y Nagano, Y Noguchi – Cancer biology & therapy, 2007 – Taylor & Francis

… For this purpose we resorted to the gene expression profile database called BioExpress developed by GeneLogic Inc., which utilizes the Affimetrix … Initially we collected 130 normal lung, 74 LAC and 51 LSCC patient samples on the BioExpress (Gene Logic Inc.) database …Cited by 48 Related articles All 3 versions

Molecular characterization of the desmoplastic tumor stroma in medullary thyroid carcinoma

O Koperek, C Scheuba, C Puri… – International …, 2007 – spandidos-publications.com

… in normal and tumor tissues. The expression levels of FAPα, Tn-C and α-SMA in thyroid cancers were analyzed by querying the Gene Logic Bioexpress database (see Materials and methods). In this database, we obtained the …Cited by 54 Related articles All 7 versions

Liver-specific activities of FGF19 require Klotho beta

BC Lin, M Wang, C Blackmore… – Journal of Biological …, 2007 – ASBMB

… KLB and FGFR4 Distribution Dictate FGF19 Tissue-specific Activity—We evaluated KLB and FGFR4 expression in a variety of human tissues by analyzing the BioExpress data base (Gene Logic, Inc.). In decreasing order of …Cited by 218 Related articles All 6 versions

Bioinformatics approaches in the study of cancer

DA Hanauer, DR Rhodes… – Current molecular …, 2007 – ingentaconnect.com

… The BioExpress® Oncology Suite offers visualization and statistical analysis tools as well … Similar to Gene Logic’s offerings is the Oncomine [13] database Fig … [19] http://www.genelogic.com/ docs/pdfs/OncologyProductSheet.pdf Accessed on April 22, 2006 …Cited by 69 Related articles All 12 versions

Death-receptor O-glycosylation controls tumor-cell sensitivity to the proapoptotic ligand Apo2L/TRAIL

KW Wagner, EA Punnoose, T Januario, DA Lawrence… – Nature medicine, 2007 – nature.com

Article. Cited by 555 Related articles All 11 versions

The Connectivity Map: a new tool for biomedical research

J Lamb – Nature reviews cancer, 2007 – nature.com

… Iconix’s DrugMatrix contains data for the effects of systemic administration of hundreds of drugs on many rat tissues 44, and Gene Logic’s BioExpress has thousands of profiles from normal, diseased and drug-treated human and animal tissues and cell lines …Cited by 655 Related articles All 7 versions

PARP1 gene over-expression in primary human cancers: A potential marker for PARP inhibition

V Ossovskaya, C Alvares, E Kaldjian, B Sherman – 2007 – AACR

Skip to main content. AACR Journals: Cancer Discovery; Cancer Epidemiology, Biomarkers & Prevention; Cancer Immunology Research; Cancer Prevention Research; Cancer Research; Clinical Cancer Research; Molecular Cancer Research; Molecular Cancer Therapeutics ..cited by 3 Related articles

From the bench to the clinic and back again: translational biomarker discovery using in silico mining of pharmacogenomic data

DL Mendrick, KK Daniels – 2007 – Future Medicine

… In silico mining of pharmacogenomic data within Gene Logic’s BioExpress ® and ToxExpress ® databases quickly reveals that the expression of Kim-1 in normal human tissues resides primarily in the kidney (Figure 1). A low level of expression was found in normal mouse …Cited by 8 Related articles All 6 versions

[CITATION] P57 The PARP1 gene is over-expressed in triple negative breast cancer

V Ossovskaya, C Alvares, E Kaldjian… – EJC …, 2007 – annalsjournal.com

… PARP1. Methods: We used the Gene Logic BioExpress® System database to analyze PARP1 expression in human ovarian, breast, uterine, lung and prostate tumor samples in comparison to normal counterpart tissues. Gene …Cited by 1 Related articles All 3 versions

[CITATION] P50 Expression of estrogens, progesterone and c-erbB-2 in patients with recurrent breast cancer in Mexico

JM Ornelas-Aguirre, LM Perez-Michel… – EJC …, 2007 – annalsjournal.com

… PARP1. Methods: We used the Gene Logic BioExpress® System database to analyze PARP1 expression in human ovarian, breast, uterine, lung and prostate tumor samples in comparison to normal counterpart tissues. Gene …

[CITATION] P10 Identification of possible metastasis associated markers expressed on the surface of a breast cancer model

N Rasmussen, HJ Ditzel – EJC Supplements, 2007 – annalsjournal.com

… PARP1. Methods: We used the Gene Logic BioExpress® System database to analyze PARP1 expression in human ovarian, breast, uterine, lung and prostate tumor samples in comparison to normal counterpart tissues. Gene …All 7 versions

[CITATION] P27 Antiangiogenic activity of combining gefitinib and rapamycin in a panel of pancreas cancer cell lines

L Pocelli, A Azzariti, GM Simone, G Gatti… – EJC …, 2007 – annalsjournal.com

… PARP1. Methods: We used the Gene Logic BioExpress® System database to analyze PARP1 expression in human ovarian, breast, uterine, lung and prostate tumor samples in comparison to normal counterpart tissues. Gene …All 3 versions

[HTML] A cardiac myosin light chain kinase regulates sarcomere assembly in the vertebrate heart

O Seguchi, S Takashima, S Yamazaki… – The Journal of …, 2007 – Am Soc Clin Investig

… peptide (BNP) mRNA levels (194 probe sets). The tissue localization of each selected probe set was then analyzed using the commercially available BioExpress database (Gene Logic Inc.). We selected 10 probe sets, for which …Cited by 126 Related articles All 14 versions

Patterns of gene expression in the limbic system of suicides with and without major depression

A Sequeira, T Klempan, L Canetti, C Benkelfat… – Molecular …, 2007 – nature.com

… (Gaithersburg, MD, USA, www.genelogic.com). All microarray data and clinical information were embedded into Gene Logic’s Genesis 2.0 software as a component of its Bioexpress system. RNA samples used in the current study had a minimum A260/A280 ratio of 1.9 …Cited by 148 Related articles All 18 versions

[BOOK] Pharmacophylogenomics: Explaining interspecies differences in drug discovery

T Hulsen – 2007 – repository.ubn.ru.nl

Page 1. PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher’s version. For additional information about this publication click this link. http://hdl.handle.net/2066/30197 …  Related articles All 5 versions 

Compositions and methods for diagnosing and treating cancers

X Be, W Liu, D Slonim, S Howes – US Patent App. 11/509,413, 2007 – Google Patents

… Genes (CRTPGs). Gene expression data in eight malignant tumor sample sets (ie, breast, colon, esophagus, kidney, liver, lung, prostate, and stomach cancer sample sets) was compared to the corresponding normal counterparts in the Gene Logic BioExpress™ database …  Cited by 2 Related articles All 2 versions 

Identification of adiponutrin-related proteins as esterases and methods of use for the same

R Gimeno, J Paulsen, JL Li, A Lake, W Liu… – US Patent App. 11 …, 2007 – Google Patents

US20070014776A1 – Identification of adiponutrin-related proteins as esterases and methods of use for the same – Google Patents. Identification of adiponutrin-related proteins as esterases and methods of use for the same. Download PDF Info …  Cited by 10 Related articles All 2 versions 

Methods and apparatuses for diagnosing AML and MDS

M Burczynski, A Dorner, N Twine… – US Patent App. 11 …, 2007 – Google Patents

Methods, systems and equipment for diagnosing or monitoring the progression or treatment of AML or MDS. This invention identifies a plurality of AML or MDS disease genes which are differentially expressed in bone marrow cells of AML or MDS patients as compared to disease …

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2006

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Expression of stromal cell markers in distinct compartments of human skin cancers

MA Huber, N Kraut, N Schweifer… – Journal of cutaneous …, 2006 – Wiley Online Library

… tumor‐relevant genes. The expression levels of FAP, endoglyx‐1, and endosialin in human skin cancers were analyzed by querying the GeneLogic Bioexpress ®database (see Materials and methods). In this database, we …

Cited by 64 Related articles All 7 versions

[HTML] Benchmarking ortholog identification methods using functional genomics data

T Hulsen, MA Huynen, J de Vlieg… – Genome …, 2006 – genomebiology.biomedcentral.com

The transfer of functional annotations from model organism proteins to human proteins is one of the main applications of comparative genomics. Various methods are used to analyze cross-species orthologous relationships according to an operational definition of orthology. Often …  Cited by 179 Related articles All 18 versions 

[HTML] A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database

S Katz, RA Irizarry, X Lin… – BMC …, 2006 – bmcbioinformatics.biomedcentral …

… We have utilized an alternate RMA workflow that includes two distinct steps: (a) training of an RMA model based on a large number of biologically distinct Affymetrix GeneChip samples from Gene Logic’s BioExpress reference database and (b) application of the resulting RMA …

TTLL7 is a mammalian β-tubulin polyglutamylase required for growth of MAP2-positive neurites

K Ikegami, M Mukai, J Tsuchida, RL Heier… – Journal of Biological …, 2006 – ASBMB

… Using BioExpress Data Base—We performed a data base search and statistical analysis on TTLL mRNA expression among various tissues in humans that were profiled by Affymetrix GeneChip technology and stored in the commercial Gene Logic BioExpress data base system …  Cited by 131 Related articles All 9 versions

Detecting and profiling tissue-selective genes

S Liang, Y Li, X Be, S Howes, W Liu – Physiological genomics, 2006 – physiology.org

Login to your account. Institutional Login. Sign In / Register. PHYSIOLOGY.ORG Skip main navigationClose Drawer MenuOpen Drawer Menu Home: Journals: AJP-Cell; AJP-Endo; AJP-GI; AJP-Heart; AJP-Lung; AJP-Regu; AJP-Renal; …  Cited by 64 Related articles All 8 versions

Translational medicine: the discovery of bridging biomarkers using pharmacogenomics

DL Mendrick – 2006 – Future Medicine

… At Gene Logic we have large reference gene expression databases with accompanying clinical annotation of normal and diseased human tissue (BioExpress ® database) and vehicle and toxicant treated tissues and cells from multiple species (ToxExpress ® database) …Cited by 7 Related articles All 4 versions

Amino acid transporter ATA2 is stored at the trans-Golgi network and released by insulin stimulus in adipocytes

T Hatanaka, Y Hatanaka, J Tsuchida… – Journal of Biological …, 2006 – ASBMB

… We performed a data base search and statistical analysis on ATA2 mRNA and GLUT4 mRNA expression among various tissues in humans, mice, and rats that were profiled by Affymetrix GeneChip technology and stored in the commercial Gene Logic BioExpress data base …  Cited by 44 Related articles All 7 versions

Toxicogenomics and cross-species biomarker discovery: applications in drug discovery and safety assessment

MS Orr – Toxicology mechanisms and methods, 2006 – Taylor & Francis

… for leveraging toxicogenomic information from rats contained in one database (ToxExpress @R database) and genomic information from human samples contained in a second database (BioExpress @ R database) in … At Gene Logic Inc., Affymetrix GeneChips @ R microarrays …Cited by 8 Related articles All 7 versions

Inhibiting HER2 shedding with matrix metalloprotease antagonists

K Carey, R Schwall, M Sliwkowski… – US Patent App. 11 …, 2006 – Google Patents

US20060177448A1 – Inhibiting HER2 shedding with matrix metalloprotease antagonists -Google Patents. Inhibiting HER2 shedding with matrix metalloprotease antagonists. Download PDF Info. Publication number US20060177448A1 …  Cited by 10 Related articles All 2 versions 

[BOOK] Application of Toxicogenomics to Cross-Species Extrapolation: A Report of a Workshop

National Research Council – 2006 – books.google.com

… For exam- ple, the fibrosis genes differentially dysregulated between dog and rat liver included INHBE (activin beta E). To determine whether these canine genes might be relevant to hu- man fibrosis, Gene Logic’s BioExpress database of normal and diseased human tissue …

Mig6 is a negative regulator of EGF receptor–mediated skin morphogenesis and tumor formation

I Ferby, M Reschke, O Kudlacek, P Knyazev, G Pantè… – Nature medicine, 2006 – nature.com

… We analyzed ERRFI1 expression levels in 3,200 normal and cancer samples using the BioExpress database, which contains transcriptional profiles obtained from … 100 divided by the trimmed mean gives the scaling factor, where 100 is the standard value used by GeneLogicCited by 213 Related articles All 12 versions

Gene encoding G-protein coupled receptor and gene product thereof

O Ohara, T Nagase, M Ohishi, D Okajima… – US Patent App. 11 …, 2006 – Google Patents

The present invention, the objects of which are to find out a gene encoding a protein having functions equivalent to those of G-protein-coupled receptor (GPCR) and the protein, and to provide a method for identifying a compound that regulates functions and/or expression of the protein …

Cited by 3 Related articles All 2 versions 

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2005

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Epithelial versus mesenchymal phenotype determines in vitro sensitivity and predicts clinical activity of erlotinib in lung cancer patients

RL Yauch, T Januario, DA Eberhard, G Cavet… – Clinical Cancer …, 2005 – AACR

Skip to main content. AACR Publications: Cancer Discovery; Cancer Epidemiology, Biomarkers & Prevention; Cancer Immunology Research; Cancer Prevention Research; Cancer Research; Clinical Cancer Research; Molecular Cancer Research; Molecular Cancer Therapeutics … Cited by 580 Related articles All 8 versions

Characterization of cancer stroma markers: in silico analysis of an mRNA expression database for fibroblast activation protein and endosialin

H Dolznig, N Schweifer, C Puri, N Kraut, WJ Rettig… – Cancer Immunity …, 2005 – AACR

Cited by 139 Related articles All 4 version 

Loss of the forkhead transcription factor FoxM1 causes centrosome amplification and mitotic catastrophe

DR Wonsey, MT Follettie – Cancer research, 2005 – AACR

Skip to main content. AACR Publications: Cancer Discovery; Cancer Epidemiology, Biomarkers & Prevention; Cancer Immunology Research; Cancer Prevention Research; Cancer Research; Clinical Cancer Research; Molecular Cancer Research; Molecular Cancer Therapeutics …Cited by 323 Related articles All 5 versions

Revealing Transforming Growth Factor–β Signaling Transduction in Human Kidney by Gene Expression Data Mining

G Hu, K Jain, M Hurle – Omics: a journal of integrative biology, 2005 – liebertpub.com

… From the BioExpress® System, Gene Logic Inc.’s (Gaithersburg, MD http://www.genelogic.com/)database of human U133 GeneChip® microarray data processed using MAS5.0, we chose 227 datasets derived from kid- ney samples that met three conditions: (i) scale factors …Cited by 6 Related articles All 3 versions

[HTML] Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data

AR Abbas, D Baldwin, Y Ma, W Ouyang, A Gurney… – Genes and …, 2005 – nature.com

Cited by 290 Related articles All 13 versions

Clusters of adjacent and similarly expressed genes across normal human tissues complicate comparative transcriptomic discovery

C Liu, S Ghosh, DB Searls, AM Saunders… – Omics: a journal of …, 2005 – liebertpub.com

… retrieved gene expression data profiled using human U133A&B chips (Affymetrix, Santa Clara, CA; http://www.affymetrix.com) for 2695 normal human samples belonging to 101 tissue types from BioExpress Sys- tem Database (Gene Logic Inc., Gaithersburg, MD; www.genelogic.com …  Cited by 6 Related articles All 3 versions

The delicate toxicity balance in drug discovery: can pricey late-stage failures–or dangerous drugs–be prevented with better products for predicting drug toxicity?

U Sankar – The Scientist, 2005 – go.galegroup.com

… Sertanty QSAR software and Knowledge-based drug services discovery Tripos Discovery informatics Preclinical development and chemical compound libraries Iconix DrugMatrix, Pharmotif Predictive toxicology Gene Logic ToxExpress, BioExpress Predictive toxicology In Vitro …Cited by 35 Related articles All 2 versions

Cell surface molecules as markers and therapeutic agents against kidney cancers

W Liu, M Whitley, D Slonim, S Howes – US Patent App. 10/671,740, 2005 – Google Patents

… [0052]. The data mining power of microarrays is encompassed in another research tool, namely BioExpress™, a comprehensive database of biological information from Gene Logic Inc. (Gaithersburg, Md.), which we used for …

  Cited by 5 Related articles All 2 versions 

[BOOK] Analyzing microarray gene expression data

G McLachlan, KA Do, C Ambroise – 2005 – books.google.com

Page 1. Analyzing Mieroarray Gene Expression Data Page 2. This Page Intentionally Left Blank Page 3. Analyzing Microarray Gene Expression Data Page 4. WILEYERIES IN PROBABILITY AND STATISTICS Established by …Cited by 685 Related articles All 8 versions

Compositions and methods for diagnosing and treating cancers

X Be, W Liu, D Slonim, S Howes – US Patent App. 10/847,918, 2005 – Google Patents

US20050119210A1 – Compositions and methods for diagnosing and treating cancers -Google Patents. Compositions and methods for diagnosing and treating cancers.Download PDF Info. Publication number US20050119210A1 …

Compositions and methods for diagnosing, preventing, and treating cancers

E Brown, W Liu – US Patent App. 10/770,726, 2005 – Google Patents

US20050266409A1 – Compositions and methods for diagnosing, preventing, and treating cancers – Google Patents. Compositions and methods for diagnosing, preventing, and treating cancers. Download PDF Info. Publication …

  Cited by 17 Related articles All 2 versions 

Methods and apparatuses for diagnosing AML and MDS

M Burczynski, A Dorner, N Twine… – US Patent App. 10 …, 2005 – Google Patents

US20050202451A1 – Methods and apparatuses for diagnosing AML and MDS – Google Patents. Methods and apparatuses for diagnosing AML and MDS. Download PDF Info. Publication number US20050202451A1. US20050202451A1 …Cited by 10 Related articles All 2 versions 

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2004

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A novel mitochondrial C1-tetrahydrofolate synthetase is upregulated in human colon adenocarcinoma

T Sugiura, Y Nagano, T Inoue, K Hirotani – Biochemical and biophysical …, 2004 – Elsevier

… We collected 117 normal and 77 adenocarcinoma colon samples on the BioExpress database (Gene Logic Inc., Gaithersburg, MA) containing Affymetrix U133 GeneChip expression profiles [3], [4]. The Fold Change analysis tool equipped in the database was utilized to identify …Cited by 33 Related articles All 6 versions

Identification and validation of novel androgen-regulated genes in prostate cancer

AM Velasco, KA Gillis, Y Li, EL Brown, TM Sadler… – …, 2004 – academic.oup.com

Abstract. Androgen-regulated genes (ARGs) are essential for the development of the prostate. Ironically, ARGs are also responsible for the pathogenesis of pros.Cited by 128 Related articles All 8 versions

[PDF] tandfonline.com

Identification of novel highly expressed genes in pancreatic ductal adenocarcinomas through a bioinformatics analysis of expressed sequence tags

D Cao, SR Hustinx, G Sui, P Bala, N Sato… – Cancer biology & …, 2004 – Taylor & Francis

… completion of the human genome sequence provides a basis for characterizing these ESTs in greater detail using computational and experimental methods.7 In this study we utilized the GeneLogic Inc. BioExpress™ platform and the most current version of Affymetrix GeneChip …Cited by 60 Related articles All 5 versions

Endothelial lipase and HDL metabolism

M Jaye, J Krawiec – Current opinion in lipidology, 2004 – journals.lww.com

Purpose of review In the past year, several laboratories taking independent approaches have provide..Cited by 61 Related articles All 8 versions

Serial analysis of gene expression (SAGE): application in cancer research

R Tuteja, N Tuteja – Medical Science Monitor, 2004 – medscimonit.com

… lack of effective treatments. In a recent study the Gene Logic Inc. BioExpress platform and Affymetrix GeneChip arrays were used to identify genes differentially expressed in pan- creatic cancer [12]. The cDNA was hybridized …

Cited by 26 Related articles All 7 versions

[PDF] Assessing the quality of clusters in microarray data–a comparison of functional and numerical measures

EVA BERGLUND – 2004 – ibg.uu.se

… This value is referred to as RNA QC. 2.4 The dataset The dataset used in this project originates from BioExpress, a non-public database from Gene Logic (Gene Logic Inc, Gaithersburg, MD, USA). The database stores post-mortem 

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2003

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Disease-associated expression profiles in peripheral blood mononuclear cells from patients with advanced renal cell carcinoma

NC Twine, JA Stover, B Marshall, G Dukart, M Hidalgo… – Cancer research, 2003 – AACR

Skip to main content. AACR Publications: Cancer Discovery; Cancer Epidemiology, Biomarkers & Prevention; Cancer Immunology Research; Cancer Prevention Research; Cancer Research; Clinical Cancer Research; Molecular Cancer Research; Molecular Cancer Therapeutics …Cited by 142 Related articles All 9 versions

[PDF] Determining the Tissue Distribution and Specificity of JM27/G antigen, family C, 1, a Prostate Cancer-associated Gene

P Kulkarni, G Logic – ocimumbio.com

… e-Northern™ and BioExpress™ Human Atlas Suite are trademarks of Gene Logic Inc. PHONE: 301-987-1700 •FAX: 301-987-1701 • www.genelogic.com • Corporate Headquarters: 708 Quince Orchard Road•Gaithersburg, Maryland 20878 BioExpress™ is a registered …

Expression profiling identifies a novel α-methylacyl-CoA racemase exon with fumarate hydratase homology

GL Shen-Ong, Y Feng, DA Troyer – Cancer research, 2003 – AACR

Skip to main content. AACR Publications: Cancer Discovery; Cancer Epidemiology, Biomarkers & Prevention; Cancer Immunology Research; Cancer Prevention Research; Cancer Research; Clinical Cancer Research; Molecular Cancer Research; Molecular Cancer Therapeutics …

Cited by 37 Related articles All 6 versions

[BOOK] Comparing NR Expression among Metabolic Syndrome Risk Factors

A Jacobsson – 2003 – diva-portal.org

… 42 5.2.1 Lifestyle analysis with the GeneLogic GUI…..43 … humans. BioExpress™ (Gene Logic Inc.) is a database that contains both clinical data and gene expression data from donors in the United States … Cited by 1 Related articles 

Highly expressed genes in pancreatic ductal adenocarcinomas: a comprehensive characterization and comparison of the transcription profiles obtained from three …

CA Iacobuzio-Donahue, R Ashfaq, A Maitra, NV Adsay… – Cancer research, 2003 – AACRCited by 456 Related articles All 12 versions

[HTML] Notch mediates TGFα-induced changes in epithelial differentiation during pancreatic tumorigenesis

Y Miyamoto, A Maitra, B Ghosh, U Zechner, P Argani… – Cancer cell, 2003 – Elsevier

Skip to main content …Cited by 701 Related articles All 11 versions

[BOOK] Using nuclear receptor interactions as biomarkers for metabolic syndrome

K Hettne – 2003 – diva-portal.org

Gene Logic is a company that provides functional genomics information products, ser- vices and bioinformatics tools, which focus on human biology and pathology (GeneLogic 2003) … BioExpress TM database, the ToxExpress TM collection of predictive models, and Gen …  Related articles 

15 The Future of Toxicogenomics

JC Rockett – An Introduction to Toxicogenomics, 2003 – books.google.com

Page 316. 15 The Future of Toxicogenomics John C. Rockett CONTENTS 15.1 Introduction….. 299 15.2 Technology … Cited by 2 Related articles

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2002

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 Discovery of novel tumor markers of pancreatic cancer using global gene expression technology

CA Iacobuzio-Donahue, A Maitra, GL Shen-Ong… – The American journal of …, 2002 – Elsevier

… to identify additional potential markers of pancreatic carcinoma, we used the Gene Logic Inc …BioExpress platform and Affymetrix GeneChip arrays to identify genes differentially expressed in a … This mismatch control is analyzed using the GeneLogic informatics filter that compares …Cited by 335 Related articles All 11 versions

Expression profiling of a human cell line model of prostatic cancer reveals a direct involvement of interferon signaling in prostate tumor progression

J Shou, R Soriano, SW Hayward… – Proceedings of the …, 2002 – National Acad Sciences

… Furthermore, in silico data-mining with the GeneLogic database revealed that expression of the IFN-inducible genes was down-regulated in approximately 30% of the 49 clinicallycharacterized samples of prostatic adenocarcinomas …Cited by 96 Related articles All 11 versions

[BOOK] Predicting gene expression using artificial neural networks

L Lindefelt – 2002 – diva-portal.org

… 2.7 Data The gene expression data used for this project is from a database that AstraZeneca has leased from the company Gene Logic Inc. The database consists of the three sub- databases BioExpress, ToxExpress and PharmExpress. BioExpress consists of gene …

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2001

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Applying data warehouse concepts to gene expression data management

VM Markowitz, T Topaloglou – Proceedings 2nd Annual IEEE …, 2001 – ieeexplore.ieee.org

Gene Logic’s GeneExpress® database products contain gene expression data generated using primarily the … GeneExpress products are available as DataSuites, such as BioExpress and ToxExpress … disease or tissue specific samples (see http://www.genelogic.com/gexpress …

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2000

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Differentiating genomics companies

R James – Nature biotechnology, 2000 – nature.com

… Another database, BioExpress, contains gene expression measurements from a wide range of human tissue samples in normal, diseased, and treated conditions, as well as extensive clinical information on all of the tissue donors. Like Incyte, Gene Logic has a number of big …Cited by 16 Related articles All 7 versions

High-throughput gene expression analysis for drug discovery

GG Lennon – Drug Discovery Today, 2000 – Elsevier

Gene Logic currently incorporates the Affymetrix GeneChip probe array in its closed gene expression studies, while using the open READS system for detecting novel genes … One GeneExpress database (BioExpress ™ ) is used primarily for target selection and prioritization …

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Ascenta 

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2016

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Methods and reagents for detecting bioactive lipids

RA Sabbadini, WA Garland, G Hansen – US Patent 9,274,129, 2016 – Google Patents

Compositions and methods for producing monoclonal antibodies and their derivatives reactive against bioactive lipid targets are described. These compositions include derivatized lipids, each of which comprises a bioactive lipid that having a polar head group and at least one hydrocarbon 

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2015

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Immune-derived moieties reactive against lysophosphatidic acid

RA Sabbadini, WA Garland, G Hansen – US Patent 9,217,749, 2015 – Google Patents

US9217749B2 – Immune-derived moieties reactive against lysophosphatidic acid – Google Patents. Immune-derived moieties reactive against lysophosphatidic acid. Download PDF Info. Publication number US9217749B2. US9217749B2 …  Cited by 6 Related articles All 4 versions 

Novel bioactive lipid derivatives, and methods of making and using the same

RA Sabbadini, WA Garland – US Patent App. 14/451,394, 2015 – Google Patents

US20150031055A1 – Novel bioactive lipid derivatives, and methods of making and using the same – Google Patents. Novel bioactive lipid derivatives, and methods of making and using the same. Download PDF Info. Publication …

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2013

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Synthesis of quinoline derivatives: discovery of a potent and selective phosphodiesterase 5 inhibitor for the treatment of Alzheimer’s disease

J Fiorito, F Saeed, H Zhang, A Staniszewski… – European journal of …, 2013 – Elsevier

… cGMP while the remaining PDEs have mixed specificity (PDE1, PDE2, PDE3, PDE10, and PDE11) [2], [3]. Among all PDEs, PDE5 is widely expressed in a variety of tissues, such as brain, smooth muscle, lung, platelets and kidney (see Gene Logic’s ASCENTA System and [4], [5 …Cited by 64 Related articles All 6 versions

Evaluation of Tyro3 expression, Gas6-mediated Akt phosphorylation, and the impact of anti-Tyro3 antibodies in melanoma cell lines

SJ Demarest, J Gardner, MC Vendel, E Ailor… – Biochemistry, 2013 – ACS Publications

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2012

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Iniparib plus paclitaxel and carboplatin as initial treatment of advanced or recurrent uterine carcinosarcoma: a Gynecologic Oncology Group Study

C Aghajanian, MW Sill, AA Secord, MA Powell… – Gynecologic …, 2012 – Elsevier

… Gene expression analysis to characterize the expression level of PARP1 and PARP1 related genes using a microarray expression generated from well annotated diseased and normal tissue samples has been performed (ASCENTA database; Gene Logic, Gaithersburg) …Cited by 27 Related articles All 5 versions

Method for treatment of pancreatitis

LA Tartaglia, TM Barnes, RM Coopersmith… – US Patent App. 13 …, 2012 – Google Patents

US20120009183A1 – Method for treatment of pancreatitis – Google Patents. Method for treatment of pancreatitis. Download PDF Info. Publication number US20120009183A1. US20120009183A1 US13/171,058 US201113171058A …All 2 versions 

Treatment of breast cancer with iodonitrobenzamides in combination with anti-tumor agents

BM Sherman, C Bradley… – US Patent App. 13/430,475, 2012 – Google Patents

US20120269861A1 – Treatment of breast cancer with iodonitrobenzamides in combination with anti-tumor agents – Google Patents. Treatment of breast cancer with iodonitrobenzamides in combination with anti-tumor agents. 

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2011

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A phase II trial of paclitaxel and carboplatin in women with advanced or recurrent uterine carcinosarcoma

RA Lacour, E Euscher, EN Atkinson, CC Sun… – International Journal of …, 2011 – ijgc.bmj.com

… Likewise, defects in DNA mismatch repair and TP53 have been recognized as factors in uterine CS tu- morigenesis.23 This, along with the suggestion of PARP over- expression in uterine CS (ASCENTA database; Gene Logic, Gaithersburg, Md), brings the exploration of novel …  Cited by 44 Related articles All 6 versions

Novel estrogen-related genes and potential biomarkers of ovarian endometriosis identified by ifferential expression analysis

K Vouk, T Šmuc, C Guggenberger… – The Journal of steroid …, 2011 – Elsevier

… These were obtained from the Genelogic ASCENTA ® System (http://www.genelogic. com), a commercial database that provides microarray gene-expression profiles from clinically relevant normal and diseased human tissue sample sets …Cited by 30 Related articles All 7 versions

Biomarker for microdomain disease

K Higashi, T Mikami – US Patent App. 13/120,843, 2011 – Google Patents

… Analysis of GM2A Gene in Obese Patient; Distribution of expression of GM2A gene in a human normal tissue was examined using Ascenta of Gene Logic Inc., which is a commercially available database listing gene expression data by the tissue and the disease of a human …

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2010

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Information technology solutions for integration of biomolecular and clinical data in the identification of new cancer biomarkers and targets for therapy

H Hackl, G Stocker, P Charoentong, B Mlecnik… – Pharmacology & …, 2010 – Elsevier

Skip to main content Skip to article … Cited by 10 Related articles All 6 versions

A novel adipokine GM2AP impairs insulin signaling

K Higashi, T Mikami, T Yamada, H Kawashima… – Biochemical and …, 2010 – Elsevier

 2.8. Gene logic ASCENTA database … With the Gene Logic ASCENTA database, p-values were calculated using the Welch’s t-test (for unequal variance) with the two sample set means for the selected gene fragment. 3. Results. 3.1 

Cited by 5 Related articles All 7 versions

Upregulation of poly (ADP-ribose) polymerase-1 (PARP1) in triple-negative breast cancer and other primary human tumor types

V Ossovskaya, IC Koo, EP Kaldjian… – Genes & …, 2010 – journals.sagepub.com

Poly (ADP-ribose) polymerase-1 (PARP1) is a key facilitator of DNA repair and is implicated in pathways of tumorigenesis. PARP inhibitors have gained recent att…  Cited by 160 Related articles All 5 versions

Selection of relevant species

M Subramanyam, N Rinaldi… – Pharmaceutical …, 2010 – Wiley Online Library

Page 1. 1 Selection of Relevant Species MEENA SUBRAMANYAM , PhD , NICOLA RINALDI , PhD , ELISABETH MERTSCHING , PhD , and DAVID HUTTO , PhD, DVM Contents 1 Introduction 1.1 Species Selection: Biologics …

 Cited by 14 Related articles All 2 versions

Treatment of breast cancer with a PARP inhibitor alone or in combination with anti-tumor agents

BM Sherman, C Bradley – US Patent 7,732,491, 2010 – Google Patents

In one aspect, the present invention provides a method of treating breast cancer that is negative for at least one of ER, PR, or HER2, comprising administering to a subject at least one PARP inhibitor. In another aspect, the present invention provides a method of treating breast cancer …  Cited by 36 Related articles All 4 versions 

Method for treating inflammatory diseases of the digestive tract

LA Tartaglia, TM Barnes, RM Coopersmith… – US Patent …, 2010 – Google Patents

US7842709B2 – Method for treating inflammatory diseases of the digestive tract – Google Patents. Method for treating inflammatory diseases of the digestive tract. Download PDF Info. Publication number US7842709B2. US7842709B2 …Cited by 

Treatment of breast cancer with a parp inhibitor alone or in combination with anti-tumor agents

BM Sherman, C Bradley – US Patent App. 12/496,593, 2010 – Google Patents

US20100003192A1 – Treatment of breast cancer with a parp inhibitor alone or in combination with anti-tumor agents – Google Patents. Treatment of breast cancer with a parp inhibitor alone or in combination with anti-tumor agents. Cited by 6 Related articles All 2 versions 

Methods for breast cancer screening and treatment

D White, S Jin, RM Coopersmith… – US Patent App. 12 …, 2010 – Google Patents

US20100029734A1 – Methods for breast cancer screening and treatment – Google Patents. Methods for breast cancer screening and treatment. Download PDF Info. Publication number US20100029734A1. US20100029734A1 …

Cited by 6 Related articles All 2 versions 

[PDF] googleapis.com

Method for reducing gastrointestinal adverse effects of cytotoxic agents

SR Donahue, JJ Byrnes – US Patent App. 12/704,286, 2010 – Google Patents

A method for moderating a gastrointestinal adverse effect induced by at least one cytotoxic agent, for example ionizing radiation and/or at least one chemotherapeutic agent, in a subject comprises administering to the subject a therapeutically effective amount of an ACE2 inhibitor …

Treatment of uterine cancer and ovarian cancer with a parp inhibitor alone or in conbination with anti-tumor agents

BM Sherman, C Bradley – US Patent App. 12/502,943, 2010 – Google Patents

US20100009930A1 – Treatment of uterine cancer and ovarian cancer with a parp inhibitor alone or in conbination with anti-tumor agents – Google Patents. Treatment of uterine cancer and ovarian cancer with a parp inhibitor …  Cited by 6 Related articles All 2 versions 

Methods and compositions for treating skin conditions

K Pojasek, D Steinberg, D Zohar – US Patent App. 12/599,911, 2010 – Google Patents

US20100278784A1 – Methods and compositions for treating skin conditions – Google Patents. Methods and compositions for treating skin conditions. Download PDF Info. Publication number US20100278784A1. US20100278784A1 …

Cited by 94 Related articles All 2 versions 

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2009

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Phosphodiesterase 5 inhibition improves synaptic function, memory, and amyloid-β load in an Alzheimer’s disease mouse model

D Puzzo, A Staniszewski, SX Deng… – Journal of …, 2009 – Soc Neuroscience Cited by 242 Related articles

[PDF] Novel PDE5 Inhibitors as a Therapeutic Tool Against Alzheimer’s Disease O Arancio – alz.washington.edu

… from APP/PS1 mice Page 13. Sildenafil decreases Aβ levels in APP/PS1 mice Page 14. Is there any PDE5 in human hippocampus? Page 15. Database of human brain Gene Logic’s ASCENTA System 0/24 20/24 3/24 0/28 23/28 3/ 28 Page 16. Relative expression (× 10 -6 ) 0 40 … All 2 versions 

Methods of treating and preventing acute myocardial infarction

WR Baumbach, H Shankar… – US Patent App. 12 …, 2009 – Google Patents

… Alternatively, commercial products such as the ASCENTA® system (GeneLogic, Gaithersburg, Md.) provide expression data from healthy and diseased tissues that have been pre-screened and analyzed. Thus, the search for

Cited by 2 Related articles All 2 versions 

Method for treating er+ breast cancer

RM Coopersmith, DW White, S Jin… – US Patent App. 12 …, 2009 – Google Patents

US20090012052A1 – Method for treating er+ breast cancer – Google Patents. Method for treating er+ breast cancer. Download PDF Info. Publication number US20090012052A1. US20090012052A1 US12/100,053 US10005308A …

Cited by 7 Related articles All 2 versions 

Method for treatment of pancreatitis

LA Tartaglia, TM Barnes, RM Coopersmith… – US Patent App. 12 …, 2009 – Google Patents

A method for treating acute or chronic pancreatitis in a subject comprises administering to the subject a therapeutically effective amount of an ACE2 inhibitor.  Related articles All 2 versions

Treatment of uterine cancer and ovarian cancer with a parp inhibitor alone or in combination with anti-tumor agents

BM Sherman, C Bradley… – US Patent App. 12/269,833, 2009 – Google Patents

US20090123419A1 – Treatment of uterine cancer and ovarian cancer with a parp inhibitor alone or in combination with anti-tumor agents – Google Patents. Treatment of uterine cancer and ovarian cancer with a parp inhibitor …

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2008

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Human rhomboid family-1 gene silencing causes apoptosis or autophagy to epithelial cancer cells and inhibits xenograft tumor growth

Z Yan, H Zou, F Tian, JR Grandis, AJ Mixson… – Molecular cancer …, 2008 – AACR

Skip to main content. AACR Journals: Cancer Discovery; Cancer Epidemiology, Biomarkers & Prevention; Cancer Immunology Research; Cancer Prevention Research; Cancer Research; Clinical Cancer Research; Molecular Cancer Research; Molecular Cancer Therapeutics …Cited by 75 Related articles All 9 versions

Breast cancer screening and treatment methods

RM Coopersmith, DW White, S Jin… – US Patent App. 11 …, 2008 – Google Patents

US20080132474A1 – Breast cancer screening and treatment methods – Google Patents. Breast cancer screening and treatment methods. Download PDF Info. Publication number US20080132474A1. US20080132474A1 US11 …Cited by 2 Related articles All 2 versions 

Method for reducing or alleviating inflammation in the digestive tract

LA Tartaglia, TM Barnes, RM Coopersmith… – US Patent App. 11 …, 2008 – Google Patents

US20080234345A1 – Method for reducing or alleviating inflammation in the digestive tract – Google Patents. Method for reducing or alleviating inflammation in the digestive tract. Download PDF Info. Publication number US20080234345A1 …Cited by 1 Related articles All 2 versions 

Immune-Derived Moieties Reactive Against Bioactive Lipids, and Methods of Making and Using Same

RA Sabbadini, WA Garland, G Hansen – US Patent App. 11/755,485, 2008 – Google Patents

Compositions and methods for producing monoclonal antibodies and their derivatives reactive against bioactive lipid targets are described. These compositions include derivatized lipids, each of which comprises a bioactive lipid that having a polar head group and at least one hydrocarbon …Cited by 4 Related articles All 2 versions 

Protein kinase inhibitors

DJ Bearss, CL Grand, XH Liu… – US Patent App. 11 …, 2008 – Google Patents

US20080207632A1 – Protein kinase inhibitors – Google Patents. Protein kinase inhibitors. Download PDF Info. Publication number US20080207632A1. US20080207632A1 US11/932,617 US93261707A US2008207632A1 US …Related articles All 2 versions 

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2007

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BREAST CANCER SCREENING AND TREATMENT METHODS

RM Coopersmith, DW White, S Jin… – US Patent App. 11/ …, 2007 – Google Patents LOUIS, MO 63105 (73) Assignee: Gene Logic Inc., Gaithersburg, MD (US) (21) Appl.No.: 11/935,870 (22) Filed: Nov. 6, 2007 Related US Application Data (60) Provisional application No. 60/865,094, filed on Nov. 9, 2006. (51) Int. CI.

Bioinformatics approaches in the study of cancer

DA Hanauer, DR Rhodes… – Current molecular …, 2007 – ingentaconnect.com

Gene Logic also offers their ASCENTA® System [20] which contains about 8,700 Affymetrix GeneChip® mouse, human, and rat arrays. projects ranging from management of clinical trials to tools for analysis of gene expression data. [19] http://www.genelogic.com/docs/pdfs Cited by 24Related articlesBL Direct – *******************************************************************

2006

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Therapeutic implications of a human neutralizing antibody to the macrophage-stimulating protein receptor tyrosine kinase (RON), a c-MET family member

JM O’toole, KE Rabenau, K Burns, D Lu… – Cancer research, 2006 – AACR

Skip to main content …Cited by 135 Related articles

Ron in Breast Development and Cancer 

SE Waltz – 2006 – apps.dtic.mil

… Western blot analyses. In addition, through access to the Gene Logic Ascenta database, we were able to assess RON expression profile in a variety of cancer tissues as well as in the NCI-60 cancer cell line panel. Table 1 is …Related articles 

[PDF] Identifizierung und funktionelle Charakterisierung neuer Interaktionspartner des renalen ROMK-Kaliumkanals

F Bundis – 2006 – core.ac.uk

Page 1. Identifizierung und funktionelle Charakterisierung neuer Interaktionspartner des renalen ROMK-Kaliumkanals Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften vorgelegt beim Fachbereich für Biochemie, Chemie und Pharmazie …Related articles 

The role of bioinformatics in genomic medicine

AHC van Kampen, AJG Horrevoets – Cardiovascular Research, 2006 – Springer

Ascenta Gene expression database www.genelogic.com Bodymap Data bank of expression bodymap.ims.u-tokyo.ac.jp information CaGE Cardiac Gene Expression www.cage.wbmei.jhu. edu knowledge base EBI European Bioinformatics http://www.ebi.ac.uk (SRS, MIAME, Institute …Cited by 4 Related articles All 7 versions

Targeting the lymphotoxin-β receptor with agonist antibodies as a potential cancer therapy

M Lukashev, D LePage, C Wilson, V Bailly, E Garber… – Cancer research, 2006 – AACR

Skip to main content. AACR Publications: Cancer Discovery; Cancer Epidemiology, Biomarkers & Prevention; Cancer Immunology Research; Cancer Prevention Research; Cancer Research; Clinical Cancer Research; Molecular Cancer Research; Molecular Cancer Therapeutics

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2005

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 Methods for enhancing gene expression analysis

U Scherf, G Hoke, D Wilson, D Barnes – US Patent App. 10/504,072, 2005 – Google Patents

… filed by Ore Pharmaceuticals Inc filed Critical Ore Pharmaceuticals Inc 2004-06-04 Priority to US10/504,072 priority patent/US20050221310A1/en 2004-06-04 Priority to PCT/US2004/017621 priority patent/WO2005003370A2/en 2005-04-11 Assigned to GENE LOGIC, INC … Cited by 1 Related articles All 2 versions 

Methods for enhancing gene expression analysis

U Scherf, G Hoke, D Wilson, D Barnes – US Patent App. 10/948,635, 2005 – Google Patents

…to PCT/US2004/017621 priority patent/WO2005003370A2/en 2004-09-24 Application filed by Ore Pharmaceuticals Inc filed Critical Ore Pharmaceuticals Inc 2004-09-24 Priority to US10/948,635 priority patent/US20050170375A1/en 2005-04-18 Assigned to GENE LOGIC

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2004

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The ASCENTA system reveals candidate cancer treatment targets by their co-regulation across the human body: Using a known target, CDC2, to seed discovery

R Nadimpalli, C Coberley, D Schwartz, G Shen, L Mertz… – 2004 – AACR

Skip to main content. AACR Publications: Cancer Discovery; Cancer Epidemiology, Biomarkers & Prevention; Cancer Immunology Research; Cancer Prevention Research; Cancer Research; Clinical Cancer Research; Molecular Cancer Research; Molecular Cancer Therapeutics …

Match/X, a gene expression pattern recognition algorithm used to identify genes which may be related to CDC2 function and cell cycle regulation

C Coberley, M Elashoff, L Mertz – Cell Cycle, 2004 – Taylor & Francis

… authors contributed equally to this work *Correspondence to: Lawence Mertz; Gene Logic Inc.; 610 … 20879 USA; Tel.: 240.364.6227; Fax: 240.364.6262; Email: lmertz@genelogic.com Received 03 … sets used for Match/X™ validation were derived from the ASCENTA™ System, an …

Cited by 3 Related articles All 3 versions

[PDF] MICROARRAYS IN MEDICAL RESEARCH

M Kamarinos, M Waltham – asbmb.org.au

… Microarray/main.html). GeneLogic’s Affymetrix subscription database (ASCENTA system; www.genelogic.com) is particularly powerful boasting expression profiles from approximately 9,000 human, mouse and rat samples. In order to …

Genchek/ Genowiz/OptGene/Irnacheck  

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2022

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Ethanol Extract of Elaeagnus glabra f. oxyphylla Branches Alleviates the Inflammatory Response Through Suppression of Cyclin D3/Cyclin-Dependent Kinase 11p58 …

HS Lim, E Sohn, YJ Kim, BY Kim… – Natural Product …, 2022 – journals.sagepub.com

… Normalized data were analyzed using Genowiz 4.0 (Ocimum Biosolutions). The

normalization decides the average intensity of all samples numerically equivalent to the average …

[HTML] Comparison of transcriptome between high-and low-marbling fineness in longissimus thoracis muscle of Korean cattle

SH Beak, M Baik – Animal Bioscience, 2022 – ncbi.nlm.nih.gov

… The read count data were processed based on the quantile normalization method using

Genowiz ver. 4.0.5.6 (Ocimum Biosolutions, Hyderabad, India). For functional annotation, we 

Anti-obesity effect of sulforaphane in broccoli leaf extract on 3T3-L1 adipocytes and ob/ob mice

SS Ranaweera, P Natraj, P Rajan… – The Journal of …, 2022 – Elsevier

… The read count data were processed based on Quantile normalization method using the

Genowiz version 4.0.5.6 (Ocimum Biosolutions, India). The PPI network was analyzed using …

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2021

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Blue laser-induced selective vasorelaxation by the activation of NOSs

SW Park, S Park, HK Choi, HJ Park, W Yu, HS Kim… – Microvascular …, 2021 – Elsevier

… The RC (Read Count) data were processed based on Global normalization method using

the Genowiz ™ version 4.0.5.6 (Ocimum Biosolutions, India). Gene classification was based 

[HTML] Association of protein Z with prediabetes and type 2 diabetes

YU Bae, JH You, NH Cho, LE Kim… – Endocrinology and …, 2021 – ncbi.nlm.nih.gov

… The numerical data were analyzed using the Genowiz 4.0 software (Ocimum Biosolutions,

Indianapolis, IN, USA). After analysis, the data on protein information were annotated using …

[HTML] Restoration of the adipogenic gene expression by naringenin and naringin in 3T3-L1 adipocytes

LA Dayarathne, SS Ranaweera, P Natraj… – Journal of Veterinary …, 2021 – ncbi.nlm.nih.gov

… The RT (read count) data were processed based on the quantile normalization method

using the Genowiz version 4.0.5.6 (Ocimum Biosolutions, India). Gene classification was …

Functional study of acetaldehyde dehydrogenase 1 (ALDH1) in keratinocytes: microarray integrating bioinformatics approaches

SJ Yin, MW Park, BN Lee, JM Yang… – Journal of …, 2021 – Taylor & Francis

… The numeric data were analyzed using Genowiz 4.0 TM (Ocimum Biosolutions, India). After

… Data were normalized with Genowiz 4.0 TM (Ocimum Biosolutions, India) software. Scatter …

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2020

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Functional study of 14-3-3 protein epsilon (YWHAE) in keratinocytes: microarray integrating bioinformatics approaches

SJ Yin, JR Lee, H Kwak, BN Lee, JW Han… – Journal of …, 2020 – Taylor & Francis

… The numeric data were analyzed using Genowiz 4.0™ (Ocimum Biosolutions, India). After …

Data were normalized with Genowiz 4.0™ (Ocimum Biosolutions, India) software. Scatter plot …

Effects of enzymatically modified chestnut starch on the gut microbiome, microbial metabolome, and transcriptome of diet-induced obese mice

ES Lee, EJ Song, YD Nam, TG Nam, HJ Kim… – International Journal of …, 2020 – Elsevier

… The read count data were processed based on the global normalization method using

Genowiz version 4.0.5.6 (Ocimum Biosolutions, Hyderabad, India). Gene classification was based …

HTML] Anti-inflammatory effect of sulforaphane on LPS-stimulated RAW 264.7 cells and ob/ob mice

SS Ranaweera, CY Dissanayake, P Natraj… – Journal of veterinary …, 2020 – ncbi.nlm.nih.gov

… The Read count (RT) data were analyzed based on the Quantile normalization method

using the Genowiz™ version 4.0.5.6 (Ocimum Biosolutions, India). The PPI network was …

[HTML] Comparison of transcriptome between high-and low-marbling fineness in longissimus thoracis muscle of Korean cattle

SH Beak, M Baik – Animal Bioscience, 2022 – ncbi.nlm.nih.gov

… The read count data were processed based on the quantile normalization method using

Genowiz ver. 4.0.5.6 (Ocimum Biosolutions, Hyderabad, India). For functional annotation, we …

Protein profiling and angiogenic effect of hypoxia-cultured human umbilical cord blood-derived mesenchymal stem cells in hindlimb ischemia

KH Han, AK Kim, MH Kim, DH Kim, HN Go, D Kang… – Tissue and Cell, 2017 – Elsevier

… The numeric data were analyzed with Genowiz 4.0TM (Ocimum Biosolutions, India) and

protein information was annotated by means of the UniProt DB. The phosphorylation ratio was 

Dynein-mediated nuclear translocation of yes-associated protein through microtubule acetylation controls fibroblast activation

E You, P Ko, J Jeong, S Keum, JW Kim, YJ Seo… – Cellular and Molecular …, 2020 – Springer

… The Read Count data were processed based on the Global normalization method using

the Genowiz™ version 4.0.5.6 (Ocimum Biosolutions, India). Hierarchical clustering analysis 

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2019

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[HTML] Enhanced Anti-Cancer Effects of Conditioned Medium from Hypoxic Human Umbilical Cord–Derived Mesenchymal Stem Cells

KH Han, AK Kim, GJ Jeong, HR Jeon… – … journal of stem cells, 2019 – ncbi.nlm.nih.gov

… The data were analyzed using Genowiz 4.0TM (Ocimum Biosolutions, India) and proteins

that were upregulated or downregulated in H-CM compared with N-CM (>1.5 fold) were …

Histone demethylase KDM3B regulates the transcriptional network of cell-cycle genes in hepatocarcinoma HepG2 cells

MJ An, DH Kim, CH Kim, M Kim, S Rhee, SB Seo… – Biochemical and …, 2019 – Elsevier

… The RC (Read Count) data were processed based on Quantile normalization method using

the Genowiz™ version 4.0.5.6 (Ocimum Biosolutions, India). Gene classification and gene …

 

Annona atemoya leaf extract ameliorates cognitive impairment in amyloid-β injected Alzheimer’s disease-like mouse model

HS Lim, YJ Kim, E Sohn, J Yoon… – Experimental …, 2019 – journals.sagepub.com

… Data normalization was conducted using the Genowiz 4.0 (Ocimum Biosolutions, Gaithersburg,

MD) and determined the average intensity of samples comparable to that of all genes. …

Dexamethasone induces a specific form of ramified dysfunctional microglia

MJ Park, HS Park, MJ You, J Yoo, SH Kim… – Molecular …, 2019 – Springer

… The RT (Read Count) data were processed based on global normalization method using

the Genowiz™ version 4.0.5.6 (Ocimum Biosolutions, India). Gene classification was based on …

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2018

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Histone demethylase KDM7A controls androgen receptor activity and tumor growth in prostate cancer

KH Lee, S Hong, M Kang, CW Jeong… – … Journal of Cancer, 2018 – Wiley Online Library

… The RT (Read Count) data were processed based on Global normalization method using

the Genowiz ™ version 4.0.5.6 (Ocimum Biosolutions, India). We performed gene clustering …

[HTML] The LuxS/AI-2 quorum-sensing system of Streptococcus pneumoniae is required to cause disease, and to regulate virulence-and metabolism-related genes in …

MK Yadav, JE Vidal, YY Go, SH Kim… – Frontiers in cellular …, 2018 – frontiersin.org

… The microarray data were analyzed using Genowiz 4.0™ (Ocimum Biosolutions,

Hyderabad, India), and normalized with Global LOWESS. The cutoffs for upregulated and …

Phytochemical allylguaiacol exerts a neuroprotective effect on hippocampal cells and ameliorates scopolamine-induced memory impairment in mice

HS Lim, BY Kim, YJ Kim, SJ Jeong – Behavioural Brain Research, 2018 – Elsevier

… Normalized data were analyzed using Genowiz 4.0 (Ocimum Biosolutions, India). The

normalization makes the average intensity of all samples numerically equivalent to the average …

Licochalcone A attenuates acne symptoms mediated by suppression of NLRP3 inflammasome

G Yang, HE Lee, SH Yeon, HC Kang… – Phytotherapy …, 2018 – Wiley Online Library

… The RT (Read Count) data were processed based on Quantile normalization method

using the Genowiz ™ version 4.0.5.6 (Ocimum Biosolutions, Hyderabad, India). …

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2017

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[HTML] Enhanced Anti-Cancer Effects of Conditioned Medium from Hypoxic Human Umbilical Cord–Derived Mesenchymal Stem Cells

KH Han, AK Kim, GJ Jeong, HR Jeon… – … journal of stem cells, 2019 – ncbi.nlm.nih.gov

… The data were analyzed using Genowiz 4.0TM (Ocimum Biosolutions, India) and proteins

that were upregulated or downregulated in H-CM compared with N-CM (>1.5 fold) were 

Expression and biochemical analysis of codon-optimized polyphenol oxidase from Camellia sinensis (L.) O. Kuntze in E. coli

S Singh, D Singh, S Kumar – Process Biochemistry, 2017 – Elsevier

… 288 bp of CsPPO. In addition, codons were optimized for the expression of CsPPO synin E. coli using OptGene™ (Ocimum Biosolutions, USA) as mentioned in supplementary data (Supplementary Fig. 1). CsPPO syn was synthesized …

 

Estimation of low-dose radiation-responsive proteins in the absence of genomic instability in normal human fibroblast cells

JH Yim, JM Yun, JY Kim, SY Nam… – International Journal of …, 2017 – Taylor & Francis

… , the normalization data were analyzed using Genewiz 4.0™ (Ocimum Biosolution, India). All

… The numerical data were analyzed using Genexiz 4.0™ (Ocimum Biosolutions, India). After …

Save Cite Cited by 9 Related articles All 3 versions

Control of cancer stem cell like population by intracellular target identification followed by the treatment with peptide-siRNA complex

JS Suh, HJ Lee, H Nam, BS Jo, DW Lee, JH Kim… – Biochemical and …, 2017 – Elsevier

… The numeric data were analyzed using Genowiz 4.0TM (Ocimum Biosolutions, Hyderabad,

India). Phosphorylation ratio was calculated as below. phosphorylation ratio = phospho …

[HTML] Characteristics of a regulator of G-protein signaling (RGS) rgsC in Aspergillus fumigatus

Y Kim, IB Heo, JH Yu, KS Shin – Frontiers in microbiology, 2017 – frontiersin.org

… Loess normalization and selection of fold-changed genes were performed using GenoWiz

4.0 (Ocimum biosolutions, India). The data is available in the Gene Expression Omnibus (GEO…

​​An ultra-effective method of generating extramultipotent cells from human fibroblasts by ultrasound

YS Lee, H Heo, J Lee, SU Moon, WY Jung, YK Park… – Biomaterials, 2017 – Elsevier

… The RC (Read Count) data were processed based on the quantile normalization method

using Genowiz ™ version 4.0.5.6 (Ocimum Biosolutions, India). Gene classification was based 

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2016

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[HTML] Identification of novel therapeutic targets in the secretome of ionizing radiation‑induced senescent tumor cells

HJ Hwang, SH Jung, HC Lee, NK Han… – Oncology …, 2016 – spandidos-publications.com

… The obtained numerical data were analyzed using Genowiz 4.0™ (Ocimum Biosolutions,

Indianapolis, IN, USA). Following analysis, the protein data were annotated using UniProt DB (…

Latent Kaposi’s sarcoma-associated herpesvirus infection in bladder cancer cells promotes drug resistance by reducing reactive oxygen species

S Lee, J Jang, H Jeon, J Lee, SM Yoo, J Park… – Journal of …, 2016 – Springer

… The numeric data were analyzed using Genowiz 4.0TM (Ocimum Biosolutions). The array

data were deposited in NCBI’s Gene Expression Omnibus (GEO) and can be accessed by 

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2015

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Process for designing diverged, codon-optimized large repeated dna sequences

DJ Merlo, I Larrinua, S Bevan – US Patent App. 14/415,115, 2015 – Google Patents

… sequence according to predetermined parameters. In particular embodiments, the computer-implemented software program may be OPTGENE™ (available from Ocimum Biosolutions). A sample amino acid repeat sequence.

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2013

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A nutrigenomic framework to identify time-resolving responses of hepatic genes in diet-induced obese mice

HS Heo, E Kim, SM Jeon, EY Kwon, SK Shin, H Paik… – Molecules and …, 2013 – Springer

… 1. Clustering of hepatic gene transcripts For clustering of hepatic gene transcripts, the Self-Organizing Map (SOM) algorithm (Quackenbush, 2001) was applied. We used Genowiz (Ocimum Biosolutions, India) with the SOM tool to arrange all data samples …Cited by 8 Related articles

Functionally redundant protein phosphatase genes PTP2 and MSG5 co-regulate the calcium signaling pathway in Saccharomyces cerevisiae upon exposure to high …

WA Laviña, M Sugiyama, Y Kaneko… – Journal of bioscience and …, 2013 – Elsevier

… All strains were cultivated in YPDA media and calcium treatment was done by supplementing the YPDA medium with 0.3 M CaCl 2 . Four independent DNA microarray data were analyzed using Genowiz (Ocimum Biosolutions) …

Cited by 13 Related articles 

Role of pilus proteins in adherence and invasion of Streptococcus agalactiae to the lung and cervical epithelial cells

P Sharma, H Lata, DK Arya, AK Kashyap… – Journal of Biological …, 2013 – ASBMB

… Hybridized chips were scanned using an Affymetrix 428TMArray scanner at three different PMT gains, and the images were analyzed using Genowiz software (Ocimum Biosolutions). Analysis was performed to detect differentially expressed genes among the groups …Cited by 27 Related articles

[HTML] Differentially expressed genes during contrasting growth stages of Artemisia annua for artemisinin content

P Nair, A Misra, A Singh, AK Shukla, MM Gupta… – PLoS …, 2013 – journals.plos.org

… chip. Hybridized chips were scanned using Affymetrix 428TM Array Scanner at three different PMT gains (40, 50 and 60) and the data was analyzed using Genowiz software (Ocimum Biosolutions, Hyderabad). Image analysis …

  Cited by 27 Related articles

[PDF] Suppression mechanism of the calcium sensitivity in Saccharomyces cerevisiae ptp2Dmsg5D double disruptant involves a novel HOG-independent function of …

WA Laviña, H Shahsavarani, A Saidi, M Sugiyama… – 2013 – researchgate.net

… was performed in triplicates. Gene enrichment analysis using Genowiz The microarray data were analyzed for distinctive expression using Genowiz 4.0 (Ocimum Biosolutions, India). Replicated gene values were combined …

  Related articles 

Decreased defense gene expression in tolerance versus resistance to Verticillium dahliae in potato

HH Tai, C Goyer, D De Koeyer, A Murphy… – Functional & integrative …, 2013 – Springer

… Analysis of microarray data. Microarray data were analyzed using the Genowiz 4.0 software (Ocimum Biosolutions, Gaithersburg, MD, USA). Double channel analysis of 07506-01 and 12120-03 data was done using print-tip loess normalization with a smoothing factor of 0.1 … Cited by 11 

Lowered expression levels of a tumor suppressor gene—caveolin-1 within dysregulated gene networks of Fanconi anemia

P Shyamsunder, P Vidyasekar, AR Shukla, S Mohan… – Gene, 2013 – Elsevier

… The statistical analysis was carried out using R package and the biological analysis was carried out using Genowiz software (Ocimum Biosolutions, USA) and Gene Spring GX 10 (Agilent Technologies, USA). 2.5. Gene ontology analysis … Cited by 14 Related articles 

The role of aldehyde/alcohol dehydrogenase (AdhE) in ethanol production from glycerol by Klebsiella pneumoniae

BR Oh, WK Hong, SY Heo, M Joe, JW Seo… – Journal of industrial …, 2013 – Springer

… expression ratios (reference vs. test) were obtained. Microarray data analysis was performed using Genowiz 4.0 (Ocimum Biosolutions, Hyderabad, India). Global lowess was used for data analysis with normalization. The cut-offs for …Cited by 6 Related articles

[HTML] Escherichia coli YmdB regulates biofilm formation independently of its role as an RNase II modulator

T Kim, J Lee, K Kim – BMC microbiology, 2013 – bmcmicrobiol.biomedcentral.com

… ratios (reference vs. test sample). Microarray data analysis was performed using Genowiz 4.0™ (Ocimum Biosolutions). Global lowess (Locally weighted scatter plot smoothing) method was used for data normalization. The cut-off …  Cited by 7 Related articles All 11 versions 

Identification of novel target genes involved in Indian Fanconi anemia patients using microarray

P Shyamsunder, KS Ganesh, P Vidyasekar, S Mohan… – Gene, 2013 – Elsevier

… obtained. The statistical analysis was carried out using the R package and the biological analysis was carried out using Genowiz TM software (Ocimum Biosolutions, USA). 2.4. Functional clustering and gene ontology analysis …  Cited by 8 Related articles All 6 versions

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2012

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[PDF] Functional annotation of expressed sequence tags of Papaver somniferum

A Priya, H Tripathi, DK Yadav, F Khan, V Gupta… – Plant Omics, 2012 – pomics.com

sequences retrieved from dbEST were cleaned, clustered and assembled through PHRED (Ewing and Green, 1998), RepeatMasker, Cross-Match, PHRAP and CAP3 (Huang and Madan, 1999) softwares with the help of Gencheck software (Ocimum Biosolutions, USA; www

Gene expression profile of early in vitro biofilms of Streptococcus pneumoniae

MK Yadav, SK Kwon, CG Cho, SW Park… – Microbiology and …, 2012 – Wiley Online Library

… ratios (planktonic vs biofilm samples). Microarray data analysis was carried out by Genowiz 4.0 (Ocimum Biosolutions, Hyderabad, India). Global Lowess was used for data analysis with normalization. The benchmarks for up …Cited by 19 Related articles All 11 versions

N-acetyl cysteine suppresses the foam cell formation that is induced by oxidized low density lipoprotein via regulation of gene expression

HJ Sung, J Kim, Y Kim, SW Jang, J Ko – Molecular biology reports, 2012 – Springer

… Data were analyzed by Genowiz 4.0 TM (Ocimum Biosolutions, Hyderabad, India) and normalized using intensity-dependent global normalization (LOWESS). To categorize the functional annotation of genes, the database of Gene Ontology TM Consortium was applied …Cited by 15 Related articles All 11 versions

The effect of secretory factors of adipose-derived stem cells on human keratinocytes

KM Moon, YH Park, JS Lee, YB Chae, MM Kim… – International journal of …, 2012 – mdpi.com

The beneficial effects of adipose-derived stem cell conditioned medium (ADSC-CM) on skin regeneration have been reported. Although the mechanism of how ADSC-CM promotes skin regeneration is unclear, ADSC-CM contained various growth factors and it is an excellent raw …Cited by 90 Related articles All 16 versions 

[PDF] Differential Gene Expression Profile in Essential Hypertension

P Yang – Genetics and Pathophysiology of Essential …, 2012 – intechopen.com

… rats treated with FPTIII kidney Codelink Uniset Rat 1Bioarrays Affymetrix Scanner 428, Imagene and Genowiz softwares by Ocimum Biosolutions (India) and subjected to arsinh transformation 2398 genes were upregulated and …Related articles All 3 versions 

[HTML] Role of position 627 of PB2 and the multibasic cleavage site of the hemagglutinin in the virulence of H5N1 avian influenza virus in chickens and ducks

KA Schat, J Bingham, JM Butler, LM Chen, S Lowther… – PloS one, 2012 – journals.plos.org

Highly pathogenic H5N1 avian influenza viruses have caused major disease outbreaks in domestic and free-living birds with transmission to humans resulting in 59% mortality amongst 564 cases. The mutation of the amino acid at position 627 of the viral polymerase basic-2 protein …Cited by 39 Related articles All 21 versions 

Activation tagging in Solanum tuberosum: Innate immune activation affects potato tuber periderm development

D Frank – 2012 – qspace.library.queensu.ca

… Page 30. ` 19 Microarray analysis Microarray data were analyzed using the Genowiz 4.1 software (Ocimum Biosolutions, Madhapur, Hyderabad). For double channel analysis, data was normalized using print-tip lowess normalization with a smoothing factor of 0.1 …Related articles All 2 versions 

[HTML] biomedcentral.com

[HTML] Non structural protein of avian influenza A (H11N1) virus is a weaker suppressor of immune responses but capable of inducing apoptosis in host cells

S Mukherjee, S Majumdar, VC Vipat… – Virology …, 2012 – virologyj.biomedcentral.com

The Non-Structural (NS1) protein of Influenza A viruses is an extensively studied multifunctional protein which is commonly considered as key viral component to fight against host immune responses. Even though there has been a lot of studies on the involvement of NS1 protein …Cited by 14 Related articles All 19 versions 

Functional Analysis of Vibrio vulnificus SmcR, a Quorum-sensing Master Regulator, as a Novel Control Target

김승민 – 2012 – s-space.snu.ac.kr

Page 1. 저작자표시-비영리-변경금지 2.0 대한민국 이용자는 아래의 조건을 따르는 경우에 한하여 자유롭게 ● 이 저작물을 복제, 배포, 전송, 전시, 공연 및 방송할 수 있습니다. 다음과 같은 조건을 따라야 합니다: ● 귀하는, 이 저작물의 …

[PDF] Yersiniosis and Food Safety

K Isshiki, RC Ray, D Montet – downloads.hindawi.com

Page 1. Journal of Pathogens Guest Editors: Latiful Bari, Dike O. Ukuku, Kenji Isshiki, Ramesh C. Ray, and Didier Montet Yersiniosis and Food Safety Page 2. Yersiniosis and Food Safety Page 3. Journal of Pathogens Yersiniosis and Food Safety …Related articles 

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2011

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HTML] A review on worldwide essential software resources in pharmacy

PY Mali, SJ Panchal – Chronicles of Young Scientists, 2011 – cysonline.org

history recording, etc. http://www.applied-maths.com/gelcompar/gelcompar.htm GenchekIt is an integral database system that can used to access, store, organize and retrieve DNA, protein and vector sequences. http://www.ocimumbio Related articles All 2 versions Cite

Differentially expressed genes in sensitive and tolerant rice varieties in response to salt-stress

A Pandit, V Rai, TR Sharma, PC Sharma… – Journal of plant …, 2011 – Springer

… genes. The array data were analyzed using GeneChip Operating Software (GCOS 1.2) and Genowiz software (Ocimum Biosolutions, India). Robust multichip average (RMA) algorithm method was used for normalization. Two 

Cited by 24 Related articles All 7 versions

Transcriptomic analysis of Haematococcus lacustris during astaxanthin accumulation under high irradiance and nutrient starvation

DK Kim, SJ Hong, JH Bae, N Yim, ES Jin… – Biotechnology and …, 2011 – Springer

… sample). Microarray data analysis was carried out by Genowiz 4.0TM (Ocimum Biosolutions,India). Global LOWESS was used for data analysis with normalization. The benchmarks for up-regulated and down-regulated genes in hybridization were 2.0 and 0.5-fold, respectively …Cited by 30 Related articles All 7 versions

[PDF] CORRELATIONS BETWEEN VARIABLE BROILER PERFORMANCE AND GENE EXPRESSION AND MICROFLORA IN THE GUT RJ MOORE, D. STANLEY …

MS GEIER, TM CROWLEY – 22 nd ANNUAL AUSTRALIAN POULTRY … – researchgate.net

… Statistical tests were carried out using Genowiz Version 4.0. 5.3 (Ocimum Biosolutions) to determine all genes that were differentially expressed (p= 0.01) between the groups under consideration, either high and low AME groups or good and poor FCR groups …Related articles All 3 versions 

[HTML] Pandemic (H1N1) 2009 influenza virus induces weaker host immune responses in vitro: a possible mechanism of high transmissibility

S Mukherjee, VC Vipat, AC Mishra… – Virology …, 2011 – virologyj.biomedcentral.com

… Data Analysis. Microarray data analysis was carried out with GENOWIZ Microarray data and pathway analysis tool (Ocimum Biosolutions, Hyderabad, India). Replicated values for genes were merged and median values of the expression ratios were considered for the dataset …Cited by 27 Related articles All 19 versions 

The application of microarray technology to the identification of Tc1-like element sequences in fish genomes

R Wenne, L Handschuh, A Pocwierz-Kotus… – Marine Biology …, 2011 – Taylor & Francis

… After normalization (double-channel normalization between arrays based on subtraction of control probe mean, followed by log2-transformation) using Genowiz 4.0 software (Ocimum Biosolutions), the probe intensity data was analysed using R (http:// http://www.R-project.org; R …Cited by 3 Related articles All 5 versions

[PDF] Gene Expression Analysis for Type-2 Diabetes Mellitus-A Case Study on Healthy vs Diabetes with ParentalHistory

CS Vasamsetty, SR Peri, AA Rao, K Srinivas… – International Journal of …, 2011 – ijetch.org

… expressed genes. ACKNOWLEDGMENT The authors acknowledge Ocimum Biosolutions, Hyderabad, India for analysis of the microarray data using their proprietary microarray analysis tool Genowiz. REFERENCES [1] John …

Related articles All 3 versions 

[PDF] Biochemical Characterization of Fermented Cucumber Spoilage using Nontargeted, Comprehensive, Two-dimensional Gas Chromatography-Time-of-Flight …

S Johanningsmeier – 2011 – repository.lib.ncsu.edu

Page 1. ABSTRACT JOHANNINGSMEIER, SUZANNE DUNN. Biochemical Characterization of Fermented Cucumber Spoilage using Non-targeted, Comprehensive, Two-dimensional Gas Chromatography-Time-of-Flight Mass …

Cited by 7 Related articles 

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2010

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Retrotransposon expression in ethanol-stressed Saccharomyces cerevisiae

D Stanley, S Fraser, GA Stanley… – Applied microbiology and …, 2010 – Springer

… reference pool (Gasch et al. 2000). Following hybridisation, the glass slides were scanned using a GenePix-Pro 4000B scanner and analysed using Genowiz™ 4.0.2.1 software (Ocimum Biosolutions). The original data from this

Cited by 16 Related articles All 19 versions

Transcriptional changes associated with ethanol tolerance in Saccharomyces cerevisiae

D Stanley, PJ Chambers, GA Stanley… – Applied microbiology …, 2010 – Springer

… Following hybridisation, the glass slides were scanned using a GenePix 4000B scanner and analysed using Genowiz™ 4.0.2.1 software (Ocimum Biosolutions). Microarray data were normalised prior to statistical analysis using a print tip Lowess (Yang et al …

Cited by 41 Related articles All 19 versions

[HTML] Host gene expression profiling in influenza A virus-infected lung epithelial (A549) cells: a comparative analysis between highly pathogenic and modified …

AK Chakrabarti, VC Vipat, S Mukherjee… – Virology …, 2010 – virologyj.biomedcentral.com

… Grid alignment was done using gene annotation files and raw data were extracted into MS EXCEL. Data Analysis. Data was analyzed using GENOWIZ Microarray and Pathway analysis tool (Ocimum Biosolutions, Hyderabad, India) 

  Cited by 58 Related articles All 20 versions 

Immunomodulatory cytokines determine the outcome of Japanese encephalitis virus infection in mice

SM Biswas, S Kar, R Singh… – Journal of medical …, 2010 – Wiley Online Library

… Data Analysis Data were analyzed using Genowiz Microarray and Pathway analysis tool (OcimumBiosolutions, Hyperabad, India). Replicated genes were merged and median values of the expression ratios of these repli- cated genes were further considered for the dataset …  Cited by 35 Related articles All 8 versions

Identification of differentially expressed genes for diabetes with parental history vs healthy using Microarray data analysis

VC Sekhar, AA Rao, PS Rao… – 2010 3rd International …, 2010 – ieeexplore.ieee.org

… is under progress. ACKNOWLEDGMENT The Authors Acknowledges Ocimum Biosolutions, Hyderabad, India. For analysis of the microarray data using their proprietary microarray analysis tool Genowiz. REFERENCES [I] M …Related articles All 2 versions

Chloroplast‐derived enzyme cocktails hydrolyse lignocellulosic biomass and release fermentable sugars

D Verma, A Kanagaraj, S Jin, ND Singh… – Plant biotechnology …, 2010 – Wiley Online Library

Skip to Main Content … Cited by 114 Related articles All 12 versions

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2009

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[HTML] TLR2 polymorphisms, Arg753Gln and Arg677Trp, are not associated with increased burden of tuberculosis in Indian patients

D Biswas, SK Gupta, G Sindhwani… – BMC research …, 2009 – biomedcentral.com

of Biochemistry, University of Delhi, India. To sense the SNPs in the selected DNA sequences, multiple sequence alignment was performed using built in interface for ClustalW[8] in Genchek software version 2.4.1.5 from Ocimum Biosolutions. Cited by 10 Related articles All 12 versions Cite

[HTML] BMC research notes Volume: 2 ISSN: 1756-0500 ISO Abbreviation: BMC Res Notes Publication Date: 2009

D Biswas, SK Gupta, G Sindhwani, A Patras – Detail: – biomedsearch.com

of Biochemistry, University of Delhi, India. To sense the SNPs in the selected DNA sequences, multiple sequence alignment was performed using built in interface for ClustalW [8 ] in Genchek software version 2.4.1.5 from Ocimum Biosolutions. Related articles 

Global upregulation of gene expression associated with renal dysfunction in DOCA–salt-induced hypertensive rats occurs via signaling cascades involving epidermal …

IF Benter, H Canatan, M Benboubetra, MHM Yousif… – Vascular …, 2009 – Elsevier

..supplier (GE Healthcare). Data analysis was performed using Imagene and Genowiz softwares by Ocimum Biosolutions (India) and subjected to arsinh transformationas described by Huber et al. (2002). The Benjamini and Cited by 24 Related articles 

A systematic approach to understanding bacterial responses to oxygen using Taverna and Webservices

S Maleki-Dizaji, M Rolfe, P Fisher… – … Conference on Biomedical …, 2009 – Springer

… (ie GeneSpring, GenoWiz) that can provide links to data- bases that define pathways, functional …Hybridisation took place to Ocimum OciChip K-12 V2 microarrays (Ocimum; Hydera- bad, India) at 42 °C overnight and washed according to the manufacturers instructions …Cited by 7 Related articles

[PDF] Transcriptional Activation of p53 gene and stabilization of p53 by its Amino-Terminus Domain

AK Sharma – 2009 – ir.inflibnet.ac.in

… information management system. Genowiz ™ incorporates an entire army of analysis tools for the efficient analysis of microarray data. Ocimum also provides analyses that are not required as a part of this study. A list of services provided in the microarray realm can be found at …Related articles 

[PDF] Generation and characterisation of ethanol-tolerant saccharomyces cerevisiae mutants

D Stanley – 2009 – vuir.vu.edu.au

Page 1. \ v;l \.TIOM AMD CHARACISRISA. jmm wBS Page 2. GENERATION AND CHARACTERISATION OF ETHANOL-TOLERANT Saccharomyces cerevisiae MUTANTS A thesis submitted for the degree of DOCTOR OF PHILOSOPHY By DRAGANA STANLEY …Related articles All 3 versions 

STATISTICAL ANALYSIS IDENTIFIES GENES IN PROSTATE CANCER

M Vidhya – International Journal of Medical Engineering and …, 2009 – Inderscience

microarray data obtained for the normal and malignant samples for 8,900 genes was taken and it was analysed to identify the genes that are differently expressed in tumour samples in comparison to the normal samples from tissues and cell lines using the tool Genowiz™ 3.1. Related articlesAll 7 versions

Application of Data Mining Algorithms in Pharmaceutical Research and Development

KV Balakin… – Pharmaceutical Data Mining, 2009 – Wiley Online Library

ac.uk/microarray/maxd/ A data warehouse and visualization environment for genomic expression data Genowizhttp://www.ocimumbio.com/ web/default.asp A comprehensive multiplatform package for tracking and analyzing Gene Expressions data Related articlesAll 3 versions

PANDEMIC (H1N1) 2009 INFLUENZA VIRUS INDUCES WEAKER HOST IMMUNE RESPONSES IN VITRO: A POSSIBLE MECHANISM OF HIGH TRANSMISSIBILITY

[PDF] from biomedcentral.com

S Mukherjee, VC Vipat, AC Mishra, SD Pawar… – Virol J, 2011 – biomedcentral.com

Grid align- ment was done by gene annotation files and raw data were extracted into MS EXCEL[15]. Data Analysis Microarray data analysis was carried out with GENOWIZ Microarray dataand pathway analysis tool (Oci- mum Biosolutions, Hyderabad, India). Cited by 6Related articlesView as HTMLAll 9 versions

A Systematic Approach to Understanding Bacterial Responses to Oxygen Using Taverna and Webservices

[PDF] from shef.ac.uk

S Maleki-Dizaji, M Rolfe, P Fisher… – … Conference on Biomedical …, 2009 – Springer

23 _____ (ie GeneSpring, GenoWiz) that can provide links to data- bases that define pathways, functional categories and gene ontologies. Many Cited by 1Related articlesAll 3 versions

 New approach to Genomics Experients Taking Advantage of Virtual Laboratory System

[PDF] from poznan.pl

L Handschuh, M Lawenda, P Stępniak… – … Methods In Science …, 2009 – man.poznan.pl

Raw data in a text file (csv, gpr or similar) are then submitted to normaliza- tion, filtration and high-level analysis, using sophisticated software (eg R Bioconductor, Multi Experiment Viewer, Gene Spring, Genowiz). Result reports are saved as text or graphic files (eg pdf, jpg). Cited by 3Related articlesView as HTMLAll 2 versions

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2008

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[PDF] Subtype selectivity in phosphodiesterase 4 (PDE4): a bottleneck in rational drug design

RD Design – Current Pharmaceutical Design, 2008 – 203.199.182.73

Page 1. 3854 Current Pharmaceutical Design, 2008,14, 3854-3872 Subtype Selectivity in Phosphodiesterase 4 (PDE4): A Bottleneck in Rational Drug Design P. Srivani1, D. Usharani2’3, Eluvathingal D. Jemmis2′” and G. Narahari Cited by 22 Related articles All 9 versions Cite

Design of microarray probes for detection of mutations

P Almeida, L Carreto, JL Oliveira – … , 2008. BIOTECHNO’08. …, 2008 – ieeexplore.ieee.org

efficiency and robustness, ie finding the best set of probes for specific hybridization conditions [4]. Several software packages already exist to assist on the design of microarray probes: AlleleID [5], Oligowiz [6], Gencheck [7], Oligo [7] OcimumBiosolutions, “GenChek,” GenChek. Cited by 1 Related articles All 4 versions Cite

Visual software tools for bioinformatics

T Arndt – Journal of Visual Languages & Computing, 2008 – Elsevier

View Within Article. Genchek [7] (available for Linux, Mac, Windows and Unix) is a comprehensive software suit. It has support for several operations on DNA and proteins. Gencheck is shown in Fig. 10. Cited by 4 Related articles All 2 versions Cite

[HTML] SERIAL CHANGES IN EXPRESSION OF FUNCTIONALLY CLUSTERED GENES IN PROGRESSION OF LIVER FIBROSIS IN HEPATITIS C PATIENTS

[HTML] from nih.gov

Y Takahara, M Takahashi, QW Zhang… – World journal of …, 2008 – ncbi.nlm.nih.gov

The gene expression data were subjected to hierarchical clustering analysis using Genowiz™ software (Ocimum Biosolutions). All genes in Figure Figure11 were subjected to hierarchical clustering analysis using Genowiz™.

Cited by 11Related articlesBL DirectAll 8 versions

Differential gene expression analysis of a known hepatotoxin, N-acetyl-p-amino-phenol (APAP) as compared to its non-toxic analog, N-acetyl-m-amino-phenol (AMAP …

P Priyadarsiny, SK Khattar, R Malik… – The Journal of …, 2008 – J-STAGE

Hierarchi- cal analysis and self-organizing maps were used to cluster the genes in different groups. Furthermore, gene annota- tion and pathway analysis was carried out using Genowiz software. RESULTS AND DISCUSSION Cited by 3Related articlesBL DirectAll 7 versions

[HTML] Nonvirally modified autologous primary hepatocytes correct diabetes and prevent target organ injury in a large preclinical model

[HTML] from plos.org

NKF Chen, J San Wong, IHC Kee, SH Lai… – PloS one, 2008 – dx.plos.org

All statistical tests and the area under the curve (AUC) were calculated with GraphPad Prism (GraphPad Software Inc., USA). Cluster analysis of GeneChip® data was performed using algorithms in Genowiz (Ocimum Biosolutions Ltd., India). P<0.05 was considered significant. Cited by 10Related articlesCachedAll 9 versions

[HTML] Nonvirally modified autologous primary hepatocytes correct diabetes and prevent target organ injury in a large preclinical model

NKF Chen, J San Wong, IHC Kee, SH Lai, CH Thng… – PLoS …, 2008 – journals.plos.org

BackgroundCurrent gene- and cell-based therapies have significant limitations which impede widespread clinical application. Taking diabetes mellitus as a paradigm, we have sought to overcome these limitations by ex vivo electrotransfer of a nonviral insulin expression vector into …  Cited by 25 Related articles All 14 versions 

[HTML] Serial changes in expression of functionally clustered genes in progression of liver fibrosis in hepatitis C patients

Y Takahara, M Takahashi, QW Zhang… – World journal of …, 2008 – ncbi.nlm.nih.gov

… This calculation was performed using SPSS (SPSS Inc., IL, USA). The gene expression data were subjected to hierarchical clustering analysis using Genowiz™ software (Ocimum Biosolutions). Pathway analysis of PCR data …Cited by 31 Related articles All 9 versions

Gene expression microarray data analysis demystified

PC Roberts – Biotechnology annual review, 2008 – Elsevier

Skip to main content Skip to article Elsevier logo: Journals & Books. Create accountSign in. Sign inCreate account. Journals & Books. Help. Download PDFDownload. Share.  Cited by 36 Related articles All 4 versions

Microarray Data Analysis Tool (MAT)

S Selvaraja – 2008 – rave.ohiolink.edu

Page 1. MICROARRAY DATA ANALYSIS TOOL (MAT) A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Sudarshan Selvaraja December, 2008 Page 2. ii …  Related articles All 3 versions 

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2007

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Genomic and morphological features of a banchine polydnavirus: comparison with bracoviruses and ichnoviruses

R Lapointe, K Tanaka, WE Barney, JB Whitfield… – Journal of …, 2007 – Am Soc Microbiol

University of Kentucky. The DNA sequences were first edited to remove vector sequences and then assembled using either SeqMan II (Lasergene DNAStar) or Genchek v. 2061 (Ocimum Biosolutions). Contigs were built using

Cited by 40 Related articles BL Direct All 8 versions Cite

< i> Pisum sativum contains a factor with strong homology to eIF5B

S Rasheedi, S Ghosh, M Suragani, N Tuteja… – Gene, 2007 – Elsevier

Multiple sequence alignments and phylogenetic tree analysis were performed by CLUSTALW version1.74 (Thompson et al., 1994) and Genchek™ sequence analysis software package (Ocimum Biosolutions, India). Hydrophilicity Cited by 2 Related articles All 6 versions Cite

Shared and species-specific features among ichnovirus genomes

K Tanaka, R Lapointe, WE Barney, AM Makkay… – Virology, 2007 – Elsevier

The DNA sequences were first edited to remove vector sequences and then assembled using either SeqMan II (Lasergene DNAStar) or Genchek v. 2061 (OcimumBiosolutions). Contigs were built with a minimum of 50 nt overlap Cited by 36 Related articles All 4 versions Cite

Automatic design of microarray probes for mutations detection

PRSG Almeida – 2007 – ria.ua.pt 26 3.3. Genchek ….. 26 3.4. 27 Figure 3.2- OligoWiz software. …. 28 Figure 3.3 –

Genchek software….. 28 Figure 3.4 – OligoDesign software. Related articles All 2 versions

Analysis of expression data: an overview

A Grewal, P Lambert, J Stockton – Current protocols in human …, 2007 – Wiley Online Library

… X. DecisionSite for Microarray Analysis (Spotfire). X. X. Expressionist (GeneData). X. X. X.

GeneSpring (Agilent Technologies). X. X. Genowiz (Ocimum Biosolutions). X. X. RMAExpress 0.4.1 (Bolstad, 2006). X. S+ArrayAnalyzer (Insightful). X. X. X. X. TeraGenomics (IMC). X. X …  Cited by 24 Related articles All 7 versions

Gene expression assays

J Kirby, PR Heath, PJ Shaw, FC Hamdy – Advances in clinical chemistry, 2007 – Elsevier

Skip to main content …

Cited by 31 Related articles 

[PDF] Data Integration and Analysis: P. falciparum Microarray Data as a Case Study

R Rao, A Sivakumar, G Rao – bioinformatics.cs.vt.edu

… 6.ACKNOWLEDGMENTS We would like to thank Dr. Sandhya Kiran, Mr. JP Mehta and Ms. Madhuri for critical comments. We would also like to thank Ocimum Biosolutions Ltd. for their technical support and the Genowiz team for their encouragement. Page 5 …  Related articles All 3 versions 

23 Visualization of Protein Microarray Data

K Clancy – Functional Protein Microarrays in Drug Discovery, 2007 – books.google.com

… s Page 442. # GeneX Genowiz Longhorn Array Database LIMaS (Laboratory Information … net Ocimum Biosolutions Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin Mammalian Genetics Unit, Harwell UK …Related articles

MICROARRAY ANALYSIS IN THE ZEBRAFISH (DANIO RERIO) LIVER AND TELENCEPHALON AFTER EXPOSURE TO LOW CONCENTRATION OF 17ALPHA-ETHINYLESTRADIOL

CJ Martyniuk, ER Gerrie, JT Popesku, M Ekker… – Aquatic toxicology, 2007 – Elsevier

2.4. Microarray analysis and gene categorization. Raw intensity data were analyzed using GenoWiz™. To normalize the microarray data, we log 2 transformed raw expression data and used the double channel normalization function in Genowiz. Cited by 40Related articlesAll 9 versions

 [HTML] Software-MIAME-FGED

[HTML] from mged.org

N Abeygunawardena – 2007 – mged.org

included! If you’d like to be informed of new developments as they occur, please join the maxd_announce mailing list.”; Genowiz™ – A comprehensive multi platform package for tracking and analyzing Gene Expressions data. Cached

[CITATION] 23 Visualization of Protein Microarray Data

K Clancy – Functional protein microarrays in drug discovery, 2007 – CRC

Related articles

Gene expression assays

J Kirby, PR Heath, PJ Shaw… – Advances in clinical chemistry, 2007 – Elsevier

Gene Sight, BioDiscovery. Expressionist, Gene Data. Chip Inspector, Genomatix. Teragenomic,IMC. JMP microarray, SAS. Genowiz, Ocimum Biosolutions. Genomics Suite, Partek. Resolver,Rosetta. Decision Site, Spotfire. Avadis, Strand Genomics. Freeware. Cited by 15Related articlesBL DirectAll 5 versions

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2006

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Analysis of expression data: an overview

A Grewal, P Lambert, J Stockton – Current protocols in human …, 2007 – Wiley Online Library

… X. DecisionSite for Microarray Analysis (Spotfire). X. X. Expressionist (GeneData). X. X. X. GeneSpring (Agilent Technologies). X. X. Genowiz (Ocimum Biosolutions). X. X. RMAExpress 0.4.1 (Bolstad, 2006). X. S+ArrayAnalyzer (Insightful). X. X. X. X. TeraGenomics (IMC). X. X …  Cited by 24 Related articles All 7 versions

Genomic and morphological features of a banchine polydnavirus: comparison with bracoviruses and ichnoviruses

R Lapointe, K Tanaka, WE Barney, JB Whitfield… – Journal of …, 2007 – Am Soc Microbiol

… The DNA sequences were first edited to remove vector sequences and then assembled

using either SeqMan II (Lasergene DNAStar) or Genchek v. 2061 (Ocimum Biosolutions). …

Gene expression assays

J Kirby, PR Heath, PJ Shaw, FC Hamdy – Advances in clinical chemistry, 2007 – Elsevier

Skip to main content …Cited by 31 Related articles All 6 versions

[PDF] Data Integration and Analysis: P. falciparum Microarray Data as a Case Study

R Rao, A Sivakumar, G Rao – bioinformatics.cs.vt.edu

… 6.ACKNOWLEDGMENTS We would like to thank Dr. Sandhya Kiran, Mr. JP Mehta and Ms. Madhuri for critical comments. We would also like to thank Ocimum Biosolutions Ltd. for their technical support and the Genowiz team for their encouragement. Page 5 …  Related articles All 3 versions 

23 Visualization of Protein Microarray Data

K Clancy – Functional Protein Microarrays in Drug Discovery, 2007 – books.google.com

… s Page 442. # GeneX Genowiz Longhorn Array Database LIMaS (Laboratory Information … Ocimum Biosolutions Section of Molecular Genetics and Microbiology, Institute for Cellular andMolecular Biology, University of Texas at Austin Mammalian Genetics Unit, Harwell UK …

[PDF] DATA INTEGRATION AND ANALYSIS: P. FALCIPARUM MICROARRAY DATA AS A CASE STUDY

[PDF] from vt.edu

R Rao, A Sivakumar… – bioinformatics.cs.vt.edu

In this paper, we explore further insights into published P. falciparum microarray data using the application Genowiz™. The genes involved in various steps of the pathway have been traced to their various clusters generated by using Genowiz™ SOM. Related articlesView as HTMLAll 3 versions

Global gene expression analysis of the effects of vinblastine on endothelial cells, when eluted from a thermo‐responsive polymer

E McLucas, H Gallagher, Y Rochev… – … Research Part A, 2006 – Wiley Online Library

analysis. Genowiz software and MAVI software (Ocimum Biosolutions) were then used to generate fold increases or decreases induced by the two different drug concentrations relative to the values generated for the polymer alone. Cited by 3Related articlesBL DirectAll 6 versions

Data Mining in Gene Expression Data Analysis: A Survey

J Han… – Processing and managing complex data for …, 2006 – books.google.com

Page 392. Data Mining in Gene Expression Data Analysis: A Survey 375 Chapter XII Data Mining in Gene Expression Data Analysis: A Survey Jilin Han, University of Oklahoma, USA Le Gruenwald, University of Oklahoma, USA Related articles

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2005

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Growth of Indian biotech companies, in the context of the international biotechnology industry

U Palnitkar – Journal of commercial biotechnology, 2005 – ingentaconnect.com

Ocimum Biosolutions Labronica Inc., USA Global marketing of Biotracker-LIMS United Bioinformatics Inc., Canada Marketing rights for Gencheck and Biotracker Hospital for JointDiseases Orthopaedic Institute (HJD), New York Research into musculoskeletal disease using Cited by 5 Related articles All 7 versions Cite

The stability of the Arabidopsis transcriptome in transgenic plants expressing the marker genes nptII and uidA

SE Ouakfaoui, B Miki – The Plant Journal, 2005 – Wiley Online Library Skip to Main Content …

Spoligotyping 

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Mapmygenome acquired the rights to sell Spoligotyping from Ocimum Biosolutions in 2014. 

Ocimum acquired the spoligotyping kit through an acquisition of the Biomolecules division of Isogen Lifesciences based in The Netherlands. Since the acquisition in 2006, Ocimum has continued to invest in additional R&D and is in the process of adding several new kits to its portfolio.

As with other products, below is a chronological publication reference to the spoligotyping kit. The earliest publication for this product is dated way back in 1997. Many publications will refer to Isogen as that was the name of our subsidiary. Recently we changed the name back to Ocimum Biosolutions but we continue to find references to Isogen.

With the large number of references of over 400 and from labs across the world, the spoligotyping kit has been validated for over 15 years now giving confidence to researchers across the globe using it.

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2022

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Era of TB elimination: Growing need to understand diversities of Mycobacterium tuberculosis lineages!

A Tejashree, PA Mahesh, MK Karthik, A Azeem… – Indian Journal of …, 2022 – Elsevier

… The Spoligotyping was carried out by amplifying the whole DR region using the commercially

available kit (Mapmygenome, Hyderabad) according to a standardized method using the …

[HTML] Molecular Epidemiology and Polymorphism Analysis in Drug-Resistant Genes in M. tuberculosis Clinical Isolates from Western and Northern India

V Rana, N Singh, C Nikam, P Kambli… – Infection and Drug …, 2022 – ncbi.nlm.nih.gov

… kit (Ocimum Biosolutions, Hyderabad). The standardized spoligotyping protocol has

been described previously. Briefly, the cycling conditions used for spoligotyping were: initial 

[HTML] Spoligotyping of Clinical Isolates of Mycobacterium tuberculosis Complex Species in the Oromia Region of Ethiopia

B Hussien, A Zewude, B Wondale, A Hailu… – Frontiers in Public …, 2022 – ncbi.nlm.nih.gov

… (29) and as per the spoligotype kit supplier’s instructions (Ocimum Biosolutions,

Ijsselstein, The Netherlands). DNA from known strains of M. bovis SB1176 and M. …

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2021

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2020

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2019

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[PDF] UPDATE ON VIRULENCE FACTORS IN MYCOBACTERIA

R Brosch – Инфекция и иммунитет, 2019 – iimmun.ru… cially available kit (Mapmygenome India Ltd., Madhapur, India) according to the manufacturer’s protocol …Spoligotypes were obtained for 127 (97.8%) isolates … When spoligotyping and MIRU-VNTR typing was used in com- bination, only tw o, out of 130 isolates, clustered both in …[HTML] plos.org

[HTML] Genetic diversity of Mycobacterium tuberculosis strains circulating in Botswana

T Mogashoa, P Melamu, SD Ley, EM Streicher… – PloS one, 2019 – journals.plos.org… A commercially available spoligotyping kit (Mapmygenome, Hyderabad India) was used for amplification, hybridization and detection of … RIF or to both INH and RIF and which clustered according to spoligotyping (n = 65 … A total of 458/461 isolates were successfully spoligotyped

Genetic diversity of Mycobacterium tuberculosis isolates causing pulmonary and extrapulmonary tuberculosis in the capital of Iran

S Hadifar, L Shamkhali, MK Kamakoli… – Molecular phylogenetics …, 2019 – Elsevier… All M.tb isolates were analyzed with Spoligotyping commercial kit (Mapmygenome Genomics company … 1. Distribution of M.tb genotypes, SIT and corresponding spoligotype patterns of all … There was 100% concordance between Spoligotyping and MIRU-VNTR data (except for …

Association of ubiA mutations and high-level of ethambutol resistance among Mycobacterium tuberculosis Thai clinical isolates

O Tulyaprawat, A Chaiprasert, P Chongtrakool… – Tuberculosis, 2019 – Elsevier… Spoligotyping was performed according to the manufacturer’s instructions (Mapmygenome, India) [17] … The octal code format of each strain was entered to assign Spoligotype International Type (SIT) and phylogenetic clade by using SITVITWEB, a database of the Pasteur …[HTML] frontiersin.org

Bayesian Assessment of the Accuracy of a PCR-Based Rapid Diagnostic Test for Bovine Tuberculosis in Swine

S Barandiaran, MS Perez Aguirreburualde… – Frontiers in veterinary …, 2019 – frontiersin.org… Spoligotyping was carried out using the spoligotyping kit (Mapmygenome India) … remaining 21% culture and PCR-negative samples (ie, 4.9% of all the samples) were M. avium complex (IS1245+)-positive (Table 3). All IS6110-positive samples showed spoligotypes that were …

Prevalence of Mycobacterium bovis infection in traditionally managed cattle at the wildlife-livestock interface in South Africa in the absence of control measures

PR Sichewo, EMC Etter, AL Michel – Veterinary Research …, 2019 – Springer… Spoligotyping assay was performed using a commercially available kit (Mapmygenome India Ltd.) to … Spoligotyping confirmed the species identification of the 12 isolates from cattle and 22 from … the isolates showed identical profiles belonging to the SB 0130 spoligotype, which is …Related articles All 2 versions

Molecular characterization of Mycobacterium bovis infection in cattle and buffalo in Amazon Region, Brazil

PAM Carneiro, TN Pasquatti, H Takatani… – Veterinary Medicine …, 2019 – Wiley Online Library… of spacer sequences, using a miniblotter according to the manufacturer’s instructions (MapMyGenome) … The spoligotyping was performed on 35 M. bovis isolates and six types of … The other municipalities presented only one spoligotype each, Manacapuru (SB0822), Itacoatiara …

MOLECULAR TYPING OF MYCOBACTERIUM KANSASII—A GLOBAL PERSPECTIVE

Z Bakuła, F Arias, E Bachiyska, E Borroni… – Инфекция и …, 2019 – iimmun.ru… cially available kit (Mapmygenome India Ltd., Madhapur, India) according to the manufacturer’s protocol … Spoligotypes were obtained for 127 (97.8%) isolates … When spoligotyping and MIRU-VNTR typing was used in com- bination, only tw o, out of 130 isolates, clustered both in …  Cited by 1 Related articles 

[HTML] Occurrence of disputed rpoB mutations among Mycobacterium tuberculosis isolates phenotypically susceptible to rifampicin in a country with a low incidence …

NM Al-Mutairi, S Ahmad… – BMC infectious …, 2019 – bmcinfectdis.biomedcentral.com

… Molecular detection of resistance for ethambutol and pyrazinamide and fingerprinting by spoligotyping were also performed for isolates with an rpoB mutation. Results … Spoligotyping showed that the isolates belonged to different M. tuberculosis lineages. Conclusions …  Cited by 5 Related articles All 8 versions 

Usefulness of 3’- 5’ IS6110-RFLP genotyping and spoligotyping of Mycobacterium tuberculosis isolated in a tertiary hospital: a retrospective study detecting unsuspected epidemiological events. Silvia Maria de Almeida, Ana Carolina Malaspina, Clarisse Queico Fujimura Leite, Maria Helena Féres SaadRev Inst Med Trop Sao Paulo. 2019; 61: e51.  Published online 2019 Sep 12. Doi: 10.1590/S1678946201961051.PMCID: PMC6746203

Genotype diversity and distribution of Mycobacterium bovis from livestock in a small, high-risk area in northeastern Sicily, Italy.Cinzia Marianelli, Benedetta Amato, Maria Beatrice Boniotti, Maria Vitale, Flavia Pruiti Ciarello, Maria Lodovica Pacciarini, Vincenzo Di Marco Lo Presti.PLoS Negl Trop Dis. 2019 Jul; 13(7): e0007546. Published online 2019 Jul 15. doi: 10.1371/journal.pntd.0007546. PMCID: PMC6658142

Genetic diversity and drug susceptibility profiles of Mycobacterium tuberculosis obtained from  Saint Peter’s TB specialized Hospital, Ethiopia.Delesa Damena, Samuel Tolosa, Milkessa Hailemariam, Aboma Zewude, Adane Worku, Biruk Mekonnen, Temesgen Mohammed, Addisu Admasu, Emile R. Chimusa, Adane  Mihret, Tamrat Abebe, Gobena Ameni.PLoS One. 2019; 14(6): e0218545.  Published online 2019 Jun 24.  doi: 10.1371/journal.pone.0218545. PMCID: PMC6590806

Exploring the “Latin American Mediterranean” family and the RDRio lineage in Mycobacterium tuberculosis isolates from Paraguay, Argentina and Venezuela. Chyntia Carolina Díaz Acosta, Graciela Russomando, Norma Candia, Viviana Ritacco, Sidra E. G. Vasconcellos, Marcia de Berrêdo Pinho  Moreira, Nilda J. de Romero, Nora Morcillo, Jacobus Henri De Waard, Harrison Magdinier Gomes, Philip Noel Suffys.BMC Microbiol. 2019; 19: 131. Published online 2019 Jun 13. doi: 10.1186/s12866-019-1479-6. PMCID: PMC6567603

Genetic diversity and drug susceptibility patterns of the Mycobacterium tuberculosis complex in Yunnan, China. Ruolan Bai, Shuijing Chi, Xiaofei Li, Xiting Dai, Zhenhua Ji, Miaomiao Jian, Yunfeng  Bi, Feng Wang, Zhe Ding, Lisha Luo, Taigui chen, Aihua Liu, Fukai Bao,Biosci Rep. 2019 May 31; 39(5): BSR20181746.  Pre-published online 2019 Apr 15. Published online 2019 May 31. doi:  10.1042/BSR20181746. PMCID: PMC6542976

Demographic risk factors for extra-pulmonary tuberculosis among adolescents and adults in Saudi ArabiaHawra Al-Ghafli, Bright Varghese, Mushira Enani, Abdulrahman Alrajhi, Sameera Al Johani, Ali  Albarrak, Sahar Althawadi, Noura Elkizzi, Sahal Al Hajoj,PLoS One. 2019; 14(3): e0213846.  Published online 2019 Mar 27. doi: 10.1371/journal.pone.0213846. PMCID: PMC6436801

Tuberculosis Caused by Mycobacterium bovis in a Sheep Flock Colocated with a Tuberculous Dairy Cattle Herd in Central Ethiopia.Benti Deresa Gelalcha, Aboma Zewude, Gobena Ameni,J Vet Med. 2019; 2019: 8315137. Published online 2019 Mar 3. doi: 10.1155/2019/8315137. PMCID: PMC6421010

Whole-Genome Sequencing of Two Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from India. Syed Beenish Rufai, Sarman Singh, Microbiol Resour Announc. 2019 Feb; 8(7): e00007-19. Published online 2019 Feb 14. doi: 10.1128/MRA.00007-19. PMCID: PMC6376416

Active and latent tuberculosis among inmates in La Esperanza prison in Guaduas, Colombia Julio Guerra, Daniel Mogollón, Deccy González, Ricardo Sanchez, Zulma Vanessa Rueda, Carlos A. Parra-López, Martha Isabel Murcia, PLoS One. 2019; 14(1): e0209895. Published online 2019 Jan 25. doi:  10.1371/journal.pone. 0209895. PMCID: PMC6347203

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Spoligotyping for Identification of Pulmonary Tuberculosis with Type 2 Diabetes Mellitus Profiles in Warangal, TS

S Tanniru, S Asha, M Jojula – Anti-Infective Agents, 2018 – ingentaconnect.com… culosis) and MDR TB (Multi Drug Resistance Tuberculosis) and different Spoligotypes are represented … Molecu- lar methods like Spoligotyping are used to differentiate and identify species of … & molecular identification methods, we found most prevalent Spoligotype pattern which …Related articles

Clofazimine drug susceptibility testing for Mycobacterium tuberculosis: the case of using the right diluent

LH Sng, JWL Peh, MTL Kee, RTH Ong, CW Wong… – Pathology, 2018 – Elsevier… The isolates were identified as MTB using the BD MGIT TBc Identification Test (TBcID; Becton Dickinson, USA) and strain typed by spoligotyping (Ocimum Biosolutions, India). DST for clofazimine had been carried out using the MGIT method 10 at a concentration of 0.5 μg/mL …

[HTML] Investigation of a cluster of multi-drug resistant tuberculosis in a high-rise apartment block in Singapore

ZJM Ho, CBE Chee, RTH Ong, LH Sng… – International Journal of …, 2018 – Elsevier… elements [Figure 1]. The isolates were determined in May 2016 to have identical spoligotype(Ocimum Biosolutions, Hyderabad) and 24-loci Mycobacterial Interspersed Repetitive Unit –Variable Number of Tandem Repeat (MIRU-VNTR: Genoscreen, France) profiles (Chee et …Cited by 3 Related articles All 6 versions

[PDF] Comparison of PFGE, IS6110-RFLP, and 24-Locus MIRU-VNTR for Molecular Epidemiologic Typing of Mycobacterium tuberculosis Isolates with Known …

S Jeon, N Lim, S Park, M Park… – Journal of microbiology …, 2018 – pdfs.semanticscholar.org… Spoligotyping Spoligotyping was performed to identify the lineages of the isolates used in this …The spoligotypes were classified according to SITVITWEB clade assignments (http://www.pasteru-guadeloupe.fr.&nbsp; There was no spoligotype match found in the SITVIT database for …  Cited by 1 Related articles All 6 versions 

[CITATION] Mycobacterium bovis Infection in a Human in Malaysia

S Suraiya, NI Farakhin – Clinical Microbiology Newsletter, 2018 – Elsevier

[HTML] Molecular clustering of patients with Mycobacterium tuberculosis strains cultured from the diabetic and non-diabetic newly diagnosed TB positive cases

JW Mburu, L Kingwara, M Esther, N Andrew – Journal of Clinical …, 2018 – Elsevier… as described by Kamerbeek et, al. [9]. Spoligotyping was performed using the spoligotype kit (Ocimum bio solutions company, Netherlands) according to the manufacturer’s instructions. The direct repeats (DR) were amplified …Related articles All 3 versions

Multi-and extensively drug resistant Mycobacterium tuberculosis in South Africa: a molecular analysis of historical isolates

NE Maningi, LT Daum, JD Rodriguez… – Journal of clinical …, 2018 – Am Soc MicrobiolCited by 2 Related articles All 6 versions

Annotated genome sequences of 16 lineage 4 Mycobacterium tuberculosis strains from guatemala

JW Saelens, D Lau-Bonilla, A Moller… – Genome …, 2018 – Am Soc Microbiol… 5 Prime GmbH, Germany). Spoligotyping was carried out using the spoligotyping kit and protocol from Isogen Biosolutions (Ocimum Biosolutions Ltd., India), identifying the isolates as lineage 4 strains. Paired-end 50-bp reads …  Cited by 1 Related articles All 5 versions

[HTML] Risk factors associated with cluster size of Mycobacterium tuberculosis (Mtb) of different RFLP lineages in Brazil

RL Peres, SA Vinhas… – BMC infectious …, 2018 – bmcinfectdis.biomedcentral.com… Of the isolates spoligotyped, 448 (52%) were classified as LAM and 412 (48%) as … Isolates were also submitted to spoligotyping by a commercial kit (Ocimum Biosolutions Inc., India … a standard protocol [17, 18], allowing the classification of strains into spoligotype-based families …  Cited by 3 Related articles All 9 versions 

[HTML] Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates

P Palittapongarnpim, P Ajawatanawong… – Scientific …, 2018 – ncbi.nlm.nih.gov… of the single nucleotide variant (SNV) phylogenetic tree and the clades defined by spoligotyping revealed some monophyletic clades representing EAI2_MNL, EAI2_NTM and EAI6_BGD1 spoligotypes. Our work demonstrates that ambiguity in spoligotype assignment could be …  Cited by 5 Related articles All 11 versions

[HTML] Genotyping and molecular detection of multidrug-resistant Mycobacterium tuberculosis among tuberculosis lymphadenitis cases in Addis Ababa, Ethiopia

O Zewdie, A Mihret, T Abebe, A Kebede, K Desta… – New microbes and new …, 2018 – Elsevier… Spoligotyping was carried out using a commercially available kit from Ocimum Biosolutions (UK …Spoligotype patterns of each strain were prepared in binary and octal format and entered intothe recently released international spoligotyping database SITVITWEB [12] for …Cited by 2 Related articles All 6 versions

[HTML] Impact of Mycobacterium tuberculosis complex lineages as a determinant of disease phenotypes from an immigrant rich moderate tuberculosis burden …

B Varghese, M Enani, A Alrajhi… – Respiratory …, 2018 – respiratory-research.biomedcentral …… according to the manufacturer’s instructions. Primary genotyping of all isolates were carried out by using the commercially available spoligotyping assay (Ocimum Biosolutions, Hyderabad, India). The 24 loci based MIRU-VNTR …  Cited by 1 Related articles All 9 versions 

Genotypes of Mycobacterium bovis strains isolated from domestic animals and wildlife in Canada in 1985–2015

O Andrievskaia, C Turcotte, G Berlie-Surujballi… – Veterinary …, 2018 – Elsevier… Isolates were spoligotyped as described by Kamerbeek et al … The spacer sequences contained in the DR locus were detected by hybridization onto spoligotyping membranes using … in the DR locus was represented in a binary code, and translated into spoligotype octal codes …  Cited by 4 Related articles All 5 versions

[HTML] Association of gyrA and rrs gene mutations detected by MTBDR sl V1 on Mycobacterium tuberculosis strains of diverse genetic background from India

SB Rufai, J Singh, P Kumar, P Mathur, S Singh – Scientific reports, 2018 – nature.com… Spoligotyping was performed using the commercially available kit (Ocimum Biosolutions,Hyderabad … The hybridization patterns obtained in the binary format were transformed to an octal code for assessment with the spoligotype patterns using SITVIT2 database …Cited by 1 Related articles All 6 versions

[HTML] Bacterial risk factors for treatment failure and relapse among patients with isoniazid resistant tuberculosis

PVK Thai, DTM Ha, NT Hanh… – BMC infectious …, 2018 – bmcinfectdis.biomedcentral.com..Drug resistant tuberculosis (TB) is increasing in prevalence worldwide. Treatment failure and relapse is known to be high for patients with isoniazid resistant TB treated with standard first line regimens. However, risk factors for unfavourable outcomes and the optimal treatment regimen …  Cited by 4 Related articles All 11 versions 

Genetic Diversity of Mycobacterium tuberculosis Isolates in the Metropolitan Area of Rome

A Cannas, S Camassa, M Sali, O Butera, A Mazzarelli… – Chemotherapy, 2018 – karger.com… All strains were analyzed by the standardized spoligotyping technique as previously described [18] using a commercial kit (Ocimum Biosolutions, India) … Spoligotype patterns were represented as octal codes and entered in the SITVIT2 proprietary database of the …Related articles All 6 versions

Comparison of methods and samples used in the diagnosis of childhood PTB and characterization of mycobacterium tuberculosis isolates

AE Ogunbayo – 2018 – scholar.ufs.ac.za… Polymorphism….. 42 2.7.2.2. Spoligotyping ….. 43 2.7.2.3 …3.10.9.1. Spoligotyping ….. 60 3.10.9.2. MIRU … Related articles All 3 versions 

[PDF] 8. Molecular typing of Mycobacterium tuberculosis complex isolates

G Skenders, D van Soolingen – Handbook on tuberculosis laboratory …, 2018 – tbonline.info… It is, however, possible to use spoligotyping as a screening method in typing (in the vast … On the other hand, when spoligotype patterns are identical, then no conclusion can be drawn … Protocol: PCR: 1. Reconstitute dry primers Dra and DRb (Ocimum Biosolutions, India) in 2.2 ml …

[HTML] Mycobacterium africanum (Lineage 6) shows slower sputum smear conversion on tuberculosis treatment than Mycobacterium tuberculosis (Lineage 4) in …

B Diarra, M Kone, ACG Togo, YDS Sarro, AB Cisse… – PloS one, 2018 – journals.plos.org… or 5M. Spoligotyping was performed on boiled bacterial lysates using a commercially available kit (Ocimum)[22] or by in-house prepared membrane. Data entry from the film was verified by a second assessor. Lineage classification …

The effect of combining natural terpenes and antituberculous agents against reference and clinical Mycobacterium tuberculosis strains

E Sieniawska, R Sawicki, M Swatko-Ossor… – Molecules, 2018 – mdpi.com… It was described in most of the common highly fragrant herbs and spices, among which Humulus lupulus, Laurus nobilis, Thymus vulgaris, Cymbopogon schoenanthus or Ocimum basilicum contain high levels of this compound [17] … 2. Results. 2.1. Spoligotyping …  Cited by 7 Related articles All 8 versions 

Molecular Characterization of Drug-Resistant Mycobacterium Tuberculosis and Evaluation of the Performance of Genexpert Mtb/Rif® Assay Using Urine Specimen to …

E Abera – 2018 – 213.55.95.56… 113 Figure 5.1: Radial UPGMA tree based on the copy numbers of MIRU-VNTR 24-loci and Spoligotyping, and it shows the pattern of drug resitance lineage and clustering of each genotype … 24 MIRU-VNTR and spoligotype. Data were analyzed using SPSS version 23 …

Impact of Mycobacterium tuberculosis complex lineages as a determinant of disease phenotypes from an immigrant rich moderate tuberculosis burden country, Bright Varghese, Mushira Enani, Abdulrahman Alrajhi, Sameera Al Johani, Ali Albarak, Sahar Althawadi, Noura Elkhizzi, Hawra AlGhafli, Mohammed Shoukri, Sahal Al – Hajoj, Respir Res. 2018; 19: 259. Published online 2018 Dec 27. doi: 10.1186/s12931-018-0966-x,PMCID: PMC6307224

Mycobacterium africanum (Lineage 6) shows slower sputum smear conversion on tuberculosis treatment than Mycobacterium tuberculosis (Lineage 4) in Bamako, Mali.Bassirou Diarra, Mahamadou Kone, Antieme Combo Georges Togo, Yeya dit Sadio Sarro, Aissata Boubakar Cisse, Amadou Somboro, Boureima Degoga, Mohamed Tolofoudie, Bourahima Kone, Moumine Sanogo, Bocar Baya, Ousmane Kodio, Mamoudou Maiga, Michael Belson, Susan Orsega, Meryam Krit, Sounkalo Dao, Ibrahim Izétiegouma Maiga, Robert L. Murphy, Leen Rigouts, Seydou Doumbia, Souleymane Diallo, Bouke Catherine de Jong PLoS One. 2018; 13(12): e0208603. Published online 2018 Dec 12. doi: 10.1371/journal.pone.0208603. PMCID: PMC6291124

Spoligotype‐based population structure of Mycobacterium tuberculosis in the Jimma Zone, southwest Ethiopia. Gemeda Abebe, Ketema Abdissa, Kedir Abdella, Mulualem Tadesse, Adane Worku, Gobena Ameni, Microbiology open. 2019 Jun; 8(6): e00744. Published online 2018 Oct 15. doi: 10.1002/mbo3.744. PMCID: PMC6562125

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates. Prasit Palittapongarnpim, Pravech Ajawatanawong, Wasna Viratyosin, Nat Smittipat, Areeya Disratthakit, Surakameth Mahasirimongkol, Hideki Yanai, Norio Yamada, Supalert Nedsuwan, Worarat Imasanguan, Pacharee Kantipong, Boonchai Chaiyasirinroje, Jiraporn Wongyai, Licht Toyo-oka, Jody Phelan, Julian Parkhill, Taane G. Clark, Martin L. Hibberd, Wuthiwat Ruengchai, Panawun Palittapongarnpim, Tada Juthayothin, Sissades Tongsima, Katsushi Tokunaga Sci Rep. 2018; 8: 11597. Published online 2018 Aug 2. doi: 10.1038/s41598-018-29986-3. PMCID: PMC6072702

Association of gyrA and rrs gene mutations detected by MTBDRsl V1 on Mycobacterium tuberculosis strains of diverse genetic background from India.Syed Beenish Rufai, Jitendra Singh, Parveen Kumar, Purva Mathur, Sarman Singh. Sci Rep. 2018; 8: 9295. Published online 2018 Jun 18. doi: 10.1038/s41598-018-27299-z. PMCID: PMC6006251

Multi- and Extensively Drug Resistant Mycobacterium tuberculosis in South Africa: a Molecular Analysis of Historical Isolates. Nontuthuko E. Maningi, Luke T. Daum, John D. Rodriguez, Halima M. Said, Remco P. H. Peters, John Osei Sekyere, Gerald W. Fischer, James P. Chambers, P. Bernard Fourie J Clin Microbiol. 2018 May; 56(5): e01214-17.  Pre-published online 2018 Mar 7. Published online 2018 Apr 25. doi: 10.1128/JCM. 01214-17.PMCID: PMC5925707

Annotated Genome Sequences of 16 Lineage 4 Mycobacterium tuberculosis Strains from Guatemal Joseph W. Saelens, Dalia Lau-Bonilla, Anneliese Moller, Ana M. Xet-Mull, Narda Medina, Brenda Guzmán, Maylena Calderón, Raúl Herrera, Jason E. Stout, Eduardo Arathoon, Blanca Samayoa, David M. Tobin Genome Announc. 2018 Feb; 6(7): e00024-18. Published online 2018 Feb 15. doi: 10.1128/genomeA.00024-18. PMCID: PMC5814500

Risk factors associated with cluster size of Mycobacterium tuberculosis (Mtb) of different RFLP lineages in Brazil. Renata Lyrio Peres, Solange Alves Vinhas, Fabíola Karla Correa Ribeiro, Moisés Palaci, Thiago Nascimento do Prado, Bárbara Reis-Santos, Eliana Zandonade, Philip Noel Suffys, Jonathan E. Golub, Lee W. Riley, Ethel Leonor Maciel,BMC Infect Dis. 2018; 18: 71. Published online 2018 Feb 8. doi: 10.1186/s12879 018-2969-0. PMCID: PMC5806441

The Effect of Combining Natural Terpenes and Antituberculous Agents against Reference and Clinical Mycobacterium tuberculosis Strains,Elwira Sieniawska, Rafal Sawicki, Marta Swatko-Ossor, Agnieszka Napiorkowska, Agata Przekora, Grazyna Ginalska, Ewa Augustynowicz-Kopec Molecules. 2018 Jan; 23(1): 176.  Published online 2018 Jan 15. doi: 10.3390/molecules23010176.PMCID: PMC6017631

Genetic diversity and distribution of Mycobacterium tuberculosis genotypes in Limpopo, South Africa.N. T. C. Maguga-Phasha, N. S. Munyai, F. Mashinya, M. E. Makgatho, E. F. Mbajiorgu .BMC Infect Dis. 2017; 17: 764.  Published online 2017 Dec 12. doi: 10.1186/s12879-017-2881-z PMCID: PMC5727936

Genotyping and molecular detection of multidrug-resistant Mycobacterium tuberculosis among tuberculosis lymphadenitis cases in Addis Ababa, Ethiopia.O. Zewdie, A. Mihret, T. Abebe, A. Kebede, K. Desta, A. Worku, G. Ameni,New Microbes New Infect. 2018 Jan; 21: 36–41.  Published online 2017.Oct 24.oi: 10.1016/j.nmni.2017.10.009.PMCID: PMC5901530

PyroTyping, a novel pyrosequencing-based assay for Mycobacterium tuberculosis genotyping. B. Molina-Moya, A. Lacoma, N. García-Sierra, S. Blanco, L. Haba, S. Samper, J. Ruiz-Manzano, C. Prat, C. Arnold, J. Domínguez,Sci Rep. 2017; 7: 6777.  Published online 2017 Jul 28. doi: 10.1038/s41598-017-06760-5,PMCID: PMC5533701

First Insight into the Fluoroquinolone and Aminoglycoside Resistance of Multidrug-Resistant Mycobacterium tuberculosis in Saudi Arabia,Bright Varghese, Sahal Al-Hajoj,Am J Trop Med Hyg. 2017 May 3; 96(5): 1066–1070.  doi: 10.4269/ajtmh.16-0579Correction in: Am J Trop Med Hyg. 2018 Feb; 98(2): 634. PMCID: PMC5417196

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Strains of Mycobacterium tuberculosis Transmitting Infection in Brazilian Households and Those Associated with Community Transmission of Tuberculosis.Solange Alves Vinhas, Edward C. Jones-López, Rodrigo Ribeiro Rodrigues, Mary Gaeddert, Renata Lyrio Peres, Patricia Marques-Rodrigues, Paola Poloni Lobo de Aguiar, Laura Forsberg White, David Alland,Padmini Salgame, David Hom, Jerrold J. Ellner, Reynaldo Dietze, Lauren F. Collins, Elena Shashkina, Barry Kreiswirth, Moisés Palaci .Tuberculosis (Edinb) Author manuscript; available in PMC 2018 May 1.Published in final edited form as: Tuberculosis (Edinb). 2017 May; 104: 79–86. Published online 2017 Mar 16.  doi: 10.1016/j.tube.2017.03.003.PMCID: PMC5716464

Molecular typing of Mycobacterium tuberculosis complex isolated from pulmonary tuberculosis patients in central Ethiopia.Zufan Bedewi, Adane Worku, Yalemtsehay Mekonnen, Getnet Yimer, Girmay Medhin, Gezahegne Mamo, Rembert Pieper, Gobena Ameni,BMC Infect Dis. 2017; 17: 184.  Published online 2017 Mar 1. doi: 10.1186/s12879-017-2267-2.PMCID: PMC5333391

[HTML] Trends in spoligotype patterns of Mycobacterium tuberculosis strains in central India

P Desikan, DS Chauhan, N Panwalkar… – Indian journal of medical …, 2017 – ijmm.org… Table 1: Year wise occurrence of spoligotype lineages over the period of five years Click here to view … Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic … Predominant tuberculosis spoligotypes, Delhi, India …Cited by 1 Related articles All 4 versions

[HTML] Molecular typing of Mycobacterium tuberculosis complex isolated from pulmonary tuberculosis patients in central Ethiopia

Z Bedewi, A Worku, Y Mekonnen… – BMC infectious …, 2017 – bmcinfectdis.biomedcentral.com… Isolates that were positive for M. tuberculosis by RD9 PCR were further characterized by spoligotyping following the procedure described by Kamerbeeket al [17] and by observing the instructions of the spoligotype kit supplier (Ocimum Biosolutions Company, Iisselstein, and the …

First Insight into the Fluoroquinolone and Aminoglycoside Resistance of Multidrug-Resistant Mycobacterium tuberculosis in Saudi Arabia

B Varghese, S Al-Hajoj – The American journal of tropical medicine and …, 2017 – ASTMH… Genotyping of MDR-TB isolates and data analysis. All the isolates reported with resistance to either amino- glycosides or fluoroquinolone were subjected to spoligotyping (Ocimum Biosolutions, Hyderabad, India) and 24-loci-based …

Cited by 1 Related articles All 4 versions

[HTML] Genetic diversity and distribution of Mycobacterium tuberculosis genotypes in Limpopo, South Africa

NTC Maguga-Phasha… – BMC infectious …, 2017 – bmcinfectdis.biomedcentral.com… They were spoligotyped and data analysed using the international spoligotyping database 4 (SpolDB4). Results … The results of spoligotyping analysis and a sample Spoligo pattern are presented in Table 1 and Fig. 2, respectively. Table 1 … Spoligotype family. Total isolates …  Cited by 2 Related articles All 7 versions 

Genetic diversity of Mycobacterium tuberculosis from Pará, Brazil, reveals a higher frequency of ancestral strains than previously reported in South America

EC Conceição, N Rastogi, D Couvin, ML Lopes… – Infection, Genetics and …, 2017 – Elsevier… In this database, Spoligotype International Type (SIT) designates patterns shared by two or … used the SpolSimilaritySearch tool to highlight the specificity of spoligotyping signatures in … Distribution of patient demographics, drug-susceptibility testing results and major spoligotypesCited by 5 Related articles All 8 versions

[HTML] Genetic diversity of Mycobacterium tuberculosis and transmission associated with first-line drug resistance: a first analysis in Jalisco, Mexico

G Lopez-Avalos, G Gonzalez-Palomar… – Journal of global …, 2017 – Elsevier… [19] using a Spoligotyping Diagnostic Kit with primers and controls (Ocimum Biosolutions LCC, Indianapolis, IN) following the manufacturer’s instructions … In this database, spoligotype international type (SIT) designates a spoligotyping pattern shared by two or more patient …Cited by 6 Related articles All 7 versions

Cross-contamination of Mycobacterium tuberculosis at the National Rference Laboratory of Tuberculosis of Cuba

MR Martínez Romero, M Sardiña Aragón… – Revista Cubana de …, 2017 – medigraphic.com… A los aislamientos se les extrajo el ADN según lo descrito por van Soolingen y otros.8 Se empleóel sistema Spoligotyping Kit IM9701 (Ocimum Biosolutions Ltd, Hyderabad, India), de acuerdocon las instrucciones del fabricante y lo descrito por Kamerbeek y otros9 Los …  Related articles All 2 versions 

[HTML] PyroTyping, a novel pyrosequencing-based assay for Mycobacterium tuberculosis genotyping

B Molina-Moya, A Lacoma, N García-Sierra, S Blanco… – Scientific reports, 2017 – nature.com… Spoligotyping was performed using the spoligokit (Ocimum Biosolutions, Hyderabad, India) following the manufacturer’s instructions … Spoligotyping International Types (SIT) were assigned according to spoligotype pattern signatures provided in SITVITWEB … Cited by 1 Related articles All 7 versions

Strains of Mycobacterium tuberculosis transmitting infection in Brazilian households and those associated with community transmission of tuberculosis

SA Vinhas, EC Jones-López, RR Rodrigues… – Tuberculosis, 2017 – Elsevier… frequencies of MTB isolates clustered assorted by RFLP and Spoligotyping in Vitoria … groups, the isolates were compared with those classified as Spoligotype International Type … Genotypes (IS6110 RFLP patterns and spoligotypes) were grouped according to three approaches … Cited by 2 Related articles All 8 versions

Genomic, Genetic, and Functional Interrogation of Mycobacterium tuberculosis Outbreak Strains

JW Saelens – 2017 – search.proquest.com… 45 2.6.3 Spoligotyping ….. 45 … xi List of Tables Table 1: Spoligotypes and patient risk factors for the 11 identified Beijing isolates from the Clínica Familiar “Luis Angel García” (CFLAG) and its associated public hospital …

Influência de fatores de risco do paciente e de características de Mycobacterium tuberculosis no desfecho dos casos novos de tuberculose pulmonar tratados com …

MC Scheffer – 2017 – repositorio.ufsc.br… de todos os spoligotypes encontrados nos isolados de M. tuberculosis incluídos no estudo, classificação segundo SITVIT-WEB….. 87 Figura 22- Distribuição das famílias e subfamílias segundo genotipagem por metodologia de Spoligotyping de isolados de M …  Related articles All 2 versions 

EPIDEMIOLOGY OF TUBERCULOSIS IN CAMELS SLAUGHTERED AT AKAKI ABATTOIR, CENTRAL ETHIOPIA

J YASMIN – 2017 – 213.55.95.56… while the rest were non-tuberculous mycobacteria (NTM). Spoligotyping of the 39 isolates indicated that majority of the isolates (94.9%) identified as orphan strains with no shared spoligotype international type (SIT) in the Spoligotype database while two …  Related articles 

[PDF] Characterization of efflux pumps genes involved in second-line drug resistance of tuberculosis

LA Malinga – 2017 – pdfs.semanticscholar.orgPage 1. Characterization of efflux pumps genes involved in second-line drug resistance of tuberculosis Lesibana Anthony Malinga © University of Pretoria Page 2. CHARACTERIZATION OF EFFLUX PUMPS GENES INVOLVED IN …

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2016

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Determination of genotypic varieties and genotyping of multiple drug-resistant tuberculosis by the RFLP and spoligotyping methods

T Karsligil, A BAYRAM, F EKŞİ – Turkish journal of medical …, 2016 – journals.tubitak.gov.tr The spoligotype patterns were encoded in triplet codes, and the types were identified (Figure 1). The obtained results were compared with the international spoligotyping database, and the spoligotypes were detected (15) …

  Related articles All 9 versions 

Role of gyrB mutations in pre-extensively and extensively drug-resistant tuberculosis in Thai clinical isolates

A Disratthakit, T Prammananan… – Antimicrobial agents …, 2016 – Am Soc Microbiol Cited by 10 Related articles All 7 versions

Secretome profiling of highly virulent Mycobacterium bovis 04-303 strain reveals higher abundance of virulence-associated proteins

F Vargas-Romero, G Mendoza-Hernández… – Microbial …, 2016 – Elsevier… From the M. bovis strains, 19 different spoligotyping patterns were observed among the 27 … M.bovis molecular typing database (Table 1). The most frequently observed spoligotypes were the … Only the 444 strain presented the spoligotype SB0140 and were used for comparison … Cited by 5 Related articles All 6 versions

[HTML] Evolutionary History and Ongoing Transmission of Phylogenetic Sublineages of Mycobacterium tuberculosis Beijing Genotype in China

Q Yin, H Liu, W Jiao, Q Li, R Han, J Tian, Z Liu… – Scientific reports, 2016 – nature.com… IS6110-RFLP or 24-VNTR) or slowly evolving phylogenetic markers (eg spoligotypes, RD and …in M. tuberculosis prevent from making any phylogenetic inference from the spoligotyping data of … For example, spoligotype SIT190 with deleted signal #40 was found in strains of both …Cited by 15 Related articles All 9 versions

[HTML] Genetic diversity of Mycobacterium tuberculosis complex strains isolated from patients with pulmonary tuberculosis in Anambra State, Nigeria

GN Uzoewulu, L Lawson, IS Nnanna, N Rastogi… – International journal of …, 2016 – Elsevier… The identified spoligotypes and five-loci ETR patterns were analyzed using the BioNumerics … result of the comparison of spoligotyping versus VNTRs demonstrated that spoligotyping analysis alone …with five-loci ETRs; for example, isolates with identical spoligotype pattern SIT61 …Cited by 8 Related articles All 15 versions

[HTML] Genetic diversity of Mycobacterium tuberculosis isolates from central India

P Desikan, DS Chauhan, P Sharma… – The Indian journal of …, 2016 – ncbi.nlm.nih.gov… Spoligotyping was carried out by using a commercial kit (Ocimum Biosolutions, Hyderabad) at …SITVIT2 database of Institute Pasteur de Guadeloupe 5 to locate families of spoligotypes … of comparison, the database consisted of a total of 7105 spoligotype patterns (corresponding …Cited by 4 Related articles All 6 versions

First insight into the molecular epidemiology of Mycobacterium tuberculosis in Santa Catarina,southern Brazil

CL Nogueira, RI Prim, SG Senna, DB Rovaris… – Tuberculosis, 2016 – Elsevier… Spoligotyping was performed by using commercially available membranes (Ocimum Biosolutions,Hyderabad … In this database, Spoligotype International Type (SIT) designates patterns shared by … The evolutionary relationships among all the observed spoligotypes were studied …Cited by 11 Related articles All 9 versions

[HTML] Analysis of Mycobacterium tuberculosis genotypic lineage distribution in Chile and neighboring countries

J Lagos, D Couvin, L Arata, J Tognarelli, C Aguayo… – PloS one, 2016 – journals.plos.org… The Fig 1B shows the spoligotyping-based MST; it is evident that LAM and T lineages … LAM9 cluster was the largest node evolved from SIT53/T1 and multiple spoligotypes were observed to be rising from it, eg, SIT33/LAM3, while the second largest spoligotype pattern SIT50/H3 … Cited by 4 Related articles All 13 versions 

[PDF] Molecular characterization of Mycobacterium tuberculosis complex in Gambella region, Southwest Ethiopia

G Asebe, A Worku, A Zewude, K Tafess… – African Journal of …, 2016 – researchgate.net… Figure 3. Spoligotype patterns of isolates obtained from Gambella … Page 7. 1092 Afr. J. Microbiol. Res. Table 3. Proportion of spoligotyping pattern of the strains with different variables … Table 4. Distribution of spoligotypes and their report status from Ethiopia … Cited by 4 Related articles All 3 versions 

[HTML] A novel molecular strategy for surveillance of multidrug resistant tuberculosis in high burden settings

HM Said, N Kushner, SV Omar, AW Dreyer… – PloS one, 2016 – journals.plos.org… Genotyping. Spoligotyping was done using a commercial kit (Ocimum Biosolutions, India) according to the manufacturer’s instructions [20]; spoligotypes were uploaded as binary codes in the SpolDB4 database for SIT (Spoligotype International Type) assignment …

[PDF] Molecular genotypes of Mycobacterium tuberculosis strains circulating in Dakar, Senegal

AB Diallo, OG Walbang, M Camara, S Lo… – African Journal of …, 2016 – researchgate.net… Spoligotyping and assignment of mycobacterial lineage and families … consecutive smear- positive TB patients out of which 15 (6.8%) did not yield a spoligotype pattern and … remaining 203 M. tuberculosis complex isolates, we identified a total of 59 different spoligotypes patterns …  Cited by 2 Related articles All 2 versions 

Molecular typing of mycobacteria isolated from tuberculous lymphadenitis cases in Addis Ababa, Ethiopia

O Zewdie, A Mihret, G Ameni, A Worku… – … of Tuberculosis and …, 2016 – ingentaconnect.com… Spoligotyping was used as the primary tool for typing MTC strains because of its ease of … SIT =spoligotype international type; CAS = Central Asian; EA = Euro-American; IO = Indo-Oceanic; LAM … A long descendant branch of spoligotypes belonged to the dominant ‘ill-defined’ T …Cited by 5 Related articles All 5 versions

[HTML] Whole-genome sequencing analysis of serially isolated multi-drug and extensively drug resistant Mycobacterium tuberculosis from Thai patients

K Faksri, JH Tan, A Disratthakit, E Xia… – PloS one, 2016 – journals.plos.org… Classical genotyping. Spoligotyping was performed according to the manufacturer’s instructions (Ocimum Biosolutions, India) as previously described [19]. Twenty four loci MIRU-VNTR typing was performed according to the …

Latin-American-Mediterranean lineage of Mycobacterium tuberculosis: Human traces across pathogen’s phylogeography

I Mokrousov, A Vyazovaya, T Iwamoto, Y Skiba… – Molecular phylogenetics …, 2016 – Elsevier… Spoligotyping was performed with in-house made membranes or using commercial kits (Ocimum Biosolutions … Profile #6 includes strains of 7 different spoligotypes from distant parts of Russia (Northwest … strains with SIT1321 and SIT64 that do not bear this spoligotype signature …

[HTML] Molecular typing of Mycobacterium Bovis from cattle reared in Midwest Brazil

RCT Carvalho, SEG Vasconcellos, M de Azevedo Issa… – PloS one, 2016 – journals.plos.org… The geographic distribution of the spoligotypes is presented in Fig 1 … bovis spoligotype found in strains isolated at municipalities of Midwest Brazil. https://doi.org/10.1371/journal.pone.0162459. g001 … by spoligotyping method. https://doi.org/10.1371/journal.pone.0162459.t001

[HTML] Chromosomal rearrangements and protein globularity changes in Mycobacterium tuberculosis isolates from cerebrospinal fluid

SH Saw, JL Tan, XY Chan, KG Chan, YF Ngeow – PeerJ, 2016 – peerj.com… The genotypes identified using the spoligotyping kit from Ocimum Biosolutions (Hyderabad, India) were Beijing ST1 (UM-CSF01, UM-CSF05, UM-CSF08, UM-CSF09 and UM-CSF17), EAI_IND (UM-CSF06), Unknown (UM-CSF04) and H3 ST50 (UM-CSF15) …  Cited by 3 Related articles All 11 versions 

[HTML] Contaminación cruzada por Mycobacterium tuberculosis en el Laboratorio Nacional de Referencia de Tuberculosis de Cuba

MR Martínez Romero, M Sardiña Aragón… – Revista Cubana de …, 2016 – scielo.sld.cu… 8 Se empleó el sistema Spoligotyping Kit IM9701 (Ocimum Biosolutions Ltd, Hyderabad, India), de acuerdo con las instrucciones del fabricante y lo descrito por Kamerbeek y otros 9 Los patrones obtenidos se compararon con la base de datos internacional SITVIT2 “en línea” …  Cited by 1 Related articles All 6 versions 

Mycobacterium Tuberculosis In Central Ethiopia: Molecular Epidemiology, Drug Sensitivity Patterns, and Evaluation of the Genotype Mtbdrplus Assay for the Detection …

Z Bedewi – 2016 – 213.55.95.56… The isolates were analyzed using region of difference (RD) 9-based polymerase chain reaction (PCR) and spoligotyping … Of these 90 spoligotypes, 32 were clustered consisting of 223 (79.3%) isolates while 58 had only a single isolate each …

The epidemiology of tuberculosis in cattle and humans living in the wildlife-livestock-human interface in the rural Mnisi community Mpumalanga province South Africa

J Musoke – 2016 – repository.up.ac.za… 85 5.3.5.2 Polymerase Chain Reaction (PCR) …. 86 5.3.5.3 Spoligotyping ….. 86 5.3.5.4 Mycobacterial interspersed repetitive-unit-variable number tandem ….. 87 …

[HTML] Molecular analysis of genetic mutations among cross-resistant second-line injectable drugs reveals a new resistant mutation in Mycobacterium tuberculosis

L Malinga, J Brand, S Olorunju, A Stoltz… – … and infectious disease, 2016 – Elsevier… Spoligotyping. The PCR products were amplified using primers purchased from manufacturer (Ocimum Biosciences, India) and the procedure was performed as … Amersham Biosciences) and by exposure to X-ray film (HyperfilmECL, Amersham).The spoligotypes were reported …

Association of Mycobacterium tuberculosis genotypes and treatment outcome in pulmonary tuberculosis patients in Tshwane metropolitan area

SR Matukane – 2016 – repository.up.ac.za

… 34 3.3.2 Data collection 35 3.3.3 DNA extraction 35 3.3.4 Spoligotyping 35 3.3.5 MIRU-VNTR typing 36 Page 8 … 38 4.1 Results 38 4.1.1 Spoligotyping and 24-loci MIRU-VNTR typing results 38 4.1.2 Association of genotypes and drug resistance with treatment outcome 39 …  Related articles All 3 versions 

Wild-type minimal inhibitory concentration distributions of secondline drugs in mycobacterium tubercolosis complex clinical isolated in relation to recommended critical …

NM Seloma – 2016 – ulspace.ul.ac.za… SpolDB4 – is an international spoligotyping database that defines M. tuberculosis complex genetic polymorphism, isolates sharing identical spoligotype pattern are defined according to SIT Spoligotype International Type) isolates with single spoligotype patterns are defined as …  Related articles All 2 versions 

Development and validation of a molecular assay and evaluation of the GeneXpert® MTB/RIF assay for the rapid detection of genital tuberculosis

MC Sokhela – 2016 – scholar.ufs.ac.za… Figure 3.1 Prevalence of spoligotypes in South Africa ….. 56 Figure 3.2 MIRU-VNTR 24 loci copy number ….. 62Figure 3.3 MIRU-VNTR and Spoligotyping results …

[HTML] Tuberculosis por Mycobacterium bovis en trabajadores de fincas en saneamiento para tuberculosis bovina, de Antioquia, Boyacá y Cundinamarca

AF Leal-Bohórquez, CM Castro-Osorio… – Revista de Salud …, 2016 – SciELO Public Health… Kremer K, Bunschoten A, Schouls L, Van Soolingen D, Van Embden J. Laboratory Spoligotyping, a PCR-based method to simultaneously detect … el producto de la reacción en cadena de la polimerasa (RCP) se hibridó en una membrana comercial (Ocimum Biosolutions India …

[PDF] Usefulness of molecular methods for detecting drug resistance and genotyping in mycobacterium tuberculosis

BM Moya – 2016 – core.ac.uk… RFLP) …. 43 1.7.2. Spoligotyping ….. 44 … RFLP) …. 64 4.4.2. Spoligotyping ….. 65 …  Related articles All 3 versions

Usefulness of molecular methods for detecting drug resistance and genotyping in mycobacterium tuberculosis

B Molina Moya – 2016 – ddd.uab.cat… RFLP) …. 43 1.7.2. Spoligotyping ….. 44 … RFLP) …. 64 4.4.2. Spoligotyping ….. 65 …  Related articles 

[HTML] Tuberculosis caused by Mycobacterium bovis in workers of bovine tuberculosis sanitation farms in Antioquia, Boyacá and Cundinamarca

AF Leal-Bohórquez, CM Castro-Osorio… – Revista de Salud …, 2016 – scielo.org.co… La metodología de Spoligotyping se realizó según lo descrito por Kremer en el 2002 … por 30 segundos y una extensión final a 72°C por 5 minutos; el producto de la reacción en cadena de la polimerasa (RCP) se hibridó en una membrana comercial (Ocimum Biosolutions India … Related articles All 3 versions 

[BOOK] Clinical and pathological characteristics of the Uganda genotype of Mycobacterium tuberculosis

D Wamala – 2016 – openarchive.ki.se… A study of the evolutionary relationships and worldwide distribution of the spoligotypes of Mtb isolates from Ugandan patients with tuberculous lymphadenitis indicated an ongoing evolution of the Uganda genotype, with Uganda at the center of this evolution (Paper II) …  Related articles All 3 versions 

Genotipificación de Mycobacterium tuberculosis en aislados clínicos obtenidos de pacientes VIH positivos de los hospitales Simón Bolívar y Santa Clara de Bogotá

MY Beltrán León – 2016 – bdigital.unal.edu.co… A total of 49 isolates of Mycobacterium tuberculosis were genotyped by spoligotyping and MIRU VNTR loci 24 … Spoligotype analysis showed 15 patterns, of which 3/49 (6,1%) were orphans and 45/49 (91,8%) belonged to the Euro American lineage …  Cited by 4 Related articles 

Genotipos de Mycobacterium tuberculosis prevalentes en Argentina y su relación con mutaciones de resistencia a isoniacida

J Monteserin – 2016 – ridaa.unq.edu.ar

… La genotipificación se realizó mediante spoligotyping, y en casos selectos, por MIRU-VNTR24. El análisis de clustering se realizó mediante RFLP IS6110 … como spoligotyping y MIRUs-VNTR (Mycobacterial interspersed repetitive units-variable …

Molecular typing of mycobacteria isolated from tuberculous lymphadenitis cases in Addis Ababa, Ethiopia.O. Zewdie, A. Mihret, G. Ameni, A. Worku, T. Gemechu, T. Abebe,Int J Tuberc Lung Dis.Author manuscript; available in PMC 2017 Nov 1.Published in final edited form as: Int J Tuberc Lung.Dis. 2016 Nov; 20(11): 1529–1534.  doi: 10.5588/ijtld.15.1023.PMCID: PMC5665165

 Evolutionary History and Ongoing Transmission of Phylogenetic Sublineages of Mycobacterium tuberculosis Beijing Genotype in China,Qing-qin Yin, Hai-can Liu, Wei-wei Jiao, Qin-jing Li, Rui Han, Jian-ling Tian, Zhi-guang Liu, Xiu-qin Zhao, Ying-jia Li, Kang-lin Wan, A-dong Shen, IgorMokrousov,Sci Rep. 2016; 6: 34353.  Published online 2016 Sep 29. doi: 10.1038/srep34353.PMCID: PMC5041183

Chromosomal rearrangements and protein globularity changes in Mycobacterium tuberculosis isolates from cerebrospinal fluid.Seow Hoon Saw, Joon Liang Tan, Xin Yue Chan, Kok Gan Chan, Yun Fong Ngeow.PeerJ. 2016; 4: e2484.  Published online 2016 Sep 21. doi: 10.7717/peerj.2484.PMCID: PMC5036109

Molecular Typing of Mycobacterium bovis from Cattle Reared in Midwest Brazil,Ricardo César Tavares Carvalho, Sidra Ezidio Gonçalves Vasconcellos, Marina de Azevedo Issa, Paulo Martins Soares Filho, Pedro Moacyr Pinto Coelho Mota, Flábio Ribeiro de Araújo, Ana Carolina da Silva Carvalho, Harrison Magdinier Gomes, Philip Noel Suffys, Eduardo Eustáquio de Souza Figueiredo, Vânia Margaret.Flosi Paschoalin.PLoS One. 2016; 11(9): e0162459.  Published online 2016 Sep 15. doi: 10.1371/journal.pone.0162459. PMCID: PMC5024986

Role of gyrB Mutations in Pre-extensively and Extensively Drug-Resistant Tuberculosis in Thai  Clinical Isolates.Areeya Disratthakit, Therdsak Prammananan, Chanwit Tribuddharat, Iyarit  Thaipisuttikul, Norio Doi, Manoon Leechawengwongs, Angkana Chaiprasert,Antimicrob Agents Chemother. 2016 Sep; 60(9): 5189–5197.  Prepublished online 2016 Jun 13. Published online 2016 Aug 22. doi: 10.1128/AAC.00539-16.PMCID: PMC4997844

Analysis of Mycobacterium tuberculosis Genotypic Lineage Distribution in Chile and Neighboring Countries.Jaime Lagos, David Couvin, Loredana Arata, Javier Tognarelli, Carolina Aguayo, TamaraLeiva, Fabiola Arias, Juan Carlos Hormazabal, Nalin Rastogi, Jorge Fernández,PLoS One. 2016; 11(8): e0160434.  Published online 2016 Aug 12. doi: 10.1371/journal.pone.0160434.PMCID: PMC4982630

Whole-Genome Sequencing Analysis of Serially Isolated Multi-Drug and Extensively Drug Resistant Mycobacterium tuberculosis from Thai Patients.Kiatichai Faksri, Jun Hao Tan, Areeya Disratthakit, Eryu Xia, Therdsak Prammananan, Prapat Suriyaphol, Chiea Chuen Khor, Yik-Ying Teo, Rick Twee-Hee Ong, Angkana Chaiprasert.PLoS One. 2016; 11(8): e0160992.  Published online 2016 Aug 12. doi: 10.1371/journal.pone.0160992.PMCID: PMC4982626

Genetic diversity of Mycobacterium tuberculosis isolates from central India.Prabha Desikan, D.S. Chauhan, Pragya Sharma, Nikita Panwalkar, Manju Chourey, Mohan Lal Patidar, Priyanka Yadav, V. Chandrasekaran, B.S. Ohri.Indian J Med Res. 2016 Apr; 143(4): 481–486.doi: 10.4103/0971-5916.184287.PMCID: PMC4928555

Association between human leukocyte antigen class II and pulmonary tuberculosis due to mycobacterium tuberculosis in Uganda.Dan Wamala, Helen Koyokoyo Buteme, Samuel Kirimunda, Gunilla Kallenius, Moses Joloba.BMC Infect Dis. 2016; 16: 23.  Published online 2016 Jan 23.doi: 10.1186/s12879-016-1346-0.PMCID: PMC4724396

A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High BurdenettingsHalima M. Said, Nicole Kushner, Shaheed V. Omar, Andries W. Dreyer, Hendrik Koornhof, Linda Erasmus,Yasmin Gardee, Ivy Rukasha, Elena Shashkina, Natalie Beylis, Gilla Kaplan, Dorothy Fallows,Nazir A. Ismail.PLoS One. 2016; 11(1): e0146106. Published online 2016 Jan 11.doi: 10.1371/journal.pone.0146106.PMCID: PMC4713439

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2015

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Genetic Diversity of Mycobacterium tuberculosis Isolates from Assam, India: Dominance of Beijing Family and Discovery of Two New Clades Related to CAS1_Delhi and EAI Family Based on Spoligotyping and MIRU-VNTR Typing.Kangjam Rekha Devi, Rinchenla Bhutia, Shovonlal Bhowmick, Kaustab Mukherjee, Jagadish Mahanta,Kanwar Narain.PLoS One. 2015; 10(12): e0145860.  Published online 2015.Dec 23. doi: 10.1371/journal.pone.0145860.PMCID: PMC4689458

Multidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazil,Elis R. Dalla Costa, Sidra E. G. Vasconcelos, Leonardo S. Esteves, Harrison M. Gomes, Lia L. Gomes, Pedro Almeida da Silva, João Perdigão, Isabel Portugal, Miguel Viveiros, Ruth McNerney, Arnab Pain, Taane G. Clark, Nalin Rastogi, Gisela Unis, Maria Lucia R. Rossetti, Philip Noel Suffys,J Clin Microbiol. 2015 Dec; 53(12): 3805–3811.  Prepublished online.2015 Sep 23. Published online 2015 Nov 18. doi: 10.1128/JCM.02012-15.PMCID: PMC4652117

 Genetic Diversity of Mycobacterium tuberculosis Complex Isolated from Tuberculosis Patients in Bahir Dar City and Its Surroundings, Northwest Ethiopia.Anwar Nuru, Gezahegne Mamo, Adane Worku, Aschalew Admasu, Girmay Medhin, Rembert Pieper, Gobena Ameni.Biomed Res Int. 2015; 2015: 174732.Published online 2015 Sep 28. doi: 10.1155/2015/174732.PMCID: PMC4600926

 Predominance of Uganda genotype of Mycobacterium tuberculosis isolated from Ugandan patients with tuberculous lymphadenitis.Dan Wamala, Moses Okee, Edgar Kigozi, David Couvin, Nalin Rastogi, Moses Joloba, Gunilla Kallenius,BMC Res Notes. 2015; 8: 398.  Published online 2015 Sep 1. doi: 10.1186/s13104-015-1362-y.PMCID: PMC4556223

Molecular Typing of Mycobacterium Tuberculosis Complex by 24-Locus Based MIRU-VNTR Typing inConjunction with Spoligotyping to Assess Genetic Diversity of Strains Circulating in Morocco .Nada Bouklata, Philip Supply, Sanae Jaouhari, Reda Charof, Fouad Seghrouchni, Khalid Sadki, Youness El Achhab, Chakib Nejjari, Abdelkarim Filali-Maltouf, Ouafae Lahlou, Rajae El Aouad,PLoS One. 2015; 10(8): e0135695.  Published online 2015 Aug 18. doi: 10.1371/journal.pone.0135695.PMCID: PMC4540494

Molecular profiling of drug resistant isolates of Mycobacterium tuberculosis in the state of Santa Catarina, southern Brazil.Rodrigo Ivan Prim, Marcos André Schörner, Simone Gonçalves Senna, Christiane Lourenço Nogueira, Anna,Carolina Cançado Figueiredo, Jaquelline Germano de Oliveira, Darcita Bürger Rovaris, Maria Luiza Bazzo.Mem Inst Oswaldo Cruz. 2015 Aug; 110(5): 618–623.  doi: 10.1590/0074-02760150100.PMCID: PMC4569824

Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples.Amanda C. Brown, Josephine M. Bryant, Katja Einer-Jensen, Jolyon Holdstock, Darren T Houniet, Jacqueline Z. M. Chan, Daniel P. Depledge, Vladyslav Nikolayevskyy, Agnieszka Broda, Madeline J. Stone,  Mette T. Christiansen, Rachel Williams, Michael B. McAndrew, Helena Tutill, Julianne Brown, Mark Melzer, Caryn Rosmarin, Timothy D. McHugh, Robert J. Shorten, Francis Drobniewski, Graham Speight, Judith Breuer.J Clin Microbiol. 2015 Jul; 53(7): 2230–2237.  Prepublished online 2015 May 13. Published online. 2015 Jun 18. doi: 10.1128/JCM.00486-15.PMCID: PMC4473240

 Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome.Vinita Periwal, Ashok Patowary, Shamsudheen Karuthedath Vellarikkal, Anju Gupta, Meghna Singh,Ashish Mittal, Shamini Jeyapaul, Rajendra Kumar Chauhan, Ajay Vir Singh, Pravin Kumar Singh, Parul,Garg, Viswa Mohan Katoch, Kiran Katoch, Devendra Singh Chauhan, Sridhar Sivasubbu, Vinod Scaria.PLoS One. 2015; 10(4): e0122979.  Published online 2015 Apr 8. doi: 10.1371/journal.pone.0122979.PMCID: PMC4390332

A First Insight on the Population Structure of Mycobacterium tuberculosis Complex as Studied by Spoligotyping and MIRU-VNTRs in Santiago, Chile.María Elvira Balcells, Patricia García, Paulina Meza, Carlos Peña, Marcela Cifuentes, David Couvin,PLoS One. 2015; 10(2): e0118007.  Published online 2015 Feb 11. doi: 10.1371/journal.pone.0118007.PMCID: PMC4324903

Multidrug-Resistant Tuberculosis Outbreak in Gaming Centers, Singapore, 2012.Cynthia B.E. Chee, Suay-Hong Gan, Rick T. Ong, Li-Hwei Sng, Christopher W. Wong, Jeffery Cutter, Min.Gong, Hui-Maan Seah, Li Yang Hsu, Suhana Solhan, Peng-Lim Ooi, Eryu Xia, Jayne T. Lim, Chwee-Kim .Koh, Soon-Kok Lim, Han-Kee Lim, Yee-Tang Wang.Emerg Infect Dis. 2015 Jan; 21(1): 179–180.  doi: 10.3201/eid2101.141159.PMCID: PMC4285258

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2014

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Study of Mycobacterium tuberculosis Complex Genotypic Diversity in Malaysia Reveals a Predominance of Ancestral East-African-Indian Lineage with a Malaysia-Specific SignatureFazli Ismail, David Couvin, Izzah Farakhin, Zaidah Abdul Rahman, Nalin Rastogi, Siti SuraiyaPLoS One. 2014; 9(12): e114832.  Published online 2014 Dec 11. doi: 10.1371/journal.pone.0114832.PMCID: PMC4263714

Diversity of Mycobacterium tuberculosis and drug resistance in different provinces of Papua New Guinea.Serej D Ley, Paul Harino, Kilagi Vanuga, Ruben Kamus, Robyn Carter, Christopher Coulter,  Sushil.Pandey, Julia Feldmann, Marie Ballif, Peter M Siba, Suparat Phuanukoonnon, Sebastien Gagneux,Hans-Peter Beck.BMC Microbiol. 2014; 14: 307.  Published online 2014 Dec 5. doi: 10.1186/s12866-014-0307-2.PMCID: PMC4264550

Molecular Confirmation of Bacillus Calmette Guerin Vaccine Related Adverse Events among Saudi Arabian Children.Sahal Al-Hajoj, Ziad Memish, Naila Abuljadayel, Raafat AlHakeem, Fahad AlRabiah, Bright Arghese,PLoS One. 2014; 9(11): e113472.  Published online 2014 Nov 9 doi: 10.1371/journal.pone.0113472.PMCID: PMC4237431

Tuberculosis recurrence in a high incidence setting for HIV and tuberculosis in Brazil. Gisela Unis, Andrezza Wolowski Ribeiro, Leonardo Souza Esteves, Fernanda Sá Spies, Pedro Dornelles Picon, Elis Regina Dalla Costa, Maria Lucia Rosa Rossetti,BMC Infect Dis. 2014; 14: 548.  Published online 2014 Oct 24. doi: 10.1186/s12879-014-0548-6.PMCID: PMC4215011

 Strain Classification of Mycobacterium tuberculosis Isolates in Brazil Based on Genotypes Obtained by Spoligotyping, Mycobacterial Interspersed Repetitive Unit Typing and the Presence of Large Sequence and Single Nucleotide Polymorphism.Sidra E. G. Vasconcellos, Chyntia Carolina Acosta, Lia Lima Gomes, Emilyn Costa Conceição, KarlaValéria Lima, Marcelo Ivens de Araujo, Maria de Lourdes Leite, Flávio Tannure, Paulo Cesar de Souza Caldas, Harrison M. Gomes, Adalberto Rezende Santos, Michel K. Gomgnimbou, Christophe Sola, David Couvin, Nalin Rastogi, Neio Boechat, Philip Noel SuffysPLoS One. 2014; 9(10): e107747.  Published online 2014 Oct 14. doi: 10.1371/journal.pone.0107747.PMCID: PMC4196770

Prevalence of Extensively Drug Resistant Tuberculosis among Archived Multidrug Resistant Tuberculosis Isolates in Zimbabwe.Tichaona Sagonda, Lucy Mupfumi, Rumbidzai Manzou, Beauty Makamure, Mqondisi Tshabalala, Lovemore Gwanzura, Peter Mason, Reggie Mutetwa.Tuberc Res Treat. 2014; 2014: 349141.  Published online 2014 May 20. doi: 10.1155/2014/349141.PMCID: PMC4054961

Clinico-pathological features of tuberculosis due to Mycobacterium tuberculosis Uganda genotype in patients with tuberculous lymphadenitis: a cross sectional study. Dan Wamala, Benon Asiimwe, Edgar Kigozi, Gerald Mboowa, Moses Joloba, Gunilla Kallenius.BMC Clin Pathol. 2014; 14: 14.  Published online 2014 Apr 2. doi: 10.1186/1472-6890-14-14.PMCID: PMC3974774

Strain Diversity of Mycobacterium tuberculosis Isolates from Pulmonary Tuberculosis Patients in Afar Pastoral Region of Ethiopia.Mulugeta Belay, Gobena Ameni, Gunnar Bjune, David Couvin, Nalin Rastogi, Fekadu Abebe.Biomed Res Int. 2014; 2014: 238532.  Published online 2014 Mar 6. doi: 10.1155/2014/238532.PMCID: PMC3966356

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2013

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Molecular Epidemiology of Mycobacterium tuberculosis Complex in Singapore, 2006-2012.Leo Kang-Yang Lim, Li Hwei Sng, Wah Win, Cynthia Bin-Eng Chee, Li Yang Hsu, Estelle Mak, Arul Earnest, Marcus Eng-Hock Ong, Jeffery Cutter, Yee Tang Wang.PLoS One. 2013; 8(12): e84487.  Published online 2013 Dec 18. doi: 10.1371/journal.pone.0084487.PMCID: PMC3867517

 Global Study of IS6110 in a Successful Mycobacterium tuberculosis Strain: Clues for Deciphering Its Behavior and for Its Rapid Detection.Maria Isabel Millán-Lou, Ana Isabel López-Calleja, Cristina Colmenarejo, Maria Antonia Lezcano, Maria Asunción Vitoria, Patricia del Portillo, Isabel Otal, Carlos Martín, Sofía Samper. J Clin Microbiol. 2013 Nov; 51(11): 3631–3637.  doi: 10.1128/JCM.00970-13.PMCID: PMC3889744

Tuberculosis Transmission among Immigrants and Autochthonous Populations of the Eastern Province of Saudi Arabia.Bright Varghese, Philip Supply, Mohammed Shoukri, Caroline Allix-Beguec, Ziad Memish, Naila Abuljadayel, Raafat Al-Hakeem, Fahad AlRabiah, Sahal Al-Hajoj.PLoS One. 2013; 8(10): e77635.  Published online 2013 Oct 17. doi: 10.1371/journal.pone.0077635.PMCID: PMC379832

 Efficacy and safety of thrice weekly DOTS in tuberculosis patients with and without HIV co-infection: an observational study.Richa Vashishtha, Krishna Mohan, Bhagteshwar Singh, Satish K Devarapu, Vishnubhatla Sreenivas, Sanjay Ranjan, Deepak Gupta, Sanjeev Sinha, Surendra K Sharma.BMC Infect Dis. 2013; 13: 468.  Published online 2013 Oct 7. doi: 10.1186/1471-2334-13-468.PMCID: PMC3852441

 Extrapulmonary Tuberculosis: Mycobacterium tuberculosis Strains and Host Risk Factors in a Large Urban Setting in Brazil.Teresa Gomes, Solange Alves Vinhas, Bárbara Reis-Santos, Moisés Palaci, Renata Lyrio Peres, Paola P. Aguiar, Fabiola Karla Correa Ribeiro, Hebert Silva Marques, Valdério do Valle Dettoni, John L.

 Johnson, Lee W. Riley, Ethel Leonor Maciel PLoS One. 2013; 8(10): e74517.  Published online 2013 Oct 2. doi: 10.1371/journal.pone.0074517.PMCID: PMC3788772

Immunogenic Mycobacterium africanum Strains Associated with Ongoing Transmission in The Gambia

Florian Gehre, Martin Antonio, Jacob K. Otu, Neneh Sallah, Oumie Secka, Tutty Faal, Patrick Owiafe, Jayne S. Sutherland, Ifedayo M. Adetifa, Martin O. Ota, Beate Kampmann, Tumani Corrah, Bouke C. de Jong .Emerg Infect Dis. 2013 Oct; 19(10): 1593–1604.  doi: 10.3201/eid1910.121023.PMCID: PMC3810728

Mycobacterium tuberculosis is the causative agent of tuberculosis in the southern ecological zones of Cameroon, as shown by genetic analysis.Jean Paul Assam Assam, Véronique Penlap Beng, Fidelis Cho-Ngwa, Michel Toukam, Ane-Anyangwe Irene Ngoh, Mercy Kitavi, Inoster Nzuki, Juliette N Nyonka, Emilienne Tata, Jean Claude Tedom, Robert A Skilton, Roger Pelle, Vincent P K Titanji BMC Infect Dis. 2013; 13: 431.  Published online 2013 Sep 13. doi: 10.1186/1471-2334-13-431.PMCID: PMC3851

 Primary Drug-Resistant Tuberculosis in Hanoi, Viet Nam: Present Status and Risk Factors Nguyen Thi Le Hang, Shinji Maeda, Luu Thi Lien, Pham Huu Thuong, Nguyen Van Hung, Tran Bich Thuy,  Akiko Nanri, Tetsuya Mizoue, Nguyen Phuong Hoang, Vu Cao Cuong, Khieu Thi Thuy Ngoc, Shinsaku Sakurada, Hiroyoshi Endo, Naoto Keicho.PLoS One. 2013; 8(8): e71867.  Published online 2013 Aug 13. doi: 10.1371/journal.pone.0071867.PMCID: PMC374246

MDR TB Transmission, Singapore Cynthia B.E. Chee, Li-Yang Hsu, Li-Hwei Sng, Yee-Sin Leo, Jeffery Cutter, Yee-Tang Wang .Emerg Infect Dis. 2013 Jul; 19(7): 1151–1152.  doi: 10.3201/eid1907.120372. PMCID: PMC3713962

Prevalence of tuberculosis in pigs slaughtered at two abattoirs in Ethiopia and molecular characterization of Mycobacterium tuberculosis isolated from tuberculous-like lesions in pigs.  Sintayehu Mulugeta Arega, Franz Josef Conraths, Gobena Ameni.BMC Vet Res. 2013; 9: 97.  Published online 2013 May 6. doi: 10.1186/1746-6148-9-97.PMCID: PMC3661388

 Abattoir-based study on the epidemiology of caprine tuberculosis in Ethiopia using conventional and molecular tools. Benti Deresa, Franz J Conraths, Gobena Ameni, Acta Vet Scand. 2013; 55(1): 15.  Published online 2013 Feb 21. doi: 10.1186/1751-0147-55-15.PMCID: PMC3639213

Admixed Phylogenetic Distribution of Drug Resistant Mycobacterium tuberculosis in Saudi Arabia. Bright Varghese, Philip Supply, Caroline Allix-Béguec, Mohammed Shoukri, Ruba Al-Omari, Mais  Herbawi, Sahal Al-Hajoj.PLoS One. 2013; 8(2): e55598.  Published online 2013 Feb 1. doi: 10.1371/journal.pone.0055598

PMCID: PMC3562184

Mycobacterium tuberculosis DNA fingerprint clusters and its relationship with RDRio genotype in Brazil

Solange Alves Vinhas, Moisés Palaci, Hebert Silva Marques, Paola Poloni Lobo de Aguiar, Fabíola Karla Ribeiro, Renata Lyrio Peres, Reynaldo Dietze, Harrison Magdinier Gomes, Philip Noel Suffys, Jonathan E. Golub, Lee W. Riley, Ethel Leonor Noia Maciel,Tuberculosis (Edinb) Author manuscript; available in PMC 2014 Mar 1. Published in final edited form as: Tuberculosis (Edinb). 2013 Mar; 93(2): 207–212. Published online 2012 Dec 8.  doi: 10.1016/j.tube.2012.09.001.PMCID: PMC3734852

Spoligotyping of multidrug-resistant Mycobacterium tuberculosis isolates in Ethiopia

B Diriba, T Berkessa, G Mamo, Y Tedla… – … International Journal of …, 2013 – ingentaconnect.com al.10 and as per the spoligotype kit supplier’s instructions (Ocimum Biosolutions, Ijssel- stein clinical isolates were represented by a unique (non-clustered) spoligotype pattern these patterns,which are already recorded in the fourth international spoligotyping database (SpolDB4

Related articles All 4 versions Cite

[PDF] from ajol.info

Modern lineages of Mycobacterium tuberculosis in Addis Ababa, Ethiopia: implications for the tuberculosis control programe

A Mihret, Y Bekele, M Aytenew, M Abebe, L Wassie… – African health …, 2013 – ajol.info... was carried out using the commercially available kit from Ocimum Biosolutions, India, using results with already existing designations in the international spoligotyping database, SpolDB4 5. In this database, two or more patient isolates sharing identical spoligotype patterns are Related articles All 7 versions Cite

[HTML] from plos.org

[HTML] Admixed Phylogenetic Distribution of Drug Resistant Mycobacterium tuberculosis in Saudi Arabia

B Varghese, P Supply, C Allix-Béguec, M Shoukri… – PloS one, 2013 – dx.plos.org grouping of the isolates with a typical Beijing spoligotype) (Figure S1). were identified based on isolates sharing identical MIRU-VNTR types and spoligotypes. loci based MIRU-VNTR typing (Genoscreen, Lille, France) and Spoligotyping (Ocimum Biosolutions, Hyderabad, India Related articles All 6 versions Cite More

[PDF] Abattoir-based study on the epidemiology of caprine tuberculosis in Ethiopia using conventional and molecular tools

B Deresa, FJ Conraths, G Ameni… – Acta Veterinaria …, 2013 – actavetscand.com Spoligotyping Spoligotyping was performed at ALIPB; following the procedure described earlier [28] and according to the spoligotype kit supplier’s instructions (Ocimum Biosolutions Company, Iisselstein, The Netherlands). Related articles All 3 versions Cite

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Molecular typing of mycobacteria isolated from extrapulmonary tuberculosis patients at Debre Birhan Referral Hospital, central Ethiopia

L Garedew, A Mihret, T Abebe… – … Journal of Infectious …, 2013 – informahealthcare.com The 34 isolates confirmed to be M. tuberculosis by deletion typing were further characterized by spoligotyping techniques, as previously described [11,12], and in accordance with the spoligotype kit supplier instructions (Ocimum Biosolutions Company, IJsselstein Related articles All 2 versions Cite

Endogenous reactivation followed by exogenous re-infection with drug resistant strains, a new challenge for tuberculosis control in Saudi Arabia

B Varghese, R al-Omari, C Grimshaw, S Al-Hajoj – Tuberculosis, 2013 – Elsevier All of the available isolates from patients were subjected to spoligotyping (Ocimum Biosolutions, Hyderabad, India) and 24 loci based MIRU-VNTR typing (Genoscreen, Lille, France) by using the commercially available kits and methods described previously. Related articles All 4 versions Cite

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2012

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Rapid spoligotyping of Mycobacterium tuberculosis complex bacteria using a microarray system with automatic data processing and assignment

A Ruettger, J Nieter, A Skrypnyk… – Journal of Clinical …, 2012 – Am Soc Microbiol Short-Form Paper 4 reverse line blot hybridization using the Spoligotyping Kit (Ocimum Biosolutions, Hydera- 79 bad, India) and the present DNA microarray. ArrayStrip spoligotyping and the assay’s capability of identifying new spoligotypes and li- 109 neages. Import into BibTeX

Rapid Test for Identification of a Highly Transmissible Mycobacterium tuberculosis Beijing Strain of Sub-Saharan Origin

MI Millán-Lou, H Alonso, P Gavín… – Journal of Clinical …, 2012 – Am Soc Microbio First, all 292 isolates were screened by spoligotyping with a commercially available kit (Ocimum Biosolutions Ltd., Hyderabad, India) by the method of Kamerbeek et al.(14). Seventy of the 292 isolates belonged to the Beijing family. Related articlesAll 3 versionsImport into BibTeX

GenoType MTBDRsl performance on clinical samples with diverse genetic background

P Miotto, AM Cabibbe, P Mantegani… – European …, 2012 – Eur Respiratory Soc Spoligotyping. The amplified direct repeat locus of clinical isolates was investigated using the Spoligotyping kit (Ocimum Biosolutions, Hyderabad, India) following the manufacturer’sinstructions. Spoligotyping results were entered, in binary format, in the MIRU-VNTRplus web Related articlesAll 2 versionsImport into BibTeX

New insight into the molecular characterization of isoniazid and rifampicin resistant< i> Mycobacterium tuberculosis</i> strains from Saudi Arabia

B Varghese, A Hillemann, DR Wijayanti… – Infection, Genetics and …, 2012 – Elsevier Of the 151 isolates, 146 with interpretable mutation results were subjected to MIRU-VNTR typingand spoligotyping. Spoligotyping was performed as previously described (Kamerbeek et al., 1997) with the commercial kit (Ocimum Biosolutions, Hyderabad, India). All 2 versionsImport into BibTeX

[HTML] DISTRIBUTION OF SPOLIGOTYPING DEFINED GENOTYPIC LINEAGES AMONG DRUG-RESISTANT MYCOBACTERIUM TUBERCULOSIS COMPLEX CLINICAL ISOLATES IN ANKARA, TURKEY

O Kisa, G Tarhan, S Gunal, A Albay, R Durmaz… – PloS one, 2012 – dx.plos.org Spoligotyping was carried out with a commercial kit (Isogen Bioscience BV, Maarssen, The Netherlands tuberculosis H37Rv and M.bovis BCG P3 were used as control for spoligotyping.Spoligotypes results were converted into octal code and in the SITVIT2 proprietary database Related articlesCachedAll 4 versionsImport into BibTeX

[HTML] SPOLIGOTYPING AND DRUG RESISTANCE ANALYSIS OF MYCOBACTERIUM TUBERCULOSIS STRAINS FROM NATIONAL SURVEY IN CHINA

Y Pang, Y Zhou, B Zhao, G Liu, G Jiang, H Xia… – PloS one, 2012 – dx.plos.org A commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands) was used as described by of the direct repeat region of Mycobacterium tuberculosis: implications for interpretation of spoligotyping data. 2004) Predominant tuberculosis spoligotypes, Delhi, India. CachedImport into BibTeX

[HTML] SPOLIGOTYPING AND VARIABLE NUMBER TANDEM REPEAT ANALYSIS OF MYCOBACTERIUM BOVIS ISOLATES FROM CATTLE IN BRAZIL

PM Parreiras, GI Andrade… – Memórias do Instituto …, 2012 – SciELO Brasil The PCR products were hybridised to a membrane (Isogen, The Netherlands) containing 43 oligonucleotides of known spacer sequences by reversed-line blot hybridisation. Spoligotyping – Complete spoligotypes were obtained from 61 isolates (Table I). In total, 17 Related articlesCachedAll 5 versionsImport into BibTeX

EVALUATION OF 24-LOCUS MIRU-VNTR IN EXTRAPULMONARY SPECIMENS: STUDY FROM A TERTIARY CENTRE IN MUMBAI

V Vadwai, A Shetty, P Supply… – Tuberculosis, 2012 – Elsevier Spoligotyping, was performed using a commercial kit (Isogen, Netherlands) as per the 13/69,18.8%) spoligo-prototypes, compared to LAM, Haarlem or T spoligotypes represented at Analysis of the congruence between MIRU-VNTR and spoligotyping results combined with the Cited by 1All 3 versionsImport into BibTeX

EPIDEMIOLOGICAL SIGNIFICANCE OF THE DOMESTIC BLACK PIG (SUS SCROFA) IN THE MAINTENANCE OF BOVINE TUBERCULOSIS IN SICILY

V Di Marco, P Mazzone, MT Capucchio… – Journal of Clinical …, 2012 – Am Soc Microbiol direct repeat locus were detected by hybridization onto a spoligotyping membrane (Isogen 231 M. bovis isolates from both field studies were genotyped by both spoligotyping 342 Fourspoligotypes were identified: SB0120 (23 isolates), SB0841 (five isolates), SB0833 (two 344 Related articlesAll 2 versionsImport into BibTeX

TRANSMISSION OF TUBERCULOSIS WITHIN FAMILY-HOUSEHOLDS

E Augustynowicz-Kopeć, T Jagielski, M Kozińska… – Journal of Infection, 2012 – Elsevier Spoligotyping was performed with a commercially available kit (Isogen Bioscience BV, Maarssen had different M. tuberculosis isolates, as evidenced by both spoligotyping and MIRU Assumingisolates revealing both identical spoligotypes and VNTR profiles are representing the All 2 versionsImport into BibTeX

[PDF] PREVALENCE OF PULMONARY TB AND SPOLIGOTYPE PATTERN OF MYCOBACTERIUM TUBERCULOSIS AMONG TB SUSPECTS IN A RURAL COMMUNITY IN SOUTHWEST ETHIOPIA

A Deribew, G Abebe, L Apers… – BMC Infectious …, 2012 – biomedcentral.com... Standard spoligotyping method [12] was done generally as described by Kamerbeek and colleagues using a commercially available kit (Isogen Bioscience BV Spoligotypes described only once (non-clustered) in this study and in the SpolDB4 were designated as View as HTMLImport into BibTeX

CHARACTERIZING< I> MYCOBACTERIUM TUBERCULOSIS</I> ISOLATES FROM KARACHI, PAKISTAN: DRUG RESISTANCE AND GENOTYPES

A Ayaz, Z Hasan, S Jafri, R Inayat, R Mangi… – International Journal of …, 2012 – Elsevier The spoligotypes were compared with the most prevalent MTB subfamilies as identified by the World Spoligotyping Database SpolDB4.0 of the Pasteur Institute, Guadeloupe. 18. 3.4. Genotypicpattern of MTB isolates. Of the 1004 isolates, 987 were spoligotyped. All 2 versionsImport into BibTeX

IMPLICATION OF THE RD< SUP> RIO</SUP>< I> MYCOBACTERIUM TUBERCULOSIS</I> SUBLINEAGE IN MULTIDRUG RESISTANT TUBERCULOSIS IN PORTUGAL

S David, EL Duarte, CQF Leite, JN Ribeiro… – Infection, Genetics and …, 2012 – Elsevier patient), were genotyped by spoligotyping according to the manufacturer’s instructions (Isogen Bioscience BV Contribution of Spoligotyping to the Characterization of the population structure of Update on the Spoligotypes of Mycobacterium tuberculosis complex isolates from the Import into BibTeX

[PDF] ÇUKUROVA BÖLGESINDE AKCIĞER TÜBERKÜLOZLU HASTALARDAN İZOLE EDILEN MYCOBACTERIUM TUBERCULOSIS SUŞLARININ SPOLIGOTIPLENDIRME VE MIRU-VNTR YÖNTEMIYLE …

ÜO ZEYTİNLİ… – Mikrobiyol Bul, 2012 – mikrobiyolbul.org… Key words: Mycobacterium tuberculosis; spoligotyping; MIRU-VNTR; molecular epidemiology; Turkey. GİRİŞ Spoligotiplendirme Spoligotiplendirme yöntemi, üretici firmanın önerileri (Isogen Bioscience BV, Hollan- da) dikkate alınarak uygulandı. View as HTMLImport into BibTeX

Rapid spoligotyping of Mycobacterium tuberculosis complex bacteria using a microarray system with automatic data processing and assignment

A Ruettger, J Nieter, A Skrypnyk… – Journal of Clinical …, 2012 – Am Soc Microbiol Short-Form Paper 4 reverse line blot hybridization using the Spoligotyping Kit (Ocimum Biosolutions, Hydera- 79 bad, India) and the present DNA microarray. ArrayStrip spoligotyping and the assay’s capability of identifying new spoligotypes and li- 109 neages. Import into BibTeX

Rapid Test for Identification of a Highly Transmissible Mycobacterium tuberculosis Beijing Strain of Sub-Saharan Origin

MI Millán-Lou, H Alonso, P Gavín… – Journal of Clinical …, 2012 – Am Soc Microbiol… First, all 292 isolates were screened by spoligotyping with a commercially available kit (Ocimum Biosolutions Ltd., Hyderabad, India) by the method of Kamerbeek et al. (14). Seventy of the 292 isolates belonged to the Beijing family. Related articlesAll 3 versionsImport into BibTeX

GenoType MTBDRsl performance on clinical samples with diverse genetic background

P Miotto, AM Cabibbe, P Mantegani… – European …, 2012 – Eur Respiratory Soc Spoligotyping. The amplified direct repeat locus of clinical isolates was investigated using the Spoligotyping kit (Ocimum Biosolutions, Hyderabad, India) following the manufacturer’s instructions. Spoligotyping results were entered, in binary format, in the MIRU-VNTRplus web Related articlesAll 2 versionsImport into BibTeX

New insight into the molecular characterization of isoniazid and rifampicin resistant< i> Mycobacterium tuberculosis</i> strains from Saudi Arabia

B Varghese, A Hillemann, DR Wijayanti… – Infection, Genetics and …, 2012 – Elsevier Of the 151 isolates, 146 with interpretable mutation results were subjected to MIRU-VNTR typing and spoligotyping. Spoligotyping was performed as previously described (Kamerbeek et al., 1997) with the commercial kit (Ocimum Biosolutions, Hyderabad, India). All 2 versionsImport into BibTeX

 [HTML] DISTRIBUTION OF SPOLIGOTYPING DEFINED GENOTYPIC LINEAGES AMONG DRUG-RESISTANT MYCOBACTERIUM TUBERCULOSIS COMPLEX CLINICAL ISOLATES IN ANKARA, TURKEY

[HTML] from plos.org

O Kisa, G Tarhan, S Gunal, A Albay, R Durmaz… – PloS one, 2012 – dx.plos.org... Spoligotyping was carried out with a commercial kit (Isogen Bioscience BV, Maarssen, TheNetherlands tuberculosis H37Rv and M.bovis BCG P3 were used as control for spoligotyping.Spoligotypes results were converted into octal code and in the SITVIT2 proprietary database Related articlesCachedAll 4 versionsImport into BibTeX

[HTML] SPOLIGOTYPING AND DRUG RESISTANCE ANALYSIS OF MYCOBACTERIUM TUBERCULOSIS STRAINS FROM NATIONAL SURVEY IN CHINA

Y Pang, Y Zhou, B Zhao, G Liu, G Jiang, H Xia… – PloS one, 2012 – dx.plos.org A commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands) was used asdescribed by of the direct repeat region of Mycobacterium tuberculosis: implications for interpretation of spoligotyping data. 2004) Predominant tuberculosis spoligotypes, Delhi, India. CachedImport into BibTeX

[HTML] SPOLIGOTYPING AND VARIABLE NUMBER TANDEM REPEAT ANALYSIS OF MYCOBACTERIUM BOVIS ISOLATES FROM CATTLE IN BRAZIL

PM Parreiras, GI Andrade… – Memórias do Instituto …, 2012 – SciELO Brasil The PCR products were hybridised to a membrane (Isogen, The Netherlands) containing 43oligonucleotides of known spacer sequences by reversed-line blot hybridisation. Spoligotyping -Complete spoligotypes were obtained from 61 isolates (Table I). In total, 17 Related articlesCachedAll 5 versionsImport into BibTeX

EVALUATION OF 24-LOCUS MIRU-VNTR IN EXTRAPULMONARY SPECIMENS: STUDY FROM A TERTIARY CENTRE IN MUMBAI

V Vadwai, A Shetty, P Supply… – Tuberculosis, 2012 – Elsevier Spoligotyping, was performed using a commercial kit (Isogen, Netherlands) as per the 13/69,18.8%) spoligo-prototypes, compared to LAM, Haarlem or T spoligotypes represented at Analysisof the congruence between MIRU-VNTR and spoligotyping results combined with the Cited by 1All 3 versionsImport into BibTeX

EPIDEMIOLOGICAL SIGNIFICANCE OF THE DOMESTIC BLACK PIG (SUS SCROFA) IN THE MAINTENANCE OF BOVINE TUBERCULOSIS IN SICILY

V Di Marco, P Mazzone, MT Capucchio… – Journal of Clinical …, 2012 – Am Soc Microbiol direct repeat locus were detected by hybridization onto a spoligotyping membrane (Isogen 231 M. bovis isolates from both field studies were genotyped by both spoligotyping 342 Four spoligotypes were identified: SB0120 (23 isolates), SB0841 (five isolates), SB0833 (two 344 Related articlesAll 2 versionsImport into BibTeX

TRANSMISSION OF TUBERCULOSIS WITHIN FAMILY-HOUSEHOLDS

E Augustynowicz-Kopeć, T Jagielski, M Kozińska… – Journal of Infection, 2012 – Elsevier Spoligotyping was performed with a commercially available kit (Isogen Bioscience BV, Maarssen had different M. tuberculosis isolates, as evidenced by both spoligotyping and MIRU Assumingisolates revealing both identical spoligotypes and VNTR profiles are representing the All 2 versionsImport into BibTeX

[PDF] PREVALENCE OF PULMONARY TB AND SPOLIGOTYPE PATTERN OF MYCOBACTERIUM TUBERCULOSIS AMONG TB SUSPECTS IN A RURAL COMMUNITY IN SOUTHWEST ETHIOPIA

A Deribew, G Abebe, L Apers… – BMC Infectious …, 2012 – biomedcentral.com Standard spoligotyping method [12] was done generally as described by Kamerbeek andcolleagues using a commercially available kit (Isogen Bioscience BV Spoligotypes described only once (non-clustered) in this study and in the SpolDB4 were designated as View as HTMLImport into BibTeX

CHARACTERIZING< I> MYCOBACTERIUM TUBERCULOSIS</I> ISOLATES FROM KARACHI, PAKISTAN: DRUG RESISTANCE AND GENOTYPES

A Ayaz, Z Hasan, S Jafri, R Inayat, R Mangi… – International Journal of …, 2012 – Elsevier The spoligotypes were compared with the most prevalent MTB subfamilies as identified by the World Spoligotyping Database SpolDB4.0 of the Pasteur Institute, Guadeloupe. 18. 3.4. Genotypic pattern of MTB isolates. Of the 1004 isolates, 987 were spoligotyped. All 2 versionsImport into BibTeX

IMPLICATION OF THE RD< SUP> RIO</SUP>< I> MYCOBACTERIUM TUBERCULOSIS</I> SUBLINEAGE IN MULTIDRUG RESISTANT TUBERCULOSIS IN PORTUGAL

S David, EL Duarte, CQF Leite, JN Ribeiro… – Infection, Genetics and …, 2012 – Elsevier patient), were genotyped by spoligotyping according to the manufacturer’s instructions (Isogen Bioscience BV Contribution of Spoligotyping to the Characterization of the population structure of Update on the Spoligotypes of Mycobacterium tuberculosis complex isolates from the Import into BibTeX

[PDF] ÇUKUROVA BÖLGESINDE AKCIĞER TÜBERKÜLOZLU HASTALARDAN İZOLE EDILEN MYCOBACTERIUM TUBERCULOSIS SUŞLARININ SPOLIGOTIPLENDIRME VE MIRU-VNTR YÖNTEMIYLE …

ÜO ZEYTİNLİ… – Mikrobiyol Bul, 2012 – mikrobiyolbul.org Key words: Mycobacterium tuberculosis; spoligotyping; MIRU-VNTR; molecular epidemiology;Turkey. GİRİŞ Spoligotiplendirme Spoligotiplendirme yöntemi, üretici firmanın önerileri(Isogen Bioscience BV, Hollan- da) dikkate alınarak uygulandı. View as HTMLImport into BibTeX

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2011

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[HTML] Bovine tuberculosis in a Nebraska herd of farmed elk and fallow deer: a failure of the tuberculin skin test and opportunities for serodiagnosis

W Waters, GE Stevens, MA Schoenbaum… – Veterinary medicine …, 2011 – hindawi.com... Isolates of M. bovis were identified by a combination of Ziehl-Neelsen acid-fast staining, nucleic acid probes (AccuProbe, Gen-Probe, San Diego, CA, USA), and spoligotyping (Ocimum Biosolutions Ltd., Hyderabad, India). Identification of atypical Mycobacteria spp. Cited by 2Related articlesCachedAll 13 versionsImport into BibTeX

 [HTML] The use of microbead-based spoligotyping for Mycobacterium tuberculosis complex to evaluate the quality of the conventional method: Providing guidelines …[HTML] from biomedcentral.com

E Abadia, J Zhang, V Ritacco… – BMC infectious …, 2011 – biomedcentral.com of hard to interpret spoligotypes and samples representative of the work flow, so we could evaluate the benefits of a new platform regarding the classical one on these samples. Most centers had performed spoligotyping using commercial membranes (Ocimum, Hyderabad, India Cited by 3Related articlesCachedAll 26 versionsImport into BibTeX

Quality assurance for molecular epidemiology of tuberculosis methods in the mycobacterum reference laboratory

PJ Freidlin, D Goldblatt, H Kaidar-Shwartz… – … and Quality Assurance: …, 2011 – Springer... for spoli- gotyping results, standardization and reproducibility depend on the quality of the commercial spoligotyping kit (Ocimum). … Spoligotyping Pattern … Both PETRA (a MIRU-VNTR lineage with central asian spoligotypes, CAS) and Beijing clusters have been observed in other …Related articlesAll 3 versionsImport into BibTeX

DETERMINATION OF DRUG SUSCEPTIBILITY PATTERNS AND GENOTYPES OF MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM KANPUR DISTRICT; …S Purwar, S Chaudhari, VM Katoch… – Infection, Genetics and …, 2011 – Elsevier… commercially available kit 126 (Isogen Biosciences , BV, Maarsen, The Netherlands now Ocimum Biosolutions) and … Owing to small sample size, the exact prevalence of various 272 spoligotypes and M … Out of the isolates clustered by spoligotyping, all 280 were unique strains by …Cited by 3Related articlesAll 4 versionsImport into BibTeX

New insight into the molecular characterization of isoniazid and rifampicin resistant< i> Mycobacterium tuberculosis</i> strains from Saudi ArabiaB Varghese, A Hillemann, DR Wijayanti… – Infection, Genetics and …, 2012 – Elsevier... Of the 151 isolates, 146 with interpretable mutation results were subjected to MIRU-VNTR typing and spoligotyping. Spoligotyping was performed as previously described (Kamerbeek et al., 1997) with the commercial kit (Ocimum Biosolutions, Hyderabad, India). …All 2 versionsImport into BibTeX

High prevalence of subclinical tuberculosis in HIV-1-infected persons without advanced immunodeficiency: implications for TB screening

T Oni, R Burke, R Tsekela, N Bangani, R Seldon… – Thorax, 2011 – thorax.highwire.org… Lowenstein–Jensen slope cultures. The DNA was used to perform spoligotyping as previously described4 using a commercially available kit from Ocimum Biosolutions BV, The Netherlands. The hybridisation patterns obtained …Cited by 1Related articlesAll 12 versionsImport into BibTeX

[HTML] Pathology of camel tuberculosis and molecular characterization of its causative agents in pastoral regions of Ethiopia

G Mamo, G Bayleyegn, TS Tessema, M Legesse… – PloS one, 2011 – dx.plos.org… Spoligotyping. Spoligotyping was performed as previously described by Kamerbeek and coauthors [22] and according to the spoligotype kit supplier’s instructions (Ocimum Biosolutions Company, Iisselstein, The Netherlands). …Cited by 3Related articlesCachedAll 9 versionsImport into BibTeX

POPULATION-BASED INVESTIGATION OF FLUOROQUINOLONES RESISTANT TUBERCULOSIS IN RURAL EASTERN CHINA Y Hu, B Mathema, W Wang, B Kreiswirth, W Jiang… – Tuberculosis, 2011 – Elsevier… Spoligotyping was carried out using commercial kits from Isogen Bioscience BV (Maarssen, The Netherlands). 15 Strain family was determined by comparison of spoligotyping patterns with the SpoligDB4 database and assigned a spoligotyping international type (SIT). …Cited by 2Related articlesAll 4 versionsImport into BibTeX

[HTML] THE GUINEA-BISSAU FAMILY OF MYCOBACTERIUM TUBERCULOSIS COMPLEX REVISITED [HTML] from plos.org R Groenheit, S Ghebremichael, J Svensson… – PLoS One, 2011 – dx.plos.org… All isolates that were subjected to RFLP were also spoligotyped. … Altogether, 414 isolates were available for spoligotyping, of which 336 isolates were grouped into 42 clusters Out of 229 isolates, 82 different spoligotypes were obtained, of which 168 (73.4%) were clustered into Cited by 4Related articlesCachedAll 5 versionsImport into BibTeX

GENETIC DIVERSITY OF MYCOBACTERIUM TUBERCULOSIS IN MBARARA, SOUTH WESTERN UGANDA [PDF] from ajol.infoJ Bazira, M Matte, BB Asiimwe… – African health sciences, 2011 – ajol.info… was performed as previously described29 using a commercially available kit (Isogen Bioscience BV Spoligotypes that did not match any existing pattern in the SpolDB4 database were tuberculosis within the Mbarara, we have used RD analysis and spoligotyping to characterize Related articlesAll 8 versionsImport into BibTeX

FLUOROQUINOLONE RESISTANCE AMONG MYCOBACTERIUM TUBERCULOSIS STRAINS FROM KARACHI, PAKISTAN: DATA FROM COMMUNITY-BASED FIELD CLINICS TML] from nih.gov  Rafiq, K Jabeen, R Hasan, S Jafri… – Antimicrobial agents …, 2011 – Am Soc Microbiol… was performed on all FQ-resistant strains using a commercially available kit provided by Isogen Life Science BV The spoligotypes were compared with the most prevalent M. tuberculosis subfamilies, as identified by the world spoligotyping database, SpolDB4.0, of Related articlesAll 6 versionsImport into BibTeX

[HTML] CHARACTERISTICS OF PNCA MUTATIONS IN MULTIDRUG-RESISTANT TUBERCULOSIS IN TAIWAN [HTML] from biomedcentral.com YC Chiu, SF Huang, KW Yu, YC Lee… – BMC infectious …, 2011 – biomedcentral.com… Genotyping. All clinical isolates were genotyped by a commercial spoligotyping kit (Isogen Bioscience BV, Maarssen, Netherlands). The “Beijing strain” was defined as deletion from spacer 1 to spacer 34 in the direct repeat region and the presence of (at least 3) spacers 35-43. Related articlesCachedAll 11 versionsImport into BibTeX

[HTML] INITIAL PRESENTATIONS PREDICT MORTALITY IN PULMONARY TUBERCULOSIS PATIENTS-A PROSPECTIVE OBSERVATIONAL STUDY [HTML] from plos.org JY Feng, WJ Su, YC Chiu, SF Huang, YY Lin… – PloS one, 2011 – dx.plos.org... All clinical isolates were genotyped using a commercial spoligotyping kit (Isogen Bioscience BV, Maarssen, Netherlands). The “Beijing strain” was defined as a deletion from spacer 1 to spacer 34 in the direct repeat region and the presence of (at least 3) spacers in 35–43. Related articlesCachedAll 4 versionsImport into BibTeX

[HTML] MOLECULAR EPIDEMIOLOGY OF MYCOBACTERIUM TUBERCULOSIS, BUENOS AIRES, ARGENTINA [HTML] from nih.govX Gonzalo, M Ambroggi, E Cordova… – Emerging Infectious …, 2011 – ncbi.nlm.nih.gov… DNA was extracted from cultures at this UK laboratory; spoligotyping was performed according to the manufacturer’s instructions (Isogen Life Science, IJsselstein, the Netherlands); and data were analyzed with SPOTCLUST (http://cgi2.cs.rpi.edu/~bennek/SPOTCLUST.html). Related articlesAll 4 versionsImport into BibTeX

CHARACTERISTICS OF MULTIDRUG-RESISTANT MYCOBACTERIUM TUBERCULOSIS IN TAIWAN: A POPULATION-BASED STUDY CW Chang, MH Wu, PC Chuang… – Infection, Genetics and Evolution, 2011 – Elsevier… 12 13 Spoligotyping 14 A commercially available kit (Isogen Bioscience BV, Maarssen, The 15 Netherlands) was used as Even through spoligotyping results 3 revealed the genetic diversities of MDR M. tuberculosis isolates in Taiwan, 4 identical spoligotypes could not Cited by 2Related articlesAll 2 versionsImport into BibTeX

MOLECULAR PATTERN OF MYCOBACTERIUM BOVIS ISOLATES AND ITS RELATIONSHIP WITH RISK FACTORS ASSOCIATED WITH THE PRESENCE OF BOVINE …[PDF] from uaemex.mx IF Padilla-Campos, JC Segura-Correa… – Tropical and …, 2011 – redalyc.uaemex.mx... Key words: Bovine tuberculosis; Spoligotypes; M. bovis; Risk factors. Spoligotyping was carried out following the protocol described by Kamerbeek et al sequences from M. tuberculosis and six spacer sequences for M. bovis BCG were covalently bound (ISOGEN, Maarssen, The Related articlesAll 2 versionsImport into BibTeX

[HTML] FINE-TUNING THE SPACE, TIME, AND HOST DISTRIBUTION OF MYCOBACTERIA IN WILDLIFE[HTML] from biomedcentral.com C Gortazar, MJ Torres, P Acevedo, J Aznar… – BMC …, 2011 – biomedcentral.com Typing. The M. bovis isolates were further characterized by spoligotyping [40]. The amplified product was detected by hybridization of the biotin-labelled PCR product onto spoligotyping membrane (Isogen Bioscience BV, Maarssen, The Netherlands). Cited by 6Related articlesCachedAll 19 versionsImport into BibTeX

MOLECULAR PATTERN OF MYCOBACTERIUM BOVIS ISOLATES AND ITS RELATIONSHIP WITH RISK FACTORS ASSOCIATED WITH THE PRESENCE OF …[PDF] from uady.mx IF Padilla, JC Segura, JC Rodriguez… – Tropical and …, 2011 – ccba.uady.mx Key words: Bovine tuberculosis; Spoligotypes; M. bovis; Risk factors. Spoligotyping was carried out following the protocol described by Kamerbeek et al sequences from M. tuberculosis and six spacer sequences for M. bovis BCG were covalently bound (ISOGEN, Maarssen, The Related articlesAll 2 versionsImport into BibTeX

EPIDEMIOLOGICAL TRENDS AND CLINICAL COMPARISONS OF< I> MYCOBACTERIUM</I>< I> TUBERCULOSIS</I> LINEAGES IN THAI TB MENINGITISK Faksri, F Drobniewski, V Nikolayevskyy, T Brown… – Tuberculosis, 2011 – Elsevier isolated from CSF samples collected from 1996 to 2004 with IS6110 RFLPs (120 RFLP patterns were available) and spoligotyping results (141 spoligotypes were available 27 Spoligotypingwas performed according to the manufacturer’s instructions (Isogen Bioscience BV Cited by 1Related articlesAll 3 versionsImport into BibTeX

A NOVEL METHOD FOR THE RAPID AND PROSPECTIVE IDENTIFICATION OF BEIJING MYCOBACTERIUM TUBERCULOSIS STRAINS BY HIGH‐RESOLUTION MELTING ANALYSISM Alonso, Y Navarro, F Barletta… – Clinical …, 2011 – Wiley Online Library... Thirty-two MTB strains (18 representatives of the Beijing genotype and 14 representatives of the non-Beijing genotype, according to their spoligotypes) were grown on Spoligotyping was performed in accordance with the manufacturer’s instructions (Isogen, De Meern, the Cited by 3Related articlesAll 3 versionsImport into BibTeX

QUALITY ASSURANCE FOR MOLECULAR EPIDEMIOLOGY OF TUBERCULOSIS METHODS IN THE MYCOBACTERIUM REFERENCE LABORATORY PJ Freidlin, D Goldblatt, H Kaidar-Shwartz… – … and Quality Assurance: …, 2011 – Springer 43 spacer spoligotyping was performed according to the manufacturer’s instructions (Isogen/Ocimun) as described previously. 27 Spoligotyping Pattern Both PETRA (a MIRU-VNTR lineage with central asian spoligotypes, CAS) and Beijing clusters have been observed in other Related articlesAll 3 versionsImport into BibTeX

EPIDEMIOLOGICAL ANALYSIS OF MYCOBACTERIUM TUBERCULOSIS STRAINS ISOLATED IN LODZ, POLANDM Krawczyk, A Brzostek, A Gorna… – … of Tuberculosis and …, 2011 – ingentaconnect.com of van Embden et al.16 Spoligotyping was performed as described by Kamerbeek et al., using the Isogen Life Science kit Spoligotyping analysis showed that 184 (78.6%) of the strains were grouped in clusters and 50 (21.4%) strains possessed unique spoligotypes.

ONE YEAR NATIONWIDE EVALUATION OF 24-LOCUS MIRU-VNTR GENOTYPING ON SLOVENIAN< I> MYCOBACTERIUM TUBERCULOSIS</I> ISOLATES U Bidovec-Stojkovic, M Zolnir-Dovc… – Respiratory Medicine, 2011 – Elsevier… 4,9,20 Spoligotyping was performed using a commercially available kit (Isogen Bioscience B identically defined by IS6110 RFLP and 24-locus MIRU-VNTR typing combined with spoligotyping. jointly defined by identical 24-locus MIRU-VNTR types and spoligotypes were only

MOLECULAR CHARACTERIZATION OF MYCOBACTERIUM TUBERCULOSIS COMPLEX (MTBC) ISOLATED FROM CATTLE IN NORTHEAST AND NORTHWEST CHINA Y Du, Y Qi, L Yu, J Lin, S Liu, H Ni… – Research in veterinary …, 2011 – Elsevier... 2.5. Spoligotyping. Spoligotyping kits and Mini-blotter MN45 were obtained from Isogen Life Science Co. (Utrecht, the Netherlands). The Streptavidin-ß-peroxidase conjugate was produced by Roche Applied Science Co. (Penzberg, Germany). Cited by 3Related articlesAll 3 versionsImport into BibTeX

[HTML] TRANSMISSION PATTERN OF DRUG-RESISTANT TUBERCULOSIS AND ITS IMPLICATION FOR TUBERCULOSIS CONTROL IN EASTERN RURAL CHINA [HTML] from plos.org Y Hu, B Mathema, W Jiang, B Kreiswirth, W Wang… – PloS one, 2011 – dx.plos.org… Hybridized DNA was detected using an enhanced chemiluminescene kit from Isogen Bioscience BV b Probaiblity that the Spoligotyping pattern belongs to the clades. N, Bennett KP (2006) Identifying Mycobacterium tuberculosis complex strain families using spoligotypes. Related articlesCachedAll 7 versionsImport into BibTeX

SUBLINEAGES OF BEIJING STRAIN OF MYCOBACTERIUM TUBERCULOSIS IN SRI LANKA US Rajapaksa… – Indian Journal of Microbiology, 2011 – Springer… Spoligotyping was carried out according to manufacturer’s guidelines using a commercially available kit (Isogen, Maarsen MV, The Netherland). Fourteen iso-lates that confirmed to be Beijing strain were further characterised. Related articlesAll 2 versionsImport into BibTeX

DETERMINATION OF DRUG SUSCEPTIBILITY PATTERNS AND GENOTYPES OF MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM KANPUR DISTRICT; …S Purwar, S Chaudhari, VM Katoch… – Infection, Genetics and …, 2011 – Elsevier… 43 spacers was done with the help of a commercially available kit 126 (Isogen Biosciences ,BV Owing to small sample size, the exact prevalence of various 272 spoligotypes and M.tuberculosis Out of the isolates clustered by spoligotyping, all 280 were unique strains by IS6110 Cited by 3Related articlesAll 4 versionsImport into BibTeX

MOLECULAR EPIDEMIOLOGY OF HUMAN AND ANIMAL TUBERCULOSIS IN IBADAN, SOUTHWESTERN NIGERIA AO Jenkins, SIB Cadmus, EH Venter… – Veterinary …, 2011 – Elsevier... Spoligotyping167 Spoligotyping confirmed the species identification of 19 M. tuberculosis and 13 M None of these CAM 173 variant spoligotypes were found in the spolDB4 database and were All M. tuberculosis strains 175 from PTB patients that were spoligotyped had identical Cited by 1Related articlesAll 5 versionsImport into BibTeX

GENETIC DIVERSITY OF THE MYCOBACTERIUM TUBERCULOSIS BEIJING FAMILY BASED ON IS6110, SNP, LSP AND VNTR PROFILES FROM THAILANDK Faksri, F Drobniewski, V Nikolayevskyy… – Infection, Genetics and …, 2011 – Elsevier… Eighty MTB Beijing isolates from CSF samples with IS6110 RFLPs (69 RFLP patterns wereavailable) and spoligotyping results (all 80 spoligotypes were available Spoligotyping was performed according to the manufacturer s instructions (Isogen Bioscience BV Cited by 2Related articlesAll 3 versionsImport into BibTeX

[PDF] 骨结核临床分离菌株基因分型的特点 [PDF] from clinicmed.net李文胜, 刘毅, 孙勇, 田苗, 刘忠泉… – 中华临床医师杂志 ( …, 2011 – clinicmed.net TM 琼脂糖购自赛百盛基因技 术有限公司。 DNA Ladder Marker 购自TaKaRa 公司。凝胶成像仪购自FOTO DYNE 公司。 Spoligotyping 试 剂盒以及Miniblotter MN45为荷兰 Isogen Bioscience 公司产品。 链霉亲和素为Sigam 公司产品。 化学发光 Related articlesView as HTMLAll 3 versionsImport into BibTeX

MOLECULAR EPIDEMIOLOGY OF MYCOBACTERIUM TUBERCULOSIS IN THE UNITED ARAB EMIRATES [PDF] from qmul.ac.uk A Saedi… – 2011 – qmro.qmul.ac.uk … 130 3.2.11 Identification of the UAE isolates by spoligotyping….. 132 3.2.12 Comparison betweenMIRU-typed and spoligotyped families in association with katG463/gyrA95 groupings ….. Related articlesAll 2 versionsImport into BibTeX 

[HTML] MYCOBACTERIUM BOVIS IN SWINE: SPOLIGOTYPING OF ISOLATES FROM ARGENTINA [HTML] from hindawi.comS Barandiaran, EV Moras, A Adri& – Veterinary Medicine …, 2011 – hindawi.com… Spoligotyping [14] was carried out by using the spoligotyping kit (Isogen Biosolutions BV, Ocimun Guerin (BCG) (ATCC 27289) were included as reference strains in each spoligotyping experiment isolates were defined as two or more M. bovis strains with identical spoligotypes. Cited by 1Related articlesCachedAll 11 versionsImport into BibTeX

[HTML] SPOLIGOTYPING OF CLINICAL MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM THE STATE OF MINAS GERAIS, BRAZIL [HTML] from scielo.brSS Miranda, WS Carvalho, PN Suffys… – Memórias do Instituto …, 2011 – SciELO Brasil was resuspended in the same TE buffer, stored at -20ºC and subjected to spoligotyping using a previously published protocol (Kamerbeek et al. 1997) and a commercially available kit (Isogen Life Science BV, Utrecht, The Netherlands). The hybridised spoligotypes in binary Related articlesCachedAll 7 versionsImport into BibTeX

EVALUATION OF SPOLIGOTYPING AND MIRU-VNTR FOR MYCOBACTERIUM BOVIS IN XINJIANG, CHINAZ Sun, R Cao, M Tian, X Zhang, X Zhang… – Research in Veterinary …, 2011 – Elsevier Additionally, two new spoligotypes (SB1903 and SB1904) and special repeat numbers of 3 loci (ETR Spoligotyping was firstly analyzed and interpreted in octal codes (Dale et al., 2001) following the instruction (http://www.mbovis.org) with a commercial kit (Isogen Bioscience BV Cited by 2Related articlesAll 2 versionsImport into BibTeX

[HTML] MYCOBACTERIUM TUBERCULOSIS SPOLIGOTYPES AND DRUG SUSCEPTIBILITY PATTERN OF ISOLATES FROM TUBERCULOSIS PATIENTS IN SOUTH-WESTERN UGANDA [HTML] from biomedcentral.comJ Bazira, BB Asiimwe, ML Joloba… – BMC infectious …, 2011 – biomedcentral.com... Spoligotyping. Standard spoligotyping was performed as previously described [29] using a commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands). Spoligotyping.All the isolates had spoligotypes characteristic of M. tuberculosis. Cited by 1Related articlesCachedAll 12 versionsImport into BibTeX

A FIRST INSIGHT ON THE POPULATION STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS COMPLEX AS STUDIED BYSPOLIGOTYPING AND MIRU-VNTRS IN BOGOTÁ, COLOMBIAI Cerezo, Y Jiménez, J Hernandez, T Zozio… – Infection, Genetics and …, 2011 – Elsevier Kamerbeek et al., 1997) according to the manufacturer s instructions (Isogen Bioscience, the Spoligotype International Type (SIT) and MIRU International Type (MIT) designate spoligotypes and MIRU was used to build minimum spanning trees based on spoligotyping and MIRU All 2 versionsImport into BibTeX

[PDF] PRELIMINARY MAPPING STUDY OF MYCOBACTERIUM TUBERCULOSIS’ COMPLEX DNA BYSPOLIGOTYPING ON ISOLATED SPUTUM OF TUBERCULOSIS PATIENT …[PDF] from digitaljournals.org V Lisdawati, I Parwati… – Bulletin of Health …, 2011 – indonesia.digitaljournals.org PCR, denaturasi menggunakan thermocycler selama 10 menit pada suhu 99,9°C. Kemudian pada mini blotter MN45 yang telah diletakkan membran spoligotyping kit (IM9702, Isogen Biosolution, BV) berlabel 43 DNA spacer Mtb complex segera hibridisasikan DNA hasil PCR. Related articlesView as HTMLImport into BibTeX

[PDF] INFECTION OF EURASIAN BADGERS (MELES MELES) WITH MYCOBACTERIUM BOVIS[PDF] from uclm.esA Balseiro, O Rodríguez, P González-Quirós… – prevalence, 2011 – uclm.es al., 2009). 125 MTC isolates were characterised hybridisation of biotin-labelled PCR products 126 onto a spoligotyping membrane (Isogen Bioscience BV), followed by spoligotyping 127 (Kamerbeek et al., 1997). Results were Cited by 2Related articlesView as HTMLAll 2 versionsImport into BibTeX

CLINICAL AND MICROBIOLOGICAL CHARACTERISTICS OF URINE CULTURE-CONFIRMED GENITOURINARY TUBERCULOSIS AT MEDICAL CENTERS IN TAIWAN FROM 1995 TO 2007HL Hsu, CC Lai, MC Yu, FL Yu, JC Lee… – European journal of …, 2011 – Springer commercially available spoligotyping kit (Isogen Bioscience BV, Maarssen, The Netherlands) was used as described by the manufacturer. The fourth international spoligotyping database (SpolDB4) database was used to assign genotype families to the spoligotypes obtained [14 Related articlesAll 5 versionsImport into BibTeX

MOLECULAR TYPING OF MYCOBACTERIUM TUBERCULOSIS CIRCULATED IN MOSCOW, RUSSIAN FEDERATIONMV Afanas’ ev, LN Ikryannikova, EN Il’ina… – European Journal of …, 2011 – Springer spacers probes from the spoligotyping kit from Isogen Lifescience (cat. no. IM9701). 182 Eur J Clin Microbiol Infect Dis (2011) 30:181–191 Page 3. Spoligotypes in binary format were entered in an Excel spreadsheet and compared with the spoligotyping database SpolDB4 [13]. Cited by 7Related articlesAll 4 versionsImport into BibTeX

ROLE OF 2-MONTH SPUTUM SMEARS IN PREDICTING CULTURE CONVERSION IN PULMONARY TUBERCULOSIS[HTML] from ersj.org.uk WJ Su, JY Feng, YC Chiu… – European Respiratory …, 2011 – Eur Respiratory Soc All clinical isolates were genotyped by commercial spoligotyping kit (Isogen Bioscience BV, Maarssen, the Netherlands). The “Beijing strain” was defined as deletion from spacer 1 to spacer 34 in the direct repeat region and the presence of (at least three of) spacers 35–43. Cited by 5Related articlesAll 6 versionsImport into BibTeX

[PDF] A TWO-STEP STRATEGY FOR MOLECULAR TYPING OF MULTIDRUG-RESISTANT MYCOBACTERIUM TUBERCULOSIS CLINICAL ISOLATES FROM POLAND. [PDF] from microbiology.pl T JAGIELSKI, EWAA KOPEĆ… – Polish journal of …, 2011 – pjm.microbiology.pl Spoligotyping was perfor- med with a commercially available kit (Isogen Bio- science BV e isolates whose spoligotype patterns were already recorded in the database, were assigned“shared types”, whereas those of spoligotypes identified for the first time, were View as HTMLAll 3 versionsImport into BibTeX

MOLECULAR TECHNOLOGIES USED IN DETECTING OF SENSITIVE AND ISONIAZID-RESISTANT MYCOBACTERIUM TUBERCULOSIS OY Limanskaya… – Cytology and Genetics, 2011 – Springer The PCR was carried out by a dry kit of reagents for DNA amplification (Isogen, Russian Federation) in 20–50 μl of reaction mixture containing 4 mM NaCl, 50 mM KCl, 12 mM Tris HCl (pH 8.0), 2.5 mM MgCl2, 200 μM dNTPs, 0.1–0.5 μM of each primer, and 1 unit of Taq DNA Related articlesAll 4 versionsImport into BibTeX

STREPTOMYCIN RESISTANCE AND LINEAGE-SPECIFIC POLYMORPHISMS IN MYCOBACTERIUM TUBERCULOSIS GIDB GENE HTML] from nih.govFS Spies, AW Ribeiro, DF Ramos… – Journal of clinical …, 2011 – Am Soc Microbiol Genotyping.Spoligotyping was performed using a commercial kit (Isogen Biosciences BV, Netherlands it was classified as LAM3 and S/convergent sublineage by spoligotyping but as non … Spoligotypes evolve through successive loss of spacer DNA sequences (16), and since Cited by 2Related articlesAll 7 versionsImport into BibTeX

GENOTYPING AND DRUG RESISTANCE PATTERNS OF MYCOBACTERIUM TUBERCULOSIS STRAINS IN FIVE PROVINCES OF CHINA YL Guo, Y Liu, SM Wang, CY Li… – … of Tuberculosis and …, 2011 – ingentaconnect.com Of the (Isogen Bioscience BV, De Meern, The Netherlands). 1–1800 = shared spoligotypes. Table 3 Results of MIRU typing and comparison of the three typing methods Isolate MIRU locus number IS6110-RFLP Cluster 2 4 10 16 20 23 24 26 27 31 39 40 Spoligotyping MIRU Cited by 3Related articlesAll 3 versionsImport into BibTeX

ASSOCIATION OF< I> MYCOBACTERIUM TUBERCULOSIS</I> GENOTYPES AND CLINICAL AND EPIDEMIOLOGICAL FEATURES-A MULTI-CENTER STUDY IN TAIWAN SF Huang, WJ Su, HY Dou, JY Feng… – Infection, Genetics and …, 2011 – Elsevier Spoligotyping was performed according to the method reported by Kamerbeek et al. (Kamerbeek et al., 1997) using a commercial kit (Isogen Biosolutions, Netherlands). The spoligotypes were identified according to the database SpoDB4.0 (Brudey et al., 2006), and the SIT Related articlesAll 5 versionsImport into BibTeX

THE GENOTYPE CHARACTERISTIC OF CLINICAL ISOLATED STRAINS GETTING FROM BONE TUBERCULOSIS[PDF] from clinicmed.netLI Wen-sheng, LIU Yi, SUN Yong… – Chinese Journal of …, 2011 – global.clinicmed.net TM 琼脂糖购自赛百盛基因技 术有限公司。 DNA Ladder Marker 购自 TaKaRa 公司。 凝胶成像仪购自 FOTO DYNE 公司。 Spoligotyping 试 剂盒以及 Miniblotter MN45为荷兰 Isogen Bioscience 公司产品。 链霉亲和素为 Sigam 公司产品。 化学发光 Related articlesImport into BibTeX

MULTIPLE STRAINS OF< I> MYCOBACTERIUM BOVIS</I> REVEALED BY MOLECULAR TYPING IN A HERD OF CATTLE EES Figueiredo, DF Ramos, L Medeiros… – The Veterinary …, 2011 – Elsevier to the spoligo-membrane was performed according to the manufacturer’s instructions (Isogen Life Sciences). The strains clustered by spoligotyping were analysed by VNTR-PCR to confirm clonal relationships Four spoligotypes were identified among the 12 M. bovis isolates. Related articlesAll 2 versionsImport into BibTeX

DETERMINAÇÃO DO CUSTO BIOLÓGICO EM ISOLADOS DE MYCOBACTERIUM TUBERCULOSIS COM MUTAÇÕES NOS GENES RPSL, RRS, GIDB, RPOB E KATG [PDF] from ufrgs.br FS Spies – 2011 – lume.ufrgs.br restriction fragment lenght polymorphism) da sequência de inserção IS6110, spoligotyping e unidade de repetição de micobactéria- repetição em tandem de número variável (MIRU- …Spoligotyping é uma técnica de genotipagem que explora a variabilidade da região Related articlesImport into BibTeX

A MAJOR SUBGROUP OF BEIJING FAMILY MYCOBACTERIUM TUBERCULOSIS IS ASSOCIATED WITH MULTIDRUG RESISTANCE AND INCREASED TRANSMISSIBILITY Y Hu, X Ma, EA Graviss, W Wang… – Epidemiology and …, 2011 – Cambridge Univ Press Spoligotyping was performed by using a com- mercial kit from Isogen Bioscience BV (Maarssen 0.04), and resistance to RIF and SM (P=0.04) (Table 1). Spoligotyping identified 243 Thirty-three(9.4%) isolates had unique/novel spoligotypes, of which similarity analysis found that Cited by 6Related articlesAll 4 versionsImport into BibTeX

[HTML] MODERN AND ANCESTRAL GENOTYPES OF MYCOBACTERIUM TUBERCULOSIS FROM ANDHRA PRADESH, INDIA [HTML] from plos.org SK Thomas, CC Iravatham, BH Moni, A Kumar… – PloS one, 2011 – dx.plos.org the help of commercially available line probe arrays (Isogen Biosciences BV tuberculosis complexgenetic diversity: mining the fourth international spoligotyping database (SpolDB4 KP (2006)Identifying Mycobacterium tuberculosis complex strain families using spoligotypes. Related articlesCachedAll 5 versionsImport into BibTeX

[HTML] TUBERCULOSIS IN SUDAN: A STUDY OF MYCOBACTERIUM TUBERCULOSIS STRAIN GENOTYPE AND SUSCEPTIBILITY TO ANTI-TUBERCULOSIS DRUGS [HTML] from biomedcentral.com GSS Eldin, I Fadl-Elmula, MS Ali… – BMC infectious …, 2011 – biomedcentral.com 21] using a commercial kit to test for 43 individual spacers (Isogen, IJsselstein, The Spoligotyping provided a relatively simple and rapid means of describing the population of improved discrimination of strains sharing the CAS1_Dehli and Beijing spoligotypes when using MIRU Related articlesCachedAll 11 versionsImport into BibTeX

[PDF] MOLECULAR CHARACTERISATION OF MYCOBACTERIUM BOVIS ISOLATED FROM AFRICAN BUFFALOES (SYNCERUS CAFFER) IN HLUHLUWE-IMFOLOZI PARK IN KWAZULU-NATAL, SOUTH AFRICA [PDF] from scielo.org.za TM Hlokwe, AO Jenkins, EM Streicher… – … Journal of Veterinary …, 2011 – scielo.org.za One of the observed spoligotypes (SB0130) was dominant and represented 75% of isolates …Spoligotyping Spoligotyping was done according to a standardised international method(Kamerbeek et al. 1997) using a commercially available kit (Isogen Biosciences BV, Maarsen). Related articlesView as HTMLAll 10 versionsImport into BibTeX

GENOTYPING DID NOT EVIDENCE ANY CONTRIBUTION OF MYCOBACTERIUM BOVIS TO HUMAN TUBERCULOSIS IN BRAZIL [PDF] from redetb.org A Rocha, AR Elias, LF Sobral, DF Soares… – Tuberculosis, 2011 – Elsevier using PCR and hybridization conditions on a commercially available membrane (Isogen Biosciene BV All isolates that yielded spoligotypes that were recognized as not previously described patterns were submitted to at least one additional spoligotyping assay and Related articlesAll 6 versionsImport into BibTeX

MOLECULAR AND EPIDEMIOLOGICAL CHARACTERIZATION OF MULTIDRUG-RESISTANT MYCOBACTERIUM TUBERCULOSIS ISOLATES IN JOHANNESBURG, SOUTH AFRICA [PDF] from wits.ac.zaCK Mlambo – 2011 – wiredspace.wits.ac.za 61 Table 3.6 Description of the orphan MIRU patterns (n=45) from this study and corresponding spoligotyping-based information (octal code, SIT, and clade)…………64 Table 3.7 MIRU profiles of the four newly created spoligotypes (10 Related articlesImport into BibTeX

USE OF SPOLIGOTYPE ANALYSIS TO DETECT LABORATORY CROSS-CONTAMINATIONB Nivin, J Driscoll, T Glaser, P Bifani… – Infection control and …, 2000 – JSTOR The spoligotyping analysis was performed using a commercially available kit (Isogen Bioscience BV In several cases of identical spoligotypes, the Wadsworth Center indicated that the …Spoligotyping is an effective, relatively inexpensive (approximately 10% the cost of RFLP Cited by 12Related articlesBL DirectAll 6 versionsImport into BibTeX

CLINICAL AND GENOTYPIC CHARACTERISTICS OF CHILDHOOD TUBERCULOSIS IN CHONGQING, CHINA L Xing, R Liu, Q Li, Z Peng… – European Journal of Clinical …, 2011 – Springer Of 105 isolates spoligotyped, the major spoligotypes found were Spoligotyping was performed according to the internation- ally standardized protocol [5]. A commercially available spoligotyping kit (Isogen Bioscience BV, Maarssen, The Netherlands) was used as described Related articlesAll 2 versionsImport into BibTeX

TUBERCULOSIS DUE TO MYCOBACTERIUM BOVIS AND MYCOBACTERIUM CAPRAE IN SHEEPM Muņoz Mendoza, L Juan, S Menéndez… – The Veterinary …, 2011 – Elsevier

by hybridisation of the biotin-labelled PCR product onto spoligotyping membrane (Isogen Bioscience BV). Isolates were characterised by spoligotyping as M. caprae SB0157 (flock A) and M. bovis close contact with cattle or goats infected by the same spoligotypes (Table 1 Cited by 3Related articlesAll 2 versionsImport into BibTeX

[HTML] MYCOBACTERIUM BOVIS INFECTION IN GOATS FROM THE NORTHEAST REGION OF BRAZIL [HTML] from scielo.br SSS Higino, SR Pinheiro, GO Souza… – Brazilian Journal of …, 2011 – SciELO Brasil Isolate was characterised by spoligotyping as described (7). The amplified product was detected by hybridization of the biotin-labelled PCR product onto spoligotyping membrane (Isogen Bioscience BV, Maarssen, The Netherlands).

EPIDEMIOLOGICAL STUDIES OF BEIJING STRAINS OF MYCOBACTERIUM TUBERCULOSIS FROM TAIPEI AND OTHER ASIAN CITIES BASED ON MIRU PROFILES JUNREN SUN, HYUN DOU, SYI LEE… – Apmis, 2011 – Wiley Online Library on isolates from areas where the Beijing strain is prevalent as most isolates in this family share the same spoligotypes (1, 5 Spoligotyping to the manufacturers’ protocol, to a set of 43 oligonucle-otides of DR spacers on a membrane using the Isogen Bioscience spoligotyping kit

Year 2012

 Diversity of Mycobacterium tuberculosis Isolates from New Pulmonary Tuberculosis Cases in Addis Ababa, Ethiopia.Adane Mihret, Yonas Bekele, Andre G. Loxton, Annemie M. Jordan, Lawrence Yamuah, Abraham Aseffa, Rawleigh Howe, Gerhard Walzl,Tuberc Res Treat. 2012; 2012: 892079.  Published online 2012 Nov 22. doi: 10.1155/2012/892079.PMCID: PMC3513727

 Plasma Level of IL-4 Differs in Patients Infected with Different Modern Lineages of M. tuberculosis.Adane Mihret, Yonas Bekele, Andre G. Loxton, Abraham Aseffa, Rawleigh Howe, Gerhard Walzl,J Trop Med. 2012; 2012: 518564.  Published online 2012 Sep 25. doi: 10.1155/2012/518564.PMCID: PMC3463165

 Modern lineages of Mycobacterium tuberculosis in Addis Ababa, Ethiopia: implications for the tuberculosis control programe.A Mihret, Y Bekele, M Aytenew, Y Assefa, M Abebe, L Wassie, GA Loxton, L Yamuah, A Aseffa, G Walzl, R Howe.Afr Health Sci. 2012 Sep; 12(3): 339–344.  PMCID: PMC3557690

 Rapid Spoligotyping of Mycobacterium tuberculosis Complex Bacteria by Use of a Microarray System with Automatic Data Processing and Assignment.Anke Ruettger, Johanna Nieter, Artem Skrypnyk, Ines Engelmann, Albrecht Ziegler, Irmgard Moser, Stefan Monecke, Ralf Ehricht, Konrad Sachse

J Clin Microbiol. 2012 Jul; 50(7): 2492–2495.  doi: 10.1128/JCM.00442-12

  Whole cell & culture filtrate proteins from prevalent genotypes of Mycobacterium tuberculosis provoke better antibody & T cell response than laboratory strain H37Rv.Gavish Kumar, Hari Shankar, Mamta Chahar, Pragya Sharma, Virendra Singh Yadav, Devendra Singh.Chauhan, Vishwa Mohan Katoch, Beenu Joshi

Indian J Med Res. 2012 May; 135(5): 745–755. PMCID: PMC3401709

 Rapid Test for Identification of a Highly Transmissible Mycobacterium tuberculosis Beijing Strain of Sub-Saharan Origin.María Isabel Millán-Lou, Henar Alonso, Patricia Gavín, Melissa Hernández-Febles, María Isolina

Campos-Herrero, Rodolfo Copado, Fernando Cañas, Kristin Kremer, José Antonio Caminero, Carlos  Martín, Sofía Samper.J Clin Microbiol. 2012 Feb; 50(2): 516–518.  doi: 10.1128/JCM.06314-11.PMCID: PMC3264144

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2011

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High prevalence of subclinical tuberculosis in HIV-1-infected persons without advanced  immunodeficiency: implications for TB screening.Tolu Oni, Rachael Burke, Relebohile Tsekela, Nonzwakazi Bangani, Ronnett Seldon, Hannah P Gideon, Kathryn Wood, Katalin A Wilkinson, Tom H M Ottenhoff, Robert J Wilkinson.Thorax. 2011 Aug; 66(8): 669–673.  Published online 2011 May 31. doi: 10.1136/thx.2011.160168

PMCID: PMC3142344

The use of microbead-based spoligotyping for Mycobacterium tuberculosis complex to evaluate the quality of the conventional method: Providing guidelines for Quality Assurance when working on membranes

Edgar Abadia, Jian Zhang, Viviana Ritacco, Kristin Kremer, Raymond Ruimy, Leen Rigouts, Harrison Magdinier Gomes, Atiná Ribeiro Elias, Maryse Fauville-Dufaux, Karolien Stoffels, Voahangy Rasolofo-Razanamparany, Darío Garcia de Viedma, Marta Herranz, Sahal Al-Hajoj, Nalin Rastogi, Carlo Garzelli, Enrico Tortoli, Philip N Suffys, Dick van Soolingen, Guislaine Refrégier, Christophe Sola.BMC Infect Dis. 2011; 11: 110.  Published online 2011 Apr 28. doi: 10.1186/1471-2334-11-110.PMCID: PMC3107175

Bovine Tuberculosis in a Nebraska Herd of Farmed Elk and Fallow Deer: A Failure of the Tuberculin Skin Test and Opportunities for Serodiagnosis.W. Ray Waters, Gary E. Stevens, Mark A. Schoenbaum, Kathy A. Orloski, Suelee Robbe-Austerman, N. Beth Harris, S. Mark Hall, Bruce V. Thomsen, Arach J. Wilson, Roger E. Brannian, Jeffrey T. Nelson, Shawn Schafer, Javan Esfandiari, Meghan Dutton, Rena Greenwald, Konstantin P. Lyashchenko.Vet Med Int. 2011; 2011: 953985.  Published online 2011 Apr 14. doi: 10.4061/2011/953985

PMCID: PMC3087612

Pathology of Camel Tuberculosis and Molecular Characterization of Its Causative Agents in astoral Regions of Ethiopia.Gezahegne Mamo, Gizachew Bayleyegn, Tesfaye Sisay Tessema, Mengistu Legesse, Girmay Medhin, Gunnar,Bjune, Fekadu Abebe, Gobena Ameni.PLoS One. 2011; 6(1): e15862.  Published online 2011 Jan 24. doi: 10.1371/journal.pone.0015862.PMCID: PMC3025912

[HTML] Bovine tuberculosis in a Nebraska herd of farmed elk and fallow deer: a failure of the tuberculin skin test and opportunities for serodiagnosis

[HTML] from hindawi.comW Waters, GE Stevens, MA Schoenbaum… – Veterinary medicine …, 2011 – hindawi.com Isolates of M. bovis were identified by a combination of Ziehl-Neelsen acid-fast staining, nucleicacid probes (AccuProbe, Gen-Probe, San Diego, CA, USA), and spoligotyping (OcimumBiosolutions Ltd., Hyderabad, India). Identification of atypical Mycobacteria spp. Cited by 2Related articlesCachedAll 13 versionsImport into BibTeX

 [HTML] The use of microbead-based spoligotyping for Mycobacterium tuberculosis complex to evaluate the quality of the conventional method: Providing guidelines …E Abadia, J Zhang, V Ritacco… – BMC infectious …, 2011 – biomedcentral.com of hard to interpret spoligotypes and samples representative of the work flow, so we could evaluatethe benefits of a new platform regarding the classical one on these samples. Most centers hadperformed spoligotyping using commercial membranes (Ocimum, Hyderabad, India Cited by 3Related articlesCachedAll 26 versionsImport into BibTeX

Quality assurance for molecular epidemiology of tuberculosis methods in the mycobacterium reference laboratoryPJ Freidlin, D Goldblatt, H Kaidar-Shwartz… – … and Quality Assurance: …, 2011 – Springer for spoli- gotyping results, standardization and reproducibility depend on the quality of thecommercial spoligotyping kit (Ocimum). Spoligotyping Pattern Both PETRA (a MIRU-VNTR lineagewith central asian spoligotypes, CAS) and Beijing clusters have been observed in other Related articlesAll 3 versionsImport into BibTeX

DETERMINATION OF DRUG SUSCEPTIBILITY PATTERNS AND GENOTYPES OF MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM KANPUR DISTRICT; …S Purwar, S Chaudhari, VM Katoch… – Infection, Genetics and …, 2011 – Elsevier commercially available kit 126 (Isogen Biosciences , BV, Maarsen, The Netherlands now OcimumBiosolutions) and Owing to small sample size, the exact prevalence of various 272 spoligotypesand M Out of the isolates clustered by spoligotyping, all 280 were unique strains by Cited by 3Related articlesAll 4 versionsImport into BibTeX

New insight into the molecular characterization of isoniazid and rifampicin resistant< i> Mycobacterium tuberculosis</i> strains from Saudi ArabiaB Varghese, A Hillemann, DR Wijayanti… – Infection, Genetics and …, 2012 – Elsevier Of the 151 isolates, 146 with interpretable mutation results were subjected to MIRU-VNTR typingand spoligotyping. Spoligotyping was performed as previously described (Kamerbeek et al., 1997)with the commercial kit (Ocimum Biosolutions, Hyderabad, India). All 2 versionsImport into BibTeX

High prevalence of subclinical tuberculosis in HIV-1-infected persons without advanced immunodeficiency: implications for TB screeningT Oni, R Burke, R Tsekela, N Bangani, R Seldon… – Thorax, 2011 – thorax.highwire.org Lowenstein–Jensen slope cultures. The DNA was used to perform spoligotypingas previously described4 using a commercially available kit from Ocimum BiosolutionsBV, The Netherlands. The hybridisation patterns obtained Cited by 1Related articlesAll 12 versionsImport into BibTeX

[HTML] Pathology of camel tuberculosis and molecular characterization of its causative agents in pastoral regions of Ethiopia

G Mamo, G Bayleyegn, TS Tessema, M Legesse… – PloS one, 2011 – dx.plos.org Spoligotyping. Spoligotyping was performed as previously described by Kamerbeekand coauthors [22] and according to the spoligotype kit supplier’s instructions (OcimumBiosolutions Company, Iisselstein, The Netherlands). Cited by 3Related articlesCachedAll 9 versionsImport into BibTeX

POPULATION-BASED INVESTIGATION OF FLUOROQUINOLONES RESISTANT TUBERCULOSIS IN RURAL EASTERN CHINA

Y Hu, B Mathema, W Wang, B Kreiswirth, W Jiang… – Tuberculosis, 2011 – Elsevier

Spoligotyping was carried out using commercial kits from Isogen Bioscience BV (Maarssen, The Netherlands). 15 Strain family was determined by comparison of spoligotyping patterns with the SpoligDB4 database and assigned a spoligotyping international type (SIT). Cited by 2Related articlesAll 4 versionsImport into BibTeX

[HTML] THE GUINEA-BISSAU FAMILY OF MYCOBACTERIUM TUBERCULOSIS COMPLEX REVISITED

R Groenheit, S Ghebremichael, J Svensson… – PLoS One, 2011 – dx.plos.org

All isolates that were subjected to RFLP were also spoligotyped. Altogether, 414 isolates were available for spoligotyping, of which 336 isolates were grouped into 42 clusters Out of 229 isolates, 82 different spoligotypes were obtained, of which 168 (73.4%) were clustered into Cited by 4Related articlesCachedAll 5 versionsImport into BibTeX

GENETIC DIVERSITY OF MYCOBACTERIUM TUBERCULOSIS IN MBARARA, SOUTH WESTERN UGANDA

J Bazira, M Matte, BB Asiimwe… – African health sciences, 2011 – ajol.info

was performed as previously described29 using a commercially available kit (Isogen Bioscience BV Spoligotypes that did not match any existing pattern in the SpolDB4 database were tuberculosis within the Mbarara, we have used RD analysis and spoligotyping to characterize Related articlesAll 8 versionsImport into BibTeX

FLUOROQUINOLONE RESISTANCE AMONG MYCOBACTERIUM TUBERCULOSIS STRAINS FROM KARACHI, PAKISTAN: DATA FROM COMMUNITY-BASED FIELD CLINICS

Y Rafiq, K Jabeen, R Hasan, S Jafri… – Antimicrobial agents …, 2011 – Am Soc Microbiol was performed on all FQ-resistant strains using a commercially available kit provided by Isogen Life Science BV The spoligotypes were compared with the most prevalent M. tuberculosis subfamilies, as identified by the world spoligotyping database, SpolDB4.0, of Related articlesAll 6 versionsImport into BibTeX

[HTML] CHARACTERISTICS OF PNCA MUTATIONS IN MULTIDRUG-RESISTANT TUBERCULOSIS IN TAIWAN

YC Chiu, SF Huang, KW Yu, YC Lee… – BMC infectious …, 2011 – biomedcentral.com

Genotyping. All clinical isolates were genotyped by a commercial spoligotyping kit (Isogen Bioscience BV, Maarssen, Netherlands). The “Beijing strain” was defined as deletion from spacer 1 to spacer 34 in the direct repeat region and the presence of (at least 3) spacers 35-43. Related articlesCachedAll 11 versionsImport into BibTeX

[HTML] INITIAL PRESENTATIONS PREDICT MORTALITY IN PULMONARY TUBERCULOSIS PATIENTS-A PROSPECTIVE OBSERVATIONAL STUDY

JY Feng, WJ Su, YC Chiu, SF Huang, YY Lin… – PloS one, 2011 – dx.plos.org

All clinical isolates were genotyped using a commercial spoligotyping kit (Isogen Bioscience BV, Maarssen, Netherlands). The “Beijing strain” was defined as a deletion from spacer 1 to spacer 34 in the direct repeat region and the presence of (at least 3) spacers in 35–43. Related articlesCachedAll 4 versionsImport into BibTeX

[HTML] MOLECULAR EPIDEMIOLOGY OF MYCOBACTERIUM TUBERCULOSIS, BUENOS AIRES, ARGENTINA

X Gonzalo, M Ambroggi, E Cordova… – Emerging Infectious …, 2011 – ncbi.nlm.nih.gov

DNA was extracted from cultures at this UK laboratory; spoligotyping was performed according to the manufacturer’s instructions (Isogen Life Science, IJsselstein, the Netherlands); and data were analyzed with SPOTCLUST (http://cgi2.cs.rpi.edu/~bennek/SPOTCLUST.html). Related articlesAll 4 versionsImport into BibTeX

CHARACTERISTICS OF MULTIDRUG-RESISTANT MYCOBACTERIUM TUBERCULOSIS IN TAIWAN: A POPULATION-BASED STUDY

CW Chang, MH Wu, PC Chuang… – Infection, Genetics and Evolution, 2011 – Elsevier

12 13 Spoligotyping 14 A commercially available kit (Isogen Bioscience BV, Maarssen, The 15 Netherlands) was used as Even through spoligotyping results 3 revealed the genetic diversities of MDR M. tuberculosis isolates in Taiwan, 4 identical spoligotypes could not Cited by 2Related articlesAll 2 versionsImport into BibTeX

MOLECULAR PATTERN OF MYCOBACTERIUM BOVIS ISOLATES AND ITS RELATIONSHIP WITH RISK FACTORS ASSOCIATED WITH THE PRESENCE OF BOVINE …

IF Padilla-Campos, JC Segura-Correa… – Tropical and …, 2011 – redalyc.uaemex.mx

Key words: Bovine tuberculosis; Spoligotypes; M. bovis; Risk factors. Spoligotyping was carried out following the protocol described by Kamerbeek et al sequences from M. tuberculosis and six spacer sequences for M. bovis BCG were covalently bound (ISOGEN, Maarssen, The Related articlesAll 2 versionsImport into BibTeX

[HTML] FINE-TUNING THE SPACE, TIME, AND HOST DISTRIBUTION OF MYCOBACTERIA IN WILDLIFE

C Gortazar, MJ Torres, P Acevedo, J Aznar… – BMC …, 2011 – biomedcentral.com

Typing. The M. bovis isolates were further characterized by spoligotyping [40]. The amplified product was detected by hybridization of the biotin-labelled PCR product onto spoligotyping membrane (Isogen Bioscience BV, Maarssen, The Netherlands). Cited by 6Related articlesCachedAll 19 versionsImport into BibTeX

MOLECULAR PATTERN OF MYCOBACTERIUM BOVIS ISOLATES AND ITS RELATIONSHIP WITH RISK FACTORS ASSOCIATED WITH THE PRESENCE OF …

IF Padilla, JC Segura, JC Rodriguez… – Tropical and …, 2011 – ccba.uady.mx

Key words: Bovine tuberculosis; Spoligotypes; M. bovis; Risk factors. Spoligotyping was carried out following the protocol described by Kamerbeek et al sequences from M. tuberculosis and six spacer sequences for M. bovis BCG were covalently bound (ISOGEN, Maarssen, The Related articlesAll 2 versionsImport into BibTeX

EPIDEMIOLOGICAL TRENDS AND CLINICAL COMPARISONS OF< I> MYCOBACTERIUM</I>< I> TUBERCULOSIS</I> LINEAGES IN THAI TB MENINGITIS

K Faksri, F Drobniewski, V Nikolayevskyy, T Brown… – Tuberculosis, 2011 – Elsevier

isolated from CSF samples collected from 1996 to 2004 with IS6110 RFLPs (120 RFLP patterns were available) and spoligotyping results (141 spoligotypes were available 27 Spoligotyping was performed according to the manufacturer’s instructions (Isogen Bioscience BV Cited by 1Related articlesAll 3 versionsImport into BibTeX

A NOVEL METHOD FOR THE RAPID AND PROSPECTIVE IDENTIFICATION OF BEIJING MYCOBACTERIUM TUBERCULOSIS STRAINS BY HIGH‐RESOLUTION MELTING ANALYSIS

M Alonso, Y Navarro, F Barletta… – Clinical …, 2011 – Wiley Online Library

Thirty-two MTB strains (18 representatives of the Beijing genotype and 14 representatives of the non-Beijing genotype, according to their spoligotypes) were grown on Spoligotyping was performed in accordance with the manufacturer’s instructions (Isogen, De Meern, the Cited by 3Related articlesAll 3 versionsImport into BibTeX

QUALITY ASSURANCE FOR MOLECULAR EPIDEMIOLOGY OF TUBERCULOSIS METHODS IN THE MYCOBACTERIUM REFERENCE LABORATORY

PJ Freidlin, D Goldblatt, H Kaidar-Shwartz… – … and Quality Assurance: …, 2011 – Springer

43 spacer spoligotyping was performed according to the manufacturer’s instructions (Isogen/Ocimun) as described previously. 27 Spoligotyping Pattern Both PETRA (a MIRU-VNTR lineage with central asian spoligotypes, CAS) and Beijing clusters have been observed in other Related articlesAll 3 versionsImport into BibTeX

EPIDEMIOLOGICAL ANALYSIS OF MYCOBACTERIUM TUBERCULOSIS STRAINS ISOLATED IN LODZ, POLAND

M Krawczyk, A Brzostek, A Gorna… – … of Tuberculosis and …, 2011 – ingentaconnect.com

of van Embden et al.16 Spoligotyping was performed as described by Kame rbeek et al., using the Isogen Life Science kit Spoligotyping analysis showed that 184 (78.6%) of the strains were grouped in clusters and 50 (21.4%) strains possessed unique spoligotypes. Cited by 1Related articlesAll 3 versionsImport into BibTeX

ONE YEAR NATIONWIDE EVALUATION OF 24-LOCUS MIRU-VNTR GENOTYPING ON SLOVENIAN< I> MYCOBACTERIUM TUBERCULOSIS</I> ISOLATES

U Bidovec-Stojkovic, M Zolnir-Dovc… – Respiratory Medicine, 2011 – Elsevier

4,9,20 Spoligotyping was performed using a commercially available kit (Isogen Bioscience BV identically defined by IS6110 RFLP and 24-locus MIRU-VNTR typing combined with spoligotyping. jointly defined by identical 24-locus MIRU-VNTR types and spoligotypes were only Related articlesAll 3 versionsImport into BibTeX

MOLECULAR CHARACTERIZATION OF MYCOBACTERIUM TUBERCULOSIS COMPLEX (MTBC) ISOLATED FROM CATTLE IN NORTHEAST AND NORTHWEST CHINA

Y Du, Y Qi, L Yu, J Lin, S Liu, H Ni… – Research in veterinary …, 2011 – Elsevier

2.5. Spoligotyping. Spoligotyping kits and Mini-blotter MN45 were obtained from Isogen Life Science Co. (Utrecht, the Netherlands). The Streptavidin-ß-peroxidase conjugate was produced by Roche Applied Science Co. (Penzberg, Germany). Cited by 3Related articlesAll 3 versionsImport into BibTeX

[HTML] TRANSMISSION PATTERN OF DRUG-RESISTANT TUBERCULOSIS AND ITS IMPLICATION FOR TUBERCULOSIS CONTROL IN EASTERN RURAL CHINA

[HTML] from plos.org

Y Hu, B Mathema, W Jiang, B Kreiswirth, W Wang… – PloS one, 2011 – dx.plos.org

Hybridized DNA was detected using an enhanced chemiluminescene kit from Isogen Bioscience BV b Probaiblity that the Spoligotyping pattern belongs to the clades. N, Bennett KP (2006) Identifying Mycobacterium tuberculosis complex strain families using spoligotypes. Related articlesCachedAll 7 versionsImport into BibTeX

SUBLINEAGES OF BEIJING STRAIN OF MYCOBACTERIUM TUBERCULOSIS IN SRI LANKA

US Rajapaksa… – Indian Journal of Microbiology, 2011 – Springer

Spoligotyping was carried out according to manufacturer’s guidelines using a commercially available kit (Isogen, Maarsen MV, The Netherland). Fourteen iso-lates that confirmed to be Beijing strain were further characterised. Related articlesAll 2 versionsImport into BibTeX

DETERMINATION OF DRUG SUSCEPTIBILITY PATTERNS AND GENOTYPES OF MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM KANPUR DISTRICT; …

S Purwar, S Chaudhari, VM Katoch… – Infection, Genetics and …, 2011 – Elsevier

43 spacers was done with the help of a commercially available kit 126 (Isogen Biosciences , BV Owing to small sample size, the exact prevalence of various 272 spoligotypes and M.tuberculosis Out of the isolates clustered by spoligotyping, all 280 were unique strains by IS6110 Cited by 3Related articlesAll 4 versionsImport into BibTeX

MOLECULAR EPIDEMIOLOGY OF HUMAN AND ANIMAL TUBERCULOSIS IN IBADAN, SOUTHWESTERN NIGERIA

AO Jenkins, SIB Cadmus, EH Venter… – Veterinary …, 2011 – Elsevier

Spoligotyping167 Spoligotyping confirmed the species identification of 19 M. tuberculosis and 13 M None of these CAM 173 variant spoligotypes were found in the spolDB4 database and were All M. tuberculosis strains 175 from PTB patients that were spoligotyped had identical Cited by 1Related articlesAll 5 versionsImport into BibTeX

GENETIC DIVERSITY OF THE MYCOBACTERIUM TUBERCULOSIS BEIJING FAMILY BASED ON IS6110, SNP, LSP AND VNTR PROFILES FROM THAILAND

K Faksri, F Drobniewski, V Nikolayevskyy… – Infection, Genetics and …, 2011 – Elsevier

Eighty MTB Beijing isolates from CSF samples with IS6110 RFLPs (69 RFLP patterns were available) and spoligotyping results (all 80 spoligotypes were available Spoligotyping wasperformed according to the manufacturer s instructions (Isogen Bioscience BV Cited by 2Related articlesAll 3 versionsImport into BibTeX

[PDF] 骨结核临床分离菌株基因分型的特点

李文胜, 刘毅, 孙勇, 田苗, 刘忠泉… – 中华临床医师杂志 ( …, 2011 – clinicmed.net

TM 琼脂糖购自赛百盛基因技 术有限公司。 DNA Ladder Marker 购自TaKaRa 公司。凝胶成像仪购自FOTO DYNE 公司。 Spoligotyping 试 剂盒以及Miniblotter MN45为荷兰Isogen Bioscience 公司产品。 链霉亲和素为Sigam 公司产品。 化学发光 Related articlesView as HTMLAll 3 versionsImport into BibTeX

MOLECULAR EPIDEMIOLOGY OF MYCOBACTERIUM TUBERCULOSIS IN THE UNITED ARAB EMIRATES

A Saedi… – 2011 – qmro.qmul.ac.uk

130 3.2.11 Identification of the UAE isolates by spoligotyping….. 132 3.2.12 Comparison between MIRU-typed and spoligotyped families in association with katG463/gyrA95 groupings ….. Related articlesAll 2 versionsImport into BibTeX

[HTML] MYCOBACTERIUM BOVIS IN SWINE: SPOLIGOTYPING OF ISOLATES FROM ARGENTINA

S Barandiaran, EV Moras, A Adri& – Veterinary Medicine …, 2011 – hindawi.com

Spoligotyping [14] was carried out by using the spoligotyping kit (Isogen Biosolutions BV, Ocimun Guerin (BCG) (ATCC 27289) were included as reference strains in each spoligotyping experiment isolates were defined as two or more M. bovis strains with identical spoligotypes. Cited by 1Related articlesCachedAll 11 versionsImport into BibTeX

[HTML] SPOLIGOTYPING OF CLINICAL MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM THE STATE OF MINAS GERAIS, BRAZIL

SS Miranda, WS Carvalho, PN Suffys… – Memórias do Instituto …, 2011 – SciELO Brasil

was resuspended in the same TE buffer, stored at -20ºC and subjected to spoligotyping using a previously published protocol (Kamerbeek et al. 1997) and a commercially available kit (Isogen Life Science BV, Utrecht, The Netherlands). The hybridised spoligotypes in binary Related articlesCachedAll 7 versionsImport into BibTeX

EVALUATION OF SPOLIGOTYPING AND MIRU-VNTR FOR MYCOBACTERIUM BOVIS IN XINJIANG, CHINA

Z Sun, R Cao, M Tian, X Zhang, X Zhang… – Research in Veterinary …, 2011 – Elsevier

Additionally, two new spoligotypes (SB1903 and SB1904) and special repeat numbers of 3 loci(ETR Spoligotyping was firstly analyzed and interpreted in octal codes (Dale et al., 2001) following the instruction (http://www.mbovis.org) with a commercial kit (Isogen Bioscience BV Cited by 2Related articlesAll 2 versionsImport into BibTeX

[HTML] MYCOBACTERIUM TUBERCULOSIS SPOLIGOTYPES AND DRUG SUSCEPTIBILITY PATTERN OF ISOLATES FROM TUBERCULOSIS PATIENTS IN SOUTH-WESTERN UGANDA

J Bazira, BB Asiimwe, ML Joloba… – BMC infectious …, 2011 – biomedcentral.com

Spoligotyping. Standard spoligotyping was performed as previously described [29] using a commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands). Spoligotyping. All the isolates had spoligotypes characteristic of M. tuberculosis. Cited by 1Related articlesCachedAll 12 versionsImport into BibTeX

A FIRST INSIGHT ON THE POPULATION STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS COMPLEX AS STUDIED BYSPOLIGOTYPING AND MIRU-VNTRS IN BOGOTÁ, COLOMBIA

I Cerezo, Y Jiménez, J Hernandez, T Zozio… – Infection, Genetics and …, 2011 – Elsevier

Kamerbeek et al., 1997) according to the manufacturer s instructions (Isogen Bioscience, the Spoligotype International Type (SIT) and MIRU International Type (MIT) designate spoligotypes and MIRU was used to build minimum spanning trees based on spoligotyping and MIRU All 2 versionsImport into BibTeX

[PDF] PRELIMINARY MAPPING STUDY OF MYCOBACTERIUM TUBERCULOSIS’ COMPLEX DNA BYSPOLIGOTYPING ON ISOLATED SPUTUM OF TUBERCULOSIS PATIENT …

[PDF] from digitaljournals.org

V Lisdawati, I Parwati… – Bulletin of Health …, 2011 – indonesia.digitaljournals.org

PCR, denaturasi menggunakan thermocycler selama 10 menit pada suhu 99,9°C. Kemudian pada mini blotter MN45 yang telah diletakkan membran spoligotyping kit (IM9702, Isogen Biosolution, BV) berlabel 43 DNA spacer Mtb complex segera hibridisasikan DNA hasil PCR. Related articlesView as HTMLImport into BibTeX

[PDF] INFECTION OF EURASIAN BADGERS (MELES MELES) WITH MYCOBACTERIUM BOVIS

A Balseiro, O Rodríguez, P González-Quirós… – prevalence, 2011 – uclm.es

al., 2009). 125 MTC isolates were characterised hybridisation of biotin-labelled PCR products 126 onto a spoligotyping membrane (Isogen Bioscience BV), followed by spoligotyping 127 (Kamerbeek et al., 1997). Results were Cited by 2Related articlesView as HTMLAll 2 versionsImport into BibTeX

CLINICAL AND MICROBIOLOGICAL CHARACTERISTICS OF URINE CULTURE-CONFIRMED GENITOURINARY TUBERCULOSIS AT MEDICAL CENTERS IN TAIWAN FROM 1995 TO 2007

HL Hsu, CC Lai, MC Yu, FL Yu, JC Lee… – European journal of …, 2011 – Springer

commercially available spoligotyping kit (Isogen Bioscience BV, Maarssen, The Netherlands) was used as described by the manufacturer. The fourth international spoligotyping database (SpolDB4) database was used to assign genotype families to the spoligotypes obtained [14 Related articlesAll 5 versionsImport into BibTeX

MOLECULAR TYPING OF MYCOBACTERIUM TUBERCULOSIS CIRCULATED IN MOSCOW, RUSSIAN FEDERATION

MV Afanas’ ev, LN Ikryannikova, EN Il’ina… – European Journal of …, 2011 – Springer

spacers probes from the spoligotyping kit from Isogen Lifescience (cat. no. IM9701). 182 Eur J Clin Microbiol Infect Dis (2011) 30:181–191 Page 3. Spoligotypes in binary format were entered in an Excel spreadsheet and compared with the spoligotyping database SpolDB4 [13]. Cited by 7Related articlesAll 4 versionsImport into BibTeX

ROLE OF 2-MONTH SPUTUM SMEARS IN PREDICTING CULTURE CONVERSION IN PULMONARY TUBERCULOSIS

WJ Su, JY Feng, YC Chiu… – European Respiratory …, 2011 – Eur Respiratory Soc

All clinical isolates were genotyped by commercial spoligotyping kit (Isogen Bioscience BV, Maarssen, the Netherlands). The “Beijing strain” was defined as deletion from spacer 1 to spacer 34 in the direct repeat region and the presence of (at least three of) spacers 35–43. Cited by 5Related articlesAll 6 versionsImport into BibTeX

[PDF] A TWO-STEP STRATEGY FOR MOLECULAR TYPING OF MULTIDRUG-RESISTANT MYCOBACTERIUM TUBERCULOSIS CLINICAL ISOLATES FROM POLAND.

T JAGIELSKI, EWAA KOPEĆ… – Polish journal of …, 2011 – pjm.microbiology.pl

Spoligotyping was perfor- med with a commercially available kit (Isogen Bio- science BV e isolates whose spoligotype patterns were already recorded in the database, were assigned “shared types”,

whereas those of spoligotypes identified for the first time, were View as HTMLAll 3 versionsImport into BibTeX

MOLECULAR TECHNOLOGIES USED IN DETECTING OF SENSITIVE AND ISONIAZID-RESISTANT MYCOBACTERIUM TUBERCULOSIS

OY Limanskaya… – Cytology and Genetics, 2011 – Springer

The PCR was carried out by a dry kit of reagents for DNA amplification (Isogen, Russian Federation) in 20–50 μl of reaction mixture containing 4 mM NaCl, 50 mM KCl, 12 mM Tris HCl (pH 8.0), 2.5 mM MgCl2, 200 μM dNTPs, 0.1–0.5 μM of each primer, and 1 unit of Taq DNA Related articlesAll 4 versionsImport into BibTeX

STREPTOMYCIN RESISTANCE AND LINEAGE-SPECIFIC POLYMORPHISMS IN MYCOBACTERIUM TUBERCULOSIS GIDB GENE

FS Spies, AW Ribeiro, DF Ramos… – Journal of clinical …, 2011 – Am Soc Microbiol

Genotyping.Spoligotyping was performed using a commercial kit (Isogen Biosciences BV, Netherlands it was classified as LAM3 and S/convergent sublineage by spoligotyping but as non …Spoligotypes evolve through successive loss of spacer DNA sequences (16), and since

Cited by 2Related articlesAll 7 versionsImport into BibTeX

GENOTYPING AND DRUG RESISTANCE PATTERNS OF MYCOBACTERIUM TUBERCULOSIS STRAINS IN FIVE PROVINCES OF CHINA

YL Guo, Y Liu, SM Wang, CY Li… – … of Tuberculosis and …, 2011 – ingentaconnect.com

Of the (Isogen Bioscience BV, De Meern, The Netherlands). 1–1800 = shared spoligotypes. Table 3 Results of MIRU typing and comparison of the three typing methods Isolate MIRU locus number IS6110-RFLP Cluster 2 4 10 16 20 23 24 26 27 31 39 40 Spoligotyping MIRU Cited by 3Related articlesAll 3 versionsImport into BibTeX

ASSOCIATION OF< I> MYCOBACTERIUM TUBERCULOSIS</I> GENOTYPES AND CLINICAL AND EPIDEMIOLOGICAL FEATURES-A MULTI-CENTER STUDY IN TAIWAN

SF Huang, WJ Su, HY Dou, JY Feng… – Infection, Genetics and …, 2011 – Elsevier

Spoligotyping was performed according to the method reported by Kamerbeek et al. (Kamerbeek et al., 1997) using a commercial kit (Isogen Biosolutions, Netherlands). The spoligotypes were identified according to the database SpoDB4.0 (Brudey et al., 2006), and the SIT Related articlesAll 5 versionsImport into BibTeX

THE GENOTYPE CHARACTERISTIC OF CLINICAL ISOLATED STRAINS GETTING FROM BONE TUBERCULOSIS

LI Wen-sheng, LIU Yi, SUN Yong… – Chinese Journal of …, 2011 – global.clinicmed.net

TM 琼脂糖购自赛百盛基因技 术有限公司。 DNA Ladder Marker 购自 TaKaRa 公司。凝胶成像仪购自 FOTO DYNE 公司。 Spoligotyping 试 剂盒以及 Miniblotter MN45为荷兰Isogen Bioscience 公司产品。 链霉亲和素为 Sigam 公司产品。 化学发光 Related articlesImport into BibTeX

MULTIPLE STRAINS OF< I> MYCOBACTERIUM BOVIS</I> REVEALED BY MOLECULAR TYPING IN A HERD OF CATTLE

EES Figueiredo, DF Ramos, L Medeiros… – The Veterinary …, 2011 – Elsevier

to the spoligo-membrane was performed according to the manufacturer’s instructions (Isogen

Life Sciences). The strains clustered by spoligotyping were analysed by VNTR-PCR to confirm

clonal relationships Four spoligotypes were identified among the 12 M. bovis isolates.

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DETERMINAÇÃO DO CUSTO BIOLÓGICO EM ISOLADOS DE MYCOBACTERIUM TUBERCULOSIS COM MUTAÇÕES NOS GENES RPSL, RRS, GIDB, RPOB E KATG

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FS Spies – 2011 – lume.ufrgs.br

restriction fragment lenght polymorphism) da sequência de inserção IS6110, spoligotyping e

unidade de repetição de micobactéria- repetição em tandem de número variável (MIRU-

Spoligotyping é uma técnica de genotipagem que explora a variabilidade da região

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A MAJOR SUBGROUP OF BEIJING FAMILY MYCOBACTERIUM TUBERCULOSIS IS ASSOCIATED WITH MULTIDRUG RESISTANCE AND INCREASED TRANSMISSIBILITY

Y Hu, X Ma, EA Graviss, W Wang… – Epidemiology and …, 2011 – Cambridge Univ Press

Spoligotyping was performed by using a com- mercial kit from Isogen Bioscience BV (Maarssen

0.04), and resistance to RIF and SM (P=0.04) (Table 1). Spoligotyping identified 243 Thirty-three

(9.4%) isolates had unique/novel spoligotypes, of which similarity analysis found that

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[HTML] MODERN AND ANCESTRAL GENOTYPES OF MYCOBACTERIUM TUBERCULOSIS FROM ANDHRA PRADESH, INDIA

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SK Thomas, CC Iravatham, BH Moni, A Kumar… – PloS one, 2011 – dx.plos.org

the help of commercially available line probe arrays (Isogen Biosciences BV tuberculosis complex

genetic diversity: mining the fourth international spoligotyping database (SpolDB4 KP (2006)

Identifying Mycobacterium tuberculosis complex strain families using spoligotypes.

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[HTML] TUBERCULOSIS IN SUDAN: A STUDY OF MYCOBACTERIUM TUBERCULOSIS STRAIN GENOTYPE AND SUSCEPTIBILITY TO ANTI-TUBERCULOSIS DRUGS

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GSS Eldin, I Fadl-Elmula, MS Ali… – BMC infectious …, 2011 – biomedcentral.com

21] using a commercial kit to test for 43 individual spacers (Isogen, IJsselstein, The Spoligotyping

provided a relatively simple and rapid means of describing the population of improved

discrimination of strains sharing the CAS1_Dehli and Beijing spoligotypes when using MIRU

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[PDF] MOLECULAR CHARACTERISATION OF MYCOBACTERIUM BOVIS ISOLATED FROM AFRICAN BUFFALOES (SYNCERUS CAFFER) IN HLUHLUWE-IMFOLOZI PARK IN KWAZULU-NATAL, SOUTH AFRICA

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TM Hlokwe, AO Jenkins, EM Streicher… – … Journal of Veterinary …, 2011 – scielo.org.za

One of the observed spoligotypes (SB0130) was dominant and represented 75% of isolates …Spoligotyping Spoligotyping was done according to a standardised international method

(Kamerbeek et al. 1997) using a commercially available kit (Isogen Biosciences BV, Maarsen).

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GENOTYPING DID NOT EVIDENCE ANY CONTRIBUTION OF MYCOBACTERIUM BOVIS TO HUMAN TUBERCULOSIS IN BRAZIL

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A Rocha, AR Elias, LF Sobral, DF Soares… – Tuberculosis, 2011 – Elsevier

using PCR and hybridization conditions on a commercially available membrane (Isogen

Bioscience BV All isolates that yielded spoligotypes that were recognized as not previously

described patterns were submitted to at least one additional spoligotyping assay and

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MOLECULAR AND EPIDEMIOLOGICAL CHARACTERIZATION OF MULTIDRUG-RESISTANT MYCOBACTERIUM TUBERCULOSIS ISOLATES IN JOHANNESBURG, SOUTH AFRICA

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CK Mlambo – 2011 – wiredspace.wits.ac.za

61 Table 3.6 Description of the orphan MIRU patterns (n=45) from this study and

corresponding spoligotyping-based information (octal code, SIT, and clade)…………

64 Table 3.7 MIRU profiles of the four newly created spoligotypes (10

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USE OF SPOLIGOTYPE ANALYSIS TO DETECT LABORATORY CROSS-CONTAMINATION

B Nivin, J Driscoll, T Glaser, P Bifani… – Infection control and …, 2000 – JSTOR

The spoligotyping analysis was performed using a commercially available kit (Isogen Bioscience

BV In several cases of identical spoligotypes, the Wadsworth Center indicated that the

Spoligotyping is an effective, relatively inexpensive (approximately 10% the cost of RFLP

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CLINICAL AND GENOTYPIC CHARACTERISTICS OF CHILDHOOD TUBERCULOSIS IN CHONGQING, CHINA

L Xing, R Liu, Q Li, Z Peng… – European Journal of Clinical …, 2011 – Springer

Of 105 isolates spoligotyped, the major spoligotypes found were Spoligotyping was performed

according to the internation- ally standardized protocol [5]. A commercially available spoligotyping

kit (Isogen Bioscience BV, Maarssen, The Netherlands) was used as described

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TUBERCULOSIS DUE TO MYCOBACTERIUM BOVIS AND MYCOBACTERIUM CAPRAE IN SHEEP

M Muņoz Mendoza, L Juan, S Menéndez… – The Veterinary …, 2011 – Elsevier by hybridisation of the biotin-labelled PCR product onto spoligotyping membrane (Isogen Bioscience BV). Isolates were characterised by spoligotyping as M. caprae SB0157 (flock A) and

M. bovis close contact with cattle or goats infected by the same spoligotypes (Table 1

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[HTML] MYCOBACTERIUM BOVIS INFECTION IN GOATS FROM THE NORTHEAST REGION OF BRAZIL

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SSS Higino, SR Pinheiro, GO Souza… – Brazilian Journal of …, 2011 – SciELO Brasil

Isolate was characterised by spoligotyping as described (7). The amplified product

was detected by hybridization of the biotin-labelled PCR product onto spoligotyping

membrane (Isogen Bioscience BV, Maarssen, The Netherlands).

 

EPIDEMIOLOGICAL STUDIES OF BEIJING STRAINS OF MYCOBACTERIUM TUBERCULOSIS FROM TAIPEI AND OTHER ASIAN CITIES BASED ON MIRU PROFILES

JUNREN SUN, HYUN DOU, SYI LEE… – Apmis, 2011 – Wiley Online Library

on isolates from areas where the Beijing strain is prevalent as most isolates in this family share

the same spoligotypes (1, 5 Spoligotyping to the manufacturers’ protocol, to a set of 43 oligonucle-

otides of DR spacers on a membrane using the Isogen Bioscience spoligotyping kit

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Comparison of restriction fragment length polymorphism with the polymorphic guanine-cytosine-rich sequence and spoligotyping for differentiation of Mycobacterium …

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L Flores, LG Jarlsberg, EY Kim… – Journal of clinical …, 2010 – Am Soc Microbiol 2004 was performed with standardized methods (15) using a membrane with 43 oligonucleotides representing the different direct variable repeats (DVRs) immobilized in specific locations (Ocimum Biosolutions, Inc., Gaithersburg, MD). Beginning in 2004, spoligotyping of the

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Fitness study of the RDRio lineage and Latin American–Mediterranean family of Mycobacterium tuberculosis in the city of Rio Grande, Brazil

A Von Groll, A Martin, C Felix… – FEMS Immunology …, 2010 – Wiley Online Library RD Rio BrgR: 5′-CACCGCCACGCTGAATGAGACCA-3′, –. Genotyping by spoligotyping. Spoligotyping was performed with a commercial kit (Ocimum Biosolutions BV, India) according to standard procedures (Kamerbeek et al., 1997).

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[HTML] Fitness of Mycobacterium tuberculosis strains of the W-Beijing and Non-W-Beijing genotype

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A Von Groll, A Martin, M Stehr, M Singh, F Portaels… – PloS one, 2010 – dx.plos.org Strains were fully characterized and analyzed for the presence of mutations conferring resistance to RMP and INH. Spoligotyping was performed with a commercial kit (Ocimum Biosolutions BV, India) according to standard procedures [29]. Molecular characterization.

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[HTML] MOLECULAR DIVERSITY OF MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM PATIENTS WITH PULMONARY TUBERCULOSIS IN MOZAMBIQUE

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SO Viegas, A Machado, R Groenheit… – BMC …, 2010 – biomedcentral.com using a commercially available kit (Isogen Life Science BV, Utrecht, The Netherlands). Spoligotyping results were analysed with the BioNumerics Software ver. 5.01 (Applied Maths, Kortrijk, Belgium). Database comparison and geographical distribution of spoligotypes.

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[PDF] ASSOCIATION AMONG THE RV2629 GENE, RPOB GENE, RFP RESISTANCE AND BEIJING GENOTYPE IN M. TUBERCULOSIS CLINICAL ISOLATES

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J Zhang, X Wu, Y Yang, Y Zhuang… – African Journal of …, 2010 – academicjournals.org The amplified PCR products were hybridized with spoligotyping Biodyne C membrane immobilized 43 oligonucleotide probes (Isogen Life Science, Holland). A total of 8 distinct spoligotyping patterns were observed. 7 isolates had unique spoligotypes (Figure 1, Tables 1 and 2

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SINGLE NUCLEOTIDE POLYMORPHISMS IN CELL WALL BIOSYNTHESIS-ASSOCIATED GENES AND PHYLOGENY OF< I> MYCOBACTERIUM TUBERCULOSIS</I> LINEAGES

PC Chuang, YMA Chen, HY Chen… – Infection, Genetics and …, 2010 – Elsevier 2.2. Genotype analysis. Spoligotyping using a commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands Spoligotypes and RFLP patterns were scanned and analyzed with Bionumerics ® software (version 4.601; Applied Maths, Kortrijk, Belgium).

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[HTML] ASSOCIATIONS BETWEEN MYCOBACTERIUM TUBERCULOSIS STRAINS AND PHENOTYPES

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T Brown, V Nikolayevskyy, P Velji… – Emerging Infectious …, 2010 – ncbi.nlm.nih.gov Spoligotyping was performed according to the manufacturer’s instructions (Isogen Lifescience, IJsselstein, the Netherlands) (9). Images were digitized and entered into BioNumerics software by using the BNIMA module (Applied Maths). Spoligotypes were assigned to families

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[HTML] SENSIBILIDAD Y ESPECIFICIDAD DE PCR ANIDADA Y SPOLIGOTYPING COMO PRUEBAS RÁPIDAS DE DIAGNÓSTICO DE TUBERCULOSIS BOVINA EN TEJIDO FRESCO

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F Milián Suazo, B Harris, C Arriaga Díaz… – Revista mexicana de …, 2010 – scielo.org.mx Spoligotyping se realizó tal como lo describe Kamerbeek et al (17) . De manera resumida, la amplificación del por 30 seg. La hibridización se realizó de acuerdo a las recomendaciones del fabricante (Isogen). El ADN hibridado

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[HTML] GENOTYPING OF MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM ALOW-ENDEMIC SETTING IN NORTHWESTERN STATE OF PARANÁ IN SOUTHERN BRAZIL

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EN Noguti, CQF Leite, AC Malaspina… – Memórias do Instituto …, 2010 – SciELO Brasil SpoligotypingSpoligotyping was performed in all 93 M. tuberculosis isolates, using the standardmethod of 43 spacer oligonucleotides covalently linked to the spoligo-membrane (Isogen Life Sciences Spoligotypes were reported using an octal code in which the 43-digit binary

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[HTML] EXTENSIVE TRANSMISSION OF ISONIAZID RESISTANT M. TUBERCULOSIS AND ITS ASSOCIATION WITH INCREASED MULTIDRUG-RESISTANT TB IN TWO RURAL COUNTIES OF EASTERN CHINA: A …

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Y Hu, S Hoffner, W Jiang… – BMC infectious …, 2010 – biomedcentral.com Spoligotyping was carried out by using the commercial kit from Isogen Bioscience BV Table 3. Spoligotyping pattern and frequency of the MTB isolates included. B, Kurepina N, Bennett KP:Identifying Mycobacterium tuberculosis complex strain families using spoligotypes.

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[HTML] MOLECULAR CHARACTERIZATION OF MYCOBACTERIUM BOVIS ISOLATES FROM ETHIOPIAN CATTLE

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D Biffa, E Skjerve, J Oloya, A Bogale… – BMC veterinary …, 2010 – biomedcentral.com spacers were then hybridized with the known oligonucleotide spacers ligated to the membrane(Isogen). The discriminatory power (HGDI) of the spoligotyping method was calculated to be 0.81. Also on the basis of the above findings (the number of distinct spoligotypes (S) = 12

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[HTML] MYCOBACTERIUM TUBERCULOSIS BEIJING STRAIN, BAMAKO, MALI

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B Diarra, S Siddiqui, D Sogoba… – Emerging infectious …, 2010 – ncbi.nlm.nih.gov See the article”Global Distribution of Mycobacterium tuberculosis Spoligotypes” in volume 8 on page 1347. Spoligotyping using a commercially available kit (Spoligotyping Isogen Life Science, De Meern, the Netherlands) showed characteristics of the Beijing clade (Appendix

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EVALUATION OF 24 LOCUS MIRU-VNTR GENOTYPING OF MYCOBACTERIUM TUBERCULOSIS ISOLATES IN CANADA

S Christianson, J Wolfe, P Orr, J Karlowsky… – Tuberculosis, 2010 – Elsevier some cases. 22 Blots were purchased from Isogen Biosolutions and run according to the manufacturer’s directions. Spoligotyping patterns were converted to the “octal” pattern using the previously described formula. 23 Data

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MYCOBACTERIUM MICROTI INFECTION ASSOCIATED WITH SPINDLE CELL PSEUDOTUMOUR AND HYPERCALCAEMIA: A POSSIBLE LINK WITH AN INFECTED ALPACA

C McGoldrick, C Coghlin, A Seagar… – BMJ Case …, 2010 – casereports.bmj.com At SMRL spoligotyping was performed using a commercial assay available from Isogen Life Science (3600 BT; Maarssen, The Netherlands) and 15-locus Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) typing, performed using the

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MOLECULAR EPIDEMIOLOGY OF HUMAN CASES OF TUBERCULOSIS BY MYCOBACTERIUM BOVIS IN MEXICO

F Milián-Suazo, L Pérez-Guerrero… – Preventive veterinary …, 2010 – Elsevier Coding allows easy comparisons of spoligotypes from different laboratories and from differentparts of Spoligotyping was performed following a standard protocol (Kemerbeek et al., 1997). 6 spacer sequences from M. bovis BCG were covalently bound (ISOGEN, Maarssen, the

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THE MOST PREDOMINANT SPOLIGOPATTERNS OF< I> MYCOBACTERIUM TUBERCULOSIS</I> ISOLATES AMONG IRANIAN, AFGHAN-IMMIGRANT, PAKISTANI AND TURKISH TUBERCULOSIS PATIENTS: …

MA Merza, P Farnia, AM Salih, MR Masjedi… – …, 2010 – content.karger.com

[19] , with a commercially available kit, according to the manufacturer’s instructions (Isogen Biosci-ence, The Analysis of Spoligotyping Data A total of 133 distinct spoligopatterns were identi- fied The distribution of spoligotypes (T, CAS, EAI, Haarlem, X, Beijing, Or- phan and

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[HTML] CHARACTERIZATION OF MYCOBACTERIUM TUBERCULOSIS BEIJING ISOLATES FROM THE MEDITERRANEAN AREA

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M Alonso, NA Rodriguez, C Garzelli… – BMC …, 2010 – biomedcentral.com deletion of the spacers 1-34 and the characteristic hybridization pattern of spacers 35-43, and the remaining seven corresponded to variant “Beijing-like” spoligotypes. Spoligotyping was performed following the manufacturer’s instructions (Isogen, Netherlands).

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SPOLIGOTYPE-BASED COMPARATIVE POPULATION STRUCTURE ANALYSIS OF MULTIDRUG-RESISTANT AND ISONIAZID-MONORESISTANT MYCOBACTERIUM TUBERCULOSIS COMPLEX CLINICAL ISOLATES …

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T Jagielski, E Augustynowicz-Kopeć… – Journal of clinical …, 2010 – Am Soc Microbiol CTAB) method (47) were stored at −20°C before being subjected to spoligotyping using a hybridized to a set of 43 oligonucleotides covalently bound to a membrane (Isogen Life Science BV Spoligotypes in binary format were converted to an octal code for comparison with the

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[HTML] FIRST INSIGHTS INTO THE GENETIC DIVERSITY OF MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM HIV-INFECTED MEXICAN PATIENTS AND MUTATIONS CAUSING MULTIDRUG RESISTANCE

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R Lopez-Alvarez, C Badillo-Lopez… – BMC …, 2010 – biomedcentral.com To determine lineage, the 57 strains (48 MTb and 9 M. bovis) from the MTC were spoligotyped and binary outcomes were compared with the shared type (ST) number and lineages and sublineages reported by Spoligotyping. Spoligotypes were reported using an octal code [74].

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MOLECULAR EVIDENCE OF FALSE-POSITIVE CULTURES FOR MYCOBACTERIUM TUBERCULOSIS IN A TAIWANESE HOSPITAL WITH A HIGH INCIDENCE OF TB

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CC Lai, CK Tan, SH Lin, CH Liao… – Chest, 2010 – chestjournal.chestpubs.org Spoligotyping was performed according to the internationally standardized protocol to identify and differentiate 10 A commercially available kit (Isogen Bioscience BV; Maarssen, The Netherlands) was database was used to assign genotype families to the spoligotypes obtained

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MOLECULAR DETECTION OF MIXED INFECTIONS OF MYCOBACTERIUM TUBERCULOSIS STRAINS IN SPUTUM SAMPLES FROM PATIENTS IN KARONGA DISTRICT, MALAWI

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K Mallard, R McNerney, AC Crampin… – Journal of clinical …, 2010 – Am Soc Microbiol on these isolates with the aid of a commercially available kit (Isogen Biosciences BV These isolates were also spoligotyped and had previously been characterized by IS6110-RFLP Spoligotyping versus Beijing and LAM PCR results for 377 clinical M. tuberculosis isolates used

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[HTML] CLUSTERING OF MYCOBACTERIUM TUBERCULOSIS CASES IN ACAPULCO: SPOLIGOTYPING AND RISK FACTORS

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E Nava-Aguilera, E Harris, S Mitchell… – Clinical and …, 2010 – hindawi.com DNA with 43 oligonucleotides covalently linked to a nylon membrane (Isogen Bioscience BV SpolTools permitted the analysis of M. tuberculosis spoligotyping data to identify emerging and visualization of the probable evolutionary relationships between the spoligotypes in our

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TRACING THE ORIGINS OF< I> MYCOBACTERIUM BOVIS</I> TUBERCULOSIS IN HUMANS IN THE USA TO CATTLE IN MEXICO USING SPOLIGOTYPING

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TC Rodwell, AJ Kapasi, M Moore… – International Journal of …, 2010 – Elsevier For this study, we also examined all available spoligotypes in the US national surveillance database of M. bovis isolates sent to the National Veterinary Services Laboratories Spoligotyping was performed by all laboratories using the Spoligo Kit (Isogen Bioscience BV

MYCOBACTERIUM TUBERCULOSIS BEIJING GENOTYPE IS AN INDEPENDENT RISK FACTOR FOR TUBERCULOSIS TREATMENT FAILURE IN INDONESIA

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I Parwati, B Alisjahbana, L Apriani… – Journal of Infectious …, 2010 – jid.oxfordjournals.org

of the Beijing genotype per se or to confounding by drug resistance, which has been linked to

the Beijing genotype in different settings [1]. We previously spoligotyped a large Spoligotyping

was performed using a commercial kit (Isogen Bioscience) according to the

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EFFECT OF SERIAL SUBCULTURING ON THE GENETIC COMPOSITION AND CYTOTOXIC ACTIVITY OF MYCOBACTERIUM TUBERCULOSIS

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CA Molina-Torres, J Castro-Garza… – Journal of medical …, 2010 – Soc General Microbiol

(1997) was used. PCR amplification of the direct repeat locus was performed on heat-treated

cell suspensions. Biotin-labelled PCR products were detected by hybridization onto a

spoligotyping membrane (Isogen Bioscience). Microarray analysis.

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[HTML] DIVERSITY OF MYCOBACTERIUM TUBERCULOSIS GENOTYPES CIRCULATING IN NDOLA, ZAMBIA

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C Mulenga, I Shamputa, D Mwakazanga… – BMC infectious …, 2010 – biomedcentral.com

Spoligotyping was performed using a commercial kit (Isogen Bioscience BV, Maarssen, The

Netherlands) according Spoligotyping and MIRU-VNTR patterns were compared to the

international Spol DB4.0 Spoligotypes that were not present in the Spol DB4.0 are referred to

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PHENOTYPIC AND GENOTYPIC ANALYSIS OF MULTIDRUG-RESISTANT TUBERCULOSIS IN ETHIOPIA

M Agonafir, E Lemma… – … of Tuberculosis and …, 2010 – ingentaconnect.com

to the extraction protocol described by van Soolingen et al.14 Spoligotyping was performed the

commercially available kit from Isogen Bioscience BV, Maarssen, The Netherlands, according

to Spoligotypes described only once (non-clustered) in this study and in the SpolDB4

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[PDF] SENSIBILIDAD Y ESPECIFICIDAD DE PCR ANIDADA Y SPOLIGOTYPING COMO PRUEBAS RÁPIDAS DE DIAGNÓSTICO DE TUBERCULOSIS BOVINA EN TEJIDO FRESCO

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FM Suazoa, B Harrisb, CA Díazc… – Revista Mexicana de …, 2010 – scielo.org.mx

Spoligotyping was performed essentially as described by Kamerbeek(17). Briefly,

amplification of DNA was run in for 30 sec. Hybridization was performed as

recommended by the manufacturer (Isogen). Hybridized DNA was detected

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CLINICAL AND GENOTYPIC CHARACTERISTICS OF EXTENSIVELY DRUG-RESISTANT AND MULTIDRUG-RESISTANT TUBERCULOSIS

CC Lai, CK Tan, SH Lin, CH Liao… – European journal of …, 2010 – Springer

by serial dilution on agar plates as described previously [1]. Spoligotyping, according to the M.

tuberculosis complex isolates [3]. A commercially available kit (Isogen Bioscience BV 1

Dendrograms of spoligotypes generated by clustered Myco- bacterium tuberculosis strains after

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IDENTIFICATION OF WILD-TYPE MYCOBACTERIUM TUBERCULOSIS ISOLATES AND POINT MUTATIONS ASSOCIATED WITH ISONIAZID RESISTANCE

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OY Limanskaya, TN Mukhina, VN Stepanshina… – Molecular Biology, 2010 – Springer

carrying AGC AGA; HB125, carrying AGC ACC, and H37Rv with the wild type codon

315 (negative control for amplification). The reaction mixture (20–50 μl) was prepared

from a dry amplification kit (Isogen, Russia). Its com

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A SNAPSHOT OF THE BIODIVERSITY AND CLUSTERING OF MYCOBACTERIUM TUBERCULOSIS IN OMAN USINGSPOLIGOTYPING

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A Al-Maniri, JPN Singh, O Al-Rawas… – … of Tuberculosis and …, 2010 – ingentaconnect.com

Figure Spoligotyped distribution of Molecular typing of Mycobacterium tuberculosis isolates

from a rural area of Kanpur by spoligotyping and mycobacterial interspersed re- petitive units

(MIRUs) typing. Predominant tubercu- losis spoligotypes, Delhi, India.

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MYCOBACTERIUM TUBERCULOSIS COMPLEX CRISPR GENOTYPING: IMPROVING EFFICIENCY, THROUGHPUT AND DISCRIMINATIVE POWER OF ‘SPOLIGOTYPING’WITH NEW SPACERS AND A …

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J Zhang, E Abadia, G Refregier… – Journal of medical …, 2010 – Soc General Microbiol

Thus, as spoligotypes are considered both as phylogenetic and epidemiological markers (Asiimwe

et al., 2008; Sola et al., 2001; Tanaka & Francis, 2006 Both sets had been previously genotyped

by spoligotyping using commercial membranes (Isogen Biosciences).

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[HTML] MOLECULAR DIVERSITY OF MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM PATIENTS WITH TUBERCULOSIS IN HONDURAS

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S Rosales, L Pineda-García… – BMC …, 2010 – biomedcentral.com

All isolates were spoligotyped in order to identify the predominant genotypes within this SG

performed and analyzed RFLP; carried out bioinformatics analysis of spoligotyping and RFLP

results NR performed database analysis of the spoligotypes and helped draft the manuscript

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[HTML] PRODUCTION OF TNF-Α, IL-12 (P40) AND IL-17 CAN DISCRIMINATE BETWEEN ACTIVE TB DISEASE AND LATENT INFECTION IN A WEST AFRICAN COHORT

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JS Sutherland, BC de Jong, DJ Jeffries, IM Adetifa… – PloS one, 2010 – dx.plos.org 10ng of DNA was used for spoligotype analysis with commercially available membranes (Isogen Biosciences, The Netherlands). Contributed reagents/materials/analysis tools: BCdJ. Wrote the paper: JSS MOCO. Performed spoligotyping: BCdJ. Statistical analysis: DJJ.

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[BOOK] RAPID TESTS FOR MULTIDRUG RESISTANT TUBERCULOSIS IN LOW INCOME SETTINGS

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F Bwanga – 2010 – mbl.mak.ac.ug

In paper V, we applied spoligotyping to study the clustering rate and predominant genotypic strains of 99 MDR-TB strains isolated from patients in Kampala. Eighty three percent of the strains occurred in clusters, and the T2 lineage was the largest single cluster. Conclusion.

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2009

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Spoligotyping for molecular epidemiology of the Mycobacterium tuberculosis complex

JR Driscoll – Methods Mol. Biol, 2009 – Springer

1. Spoligotyping membrane (Ocimum Biosolutions Inc., for- merly Isogen Biosciences BV potential

of additional spacer sequences for “expanded” or “extended” spoligotyping (25, 26). spacer

sequences would improve the differentiability of the commonly observed spoligotypes.

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Polymorphic Exact Tandem Repeat A (PETRA): a Newly Defined Lineage of Mycobacterium tuberculosis in Israel Originating Predominantly in Sub-Saharan Africa

[HTML] from nih.gov

PJ Freidlin, D Goldblatt… – Journal of clinical …, 2009 – Am Soc Microbiol

The fast DNA extraction method (amount used, 2 μl) was also successfully employed for

spoligotyping (Ocimum Biosolution Company, India). In addition, further CAS MIRU-VNTR types

and associated spoligotypes were identified in the literature (3, 6, 7, 58, 61, 62).

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MOLECULAR EPIDEMIOLOGY OF MYCOBACTERIUM TUBERCULOSIS IN THE UNITED ARAB EMIRATES (UAE)

[DOC] from qmul.ac.uk

A Saaidi… – 2009 – qmro.qmul.ac.uk

HYPERLINK \l “_Toc237239861” **3.2.11 Identification of the UAE isolates by spoligotyping *

PAGEREF _Toc237239861 \h **133**. * HYPERLINK \l “_Toc237239862” **3.2.12 Comparison

between MIRU-typed and spoligotyped families in association with katG463/gyrA95

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BEIJING GENOTYPE OF MYCOBACTERIUM TUBERCULOSIS IS SIGNIFICANTLY ASSOCIATED WITH HIGH-LEVEL FLUOROQUINOLONE RESISTANCE IN VIETNAM

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DD An, NTH Duyen, NTN Lan, DTM Ha… – Antimicrobial agents …, 2009 – Am Soc Microbiol

with primers Dra (biotin labeled) and Drb, hybridized to the spoligotype membrane (Isogen

Bioscience BV were assigned to the Euro-American clade on the basis of spoligotyping patterns

LSP types and spoligotypes of 109 consecutive FQ-resistant isolates and 109 consecutive

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[PDF] NOSOCOMIAL TUBERCULOSIS IN THE ERA OF DRUG RESISTANT TUBERCULOSIS

[PDF] from lrsitbrd.nic.in

TB Nosocomial – Indian J Tuberc, 2009 – lrsitbrd.nic.in

Page 1. Indian Journal of Tuberculosis [Indian J Tuberc 2009; 56:59-61] Editorial

NOSOCOMIAL TUBERCULOSIS IN THE ERA OF DRUG RESISTANT TUBERCULOSIS

Indian Journal of Tuberculosis Vol. 56 New Delhi, April 2009 No. 2

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[HTML] SUPERVISED LEARNING FOR THE AUTOMATED TRANSCRIPTION OF SPACER CLASSIFICATION FROM SPOLIGOTYPE FILMS

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D Jeffries, N Abernethy… – BMC bioinformatics, 2009 – biomedcentral.com

a standardized method [4] using commercially prepared membranes from Isogen Biosciences

(Maarsen Crawford JT: Transfer of a Mycobacterium tuberculosis genotyping method,

Spoligotyping, from a AR, Tanaka MM: spolTools: online utilities for analyzing spoligotypes of

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POLYMORPHIC EXACT TANDEM REPEAT A (PETRA): A NEWLY DEFINED LINEAGE OF MYCOBACTERIUM TUBERCULOSIS IN ISRAEL ORIGINATING PREDOMINANTLY IN SUB-SAHARAN AFRICA

[HTML] from nih.gov

PJ Freidlin, D Goldblatt… – Journal of clinical …, 2009 – Am Soc Microbiol In addition, further CAS MIRU-VNTR types and associated spoligotypes were identified in …Spoligotyping.Spacer oligonucleotide typing (spoligotyping) for 43 spacers of the direct repeat region (9 performed using a kit according to the manufacturer’s instructions (Isogen/Omicium

A RAPID AND SIMPLE METHOD FOR IDENTIFYING MYCOBACTERIUM TUBERCULOSIS W-BEIJING STRAINS BASED ON DETECTION OF A UNIQUE MUTATION IN RV0927C BY PCR-SSCP

X Jiang, C Lu, F Gao, F Wang, W Zhang… – Microbes and …, 2009 – Elsevier

Spoligotyping was performed as previously described [16 in 2 × SSPE (1 × SSPE is 0.18 M NaCl, 10 mM NaH 2 PO 4 , and 1 mM EDTA) −0.5% sodium dodecyl sulfate (SDS) at 60 °C and then incubated in 1:4000 diluted streptavidin peroxidase conjugate (Isogen Bioscience) for

Using a multiplex polymerase chain reaction for the identification of Beijing strains of Mycobacterium tuberculosis

JR Sun, SY Lee, HY Dou… – European Journal of Clinical …, 2009 – Springer Page 2. in the Isogen Bioscience spoligotyping kit (Isogen Life Science, the Netherlands). Among the 323 clinical MTB isolates, a total of 78 different spoligotypes were found. One hundred and sixty-nine isolates were determined to belong to the Beijing family.

[HTML] Mycobacterium bovis en Argentina: aislamientos de gatos tipificados por spoligotyping

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MJ Zumárraga, M Martínez Vivot… – Revista argentina de …, 2009 – SciELO Argentina

(8) , and using the spoligotyping kit (Isogen Biosolutions BV Each of the different spoligotypes were allocated a number. H37Rv (ATCC 27294) and M. bovis Bacillus Calmette-Guerin (BCG)(ATCC 27289) were included as reference strains in each spoligotyping experiment.

Spoligotyping for molecular epidemiology of the Mycobacterium tuberculosis complex

JR Driscoll – Methods Mol. Biol, 2009 – Springer 1. Spoligotyping membrane (Ocimum Biosolutions Inc., for- merly Isogen Biosciences BV potential of additional spacer sequences for “expanded” or “extended” spoligotyping (25, 26). spacer sequences would improve the differentiability of the commonly observed spoligotypes.

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Use of spoligotyping and large sequence polymorphisms to study the population structure of the Mycobacterium tuberculosis complex in a cohort study of consecutive …

[HTML] from nih.gov

BC De Jong, M Antonio, T Awine… – Journal of clinical …, 2009 – Am Soc Microbiol After spectrophotometry, we used 10 ng of DNA for spoligotype analysis (16) with commercially available membranes (Isogen Biosciences, Maarssen, The Netherlands If spoligotype analysis did not result in a clear pattern of spacers, the isolate underwent repeat spoligotyping.

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Isoniazid and rifampicin resistance-associated mutations in Mycobacterium tuberculosis isolates from Yangon, Myanmar: implications for rapid molecular testing

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H Valvatne, H Syre, M Kross… – Journal of …, 2009 – Br Soc Antimicrob Chemo

identification test (GenProbe Incorporated, San Diego, CA, USA) and by spoligotyping (Isogen Bioscience BV A total of 43 different spoligotypes were observed among the 96 isoniazid-resistant of the 63 isolates that could not be differentiated by spoligotyping produced diverse

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… of the Mycobacterium tuberculosis complex in Albania obtained by multilocus variable-number tandem-repeat analysis and spoligotyping reveals the presence of …

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S Tafaj, J Zhang, Y Hauck, C Pourcel… – Journal of clinical …, 2009 – Am Soc Microbiol ethambutol (2.0 μg/ml) (5). Identification at the species level was performed by phenotypic methods and verified by a genotypic method on isolates with rare spoligotypes and/or Spoligotyping was performed using a commercial membrane (Isogen, The Netherlands

Prospective study applying spoligotyping directly to DNA from sputum samples of patients suspected of having tuberculosis

PICPI Cafrune, LGPLG Possuelo… – Canadian Journal …, 2009 – NRC Research Press was performed using a commercial kit according to the manufacturer’s instructions (Isogen Biosciences BV Table 1. Accuracy of spoligotyping results according to culture grading. A total of 44 different spoligotypes were identified; 112 isolates (83%) were included in 21 shared

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Molecular typing of Mycobacterium bovis strains isolated in Italy from 2000 to 2006 and evaluation of variable-number tandem repeats for geographically optimized …

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MB Boniotti, M Goria, D Loda… – Journal of clinical …, 2009 – Am Soc Microbiol repeat locus were detected by hybridization onto a spoligotyping membrane (Isogen Bioscience BV into 64 different patterns, while the seven M. caprae spoligotypes were subdivided Thediscrimination provided by combination of spoligotyping and ETR methods allowed for a

Cited by 21Related articlesAll 7 versionsImport into BibTeX

Utility and evaluation of new variable-number tandem-repeat systems for genotyping mycobacterial tuberculosis isolates

HY Dou, JJ Lu, CW Lin, JR Chang, JR Sun… – Journal of microbiological …, 2009 – Elsevier Spoligotyping was carried out using a spoligotyping kit according to the manufacturer’s instructions (Isogen Bioscience BV). Spoligotypes common to more than one strain were designated as shared types (ST) and assigned a shared international type number (SIT) according to

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[PDF] Comparison of phenotypic and genotypic methods for pyrazinamide susceptibility testing

[PDF] from medind.nic.in

S Shenai, C Rodrigues, M Sadani, N Sukhadia… – Indian J Tuberc, 2009 – medind.nic.in All the PZA resistant isolates were further spoligotyped to identify M. bovis, if present. Finger printing – Spoligotyping All the 63 culture isolates were subjected to spoligotyping using a commercially available Isogen kit, Netherlands as described by Kamerbeek et al.11 Briefly

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Molecular analysis of< i> Mycobacterium tuberculosis</i> from tuberculous meningitis patients in Thailand

J Yorsangsukkamol, A Chaiprasert, T Prammananan… – Tuberculosis, 2009 – Elsevier 2.4. Spoligotyping. Spoligotyping was performed with a commercially available kit (Isogen Bioscience BV, Maarsen, The Netherlands). 25 All obtained spoligotypes were compared to SpolDB4 for analysis. 2.5. Data analysis.

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Prevalence of ST26 among untreated smear-positive tuberculosis patients from Karachi indicating ongoing transmission

S Shakoor, M Tanveer, Y Rafiq… – Scandinavian …, 2009 – informahealthcare.com Five different resistance phenotypes were identified among the isolates spoligotyped: isolated low-level isoniazid resistance (resistant to 0.2 µg/ml) in 1 isolate; high-level isoniazid resistance(resistant to 1 Spoligotypes Spoligotyping grouped 66 isolates into 9 different clusters.

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[PDF] Reinout van Crevel1, Ida Parwati2, Edhyana Sahiratmadja2, Sangkot Marzuki3, Tom HM Ottenhoff4, Mihai G. Netea1, Andre van der Ven1, Ronald H. Nelwan5, …

[PDF] from kun.nl

BA van der Meer… – Factors Underlying the Success … – repository.ubn.kun.nl min. Spoligotyping was performed using a commercial kit (Isogen Bioscience,Maarssen, The Netherlands). The min. Spoligotyping was performed using acommercial kit (Isogen Bioscience, Maarssen, The Netherlands). The

Emergence of new forms of totally drug-resistant tuberculosis bacilli

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AA Velayati, MR Masjedi, P Farnia… – Chest, 2009 – chestjournal.chestpubs.org by polymerase chain reaction (PCR) using primers derived from the direct repeat sequence (Isogen Bioscience; Maarssen, the and CAS (n = 4; 17.5%) [Table 2]. The VNTR profiles of spoligotypes strains were Spoligotyping Patterns and VNTR Profiles of XDR and TDR Patients.

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[PDF] Mycobacterium tuberculosis Beijing genotype in Indonesia is associated with drug resistance gene mutations in katG, rpoB and embB

[PDF] from kun.nl

I Parwati, R van Crevel, J de Beer… – Factors Underlying the … – repository.ubn.kun.nl

of rpoB-hotspot region Three hundred and twenty five spoligotyped isolates were Mycobacteriumtuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4 mutations in katG, rpoB, rpsL and rrs genes with spoligotypes of multidrug

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Infection with Mycobacterium tuberculosis Beijing genotype strains is associated with polymorphisms in SLC11A1/NRAMP1 in Indonesian patients with tuberculosis

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R Van Crevel, I Parwati… – Journal of Infectious …, 2009 – jid.oxfordjournals.org Mycobacterial DNA was extracted by bringing 2 loops of bacterial mass from a M. tuberculosis culture in saline and subsequently heating it at 95°C for 5 min. Spoligotyping was performed using a commercial kit (Isogen Bioscience).

Unexpectedly high proportion of ancestral Manu genotype Mycobacterium tuberculosis strains cultured from tuberculosis patients in Egypt

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ZH Helal, MSED Ashour, SA Eissa… – Journal of clinical …, 2009 – Am Soc Microbiol was amplified with primers DRa and DRb, and the amplified biotinylated products were hybridized to a set of 43 oligonucleotides covalently bound to a membrane (Isogen Life Science BV Comparison of spoligotyping results with database types.Spoligotypes in binary

Differences in Cell Wall Thickness between Resistant and Nonresistant Strains of< i> Mycobacterium tuberculosis</i>: Using Transmission Electron Microscopy

[PDF] from mrc.ac.ir

AA Velayati, P Farnia, TA Ibrahim… – …, 2009 – content.karger.com For spoligotyping, the direct repeat region was am- plified by PCR using primers derived fromthe direct repeat se- quence (Isogen Bioscience). Spoligopatterns and VNTR Profiles When the spoligotype patterns were compared with earlier published spoligotypes [5] , our

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Mycobacterium tuberculosis genotypic diversity in pyrazinamide-resistant isolates of Iran

[PDF] from mrc.ac.ir

F Doustdar, AD Khosravi… – Microbial Drug …, 2009 – online.liebertpub.com Spoligotyping was performed with a commercial kit (Isogen Bioscience BV, Maarsen, The Only1 (5.0%) of the 20 PZA-monoresistant isolates had spoligotyping patterns characteristic Therefore,the CAS superfamily spoligotypes showed no important correlation with MDR-TB as

Molecular characterisation of Mycobacterium bovis isolates from cattle carcases at a city slaughterhouse in Uganda

BB Asiimwe, J Asiimwe, G Kallenius… – Veterinary …, 2009 – veterinaryrecord.bmj.com The isolates were spoligotyped using the DNA extracted at the identification stage. Thespoligotypes were analysed by BioNumerics software, version 5.0 (Applied Maths) as character were compared with those in SpolDB4.0, the international spoligotyping database (Brudey

High resolution typing system for pathogenic Mycobacterium tuberculosum

PS Keim, RS Spurgiesz… – US Patent 7,592,135, 2009 – Google Patents Spoligotyping is currently the most widely used PCR- based method of M. tuberculosum genotyping due to the 65 relative technical ease of In a database of 3,319 spoligotypes from isolates collected in geographically distinct areas, seven spoligotype patterns were found for

Frequency of Mycobacterium bovis as an etiologic agent in extrapulmonary tuberculosis in HIV-positive and-negative Mexican patients

R Cicero, H Olivera, A Hernández-Solis… – European journal of …, 2009 – Springer

a commercially available kit in accordance with the manufacturer’s recommendations (Isogen Bioscience BV and consistent identification of M. bovis was obtained by spoligotyping, showing a cattle, where even isolates from the same herd show different spoligotypes [26] and

[HTML] In-depth molecular characterization of Mycobacterium tuberculosis from New Delhi–predominance of drug resistant isolates of the ‘modern'(TbD1−) type

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R Stavrum, VP Myneedu, VK Arora, N Ahmed… – PloS one, 2009 – dx.plos.org C membranes with the 43 synthetic oligonucleotides covalently bound to the membranes (Isogen Bioscience BV (2004) Predominant tuberculosis spoligotypes, Delhi, India. repetitive-unit-variable-number tandem-repeat typing system combined with spoligotyping for population

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Predominance of Mycobacterium tuberculosis EAI and Beijing lineages in Yangon, Myanmar

[HTML] from nih.gov

S Phyu, R Stavrum, T Lwin… – Journal of clinical …, 2009 – Am Soc Microbiol (35). Spoligotyping was performed with commercially available activated Biodyne C membranesthat had 43 synthetic oligonucleotides covalently bound to the membranes (Isogen BioscienceBV Prevalence of spoligotypes in Yangon.The spoligotyping results obtained

[HTML] Tokyo-172 BCG vaccination complications, Taiwan

[HTML] from nih.gov

R Jou, WL Huang… – Emerging Infectious Diseases, 2009 – ncbi.nlm.nih.gov BCG, DNA samples were initially screened using a GenoType kit (Hain Lifescience GmbH, Nehren,Germany), multiplex PCR (7), and pncA sequencing (8). In addition, spoligotyping was performedwith a commercial kit (Isogen Bioscience BV, Maarssen, the Netherlands).

Immunologic analysis of HIV-uninfected taiwanese children with BCG-induced disease

WI Lee, FC Liang, JL Huang, TH Jaing… – Journal of clinical …, 2009 – Springer also used to identify and differentiate M. tuberculosis complex isolates in this study [38], using a commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands). The resolved spoligotypes were M. tuberculosis complex strain specific. The spoligotyping profile of

A rapid and simple method for identifying Mycobacterium tuberculosis W-Beijing strains based on detection of a unique mutation in Rv0927c by PCR-SSCP

X Jiang, C Lu, F Gao, F Wang, W Zhang… – Microbes and …, 2009 – Elsevier Spoligotyping was performed as previously described [16 in 2 × SSPE (1 × SSPE is 0.18 M NaCl,10 mM NaH 2 PO 4 , and 1 mM EDTA) −0.5% sodium dodecyl sulfate (SDS) at 60 °C and thenincubated in 1:4000 diluted streptavidin peroxidase conjugate (Isogen Bioscience) for

[PDF] NOSOCOMIAL TUBERCULOSIS IN THE ERA OF DRUG RESISTANT TUBERCULOSIS

[PDF] from lrsitbrd.nic.in

TB Nosocomial – Indian J Tuberc, 2009 – lrsitbrd.nic.inPage 1. Indian Journal of Tuberculosis [Indian J Tuberc 2009; 56:59-61] EditorialNOSOCOMIAL TUBERCULOSIS IN THE ERA OF DRUG RESISTANT TUBERCULOSISIndian Journal of Tuberculosis Vol. 56 New Delhi, April 2009 No. 2

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Beijing genotype of Mycobacterium tuberculosis is significantly associated with high-level fluoroquinolone resistance in Vietnam

[HTML] from nih.gov

DD An, NTH Duyen, NTN Lan, DTM Ha… – Antimicrobial agents …, 2009 – Am Soc Microbiol with primers Dra (biotin labeled) and Drb, hybridized to the spoligotype membrane (IsogenBioscience BV were assigned to the Euro-American clade on the basis of spoligotyping patterns LSP types and spoligotypes of 109 consecutive FQ-resistant isolates and 109 consecutive

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Polymorphic Exact Tandem Repeat A (PETRA): a Newly Defined Lineage of Mycobacterium tuberculosis in Israel Originating Predominantly in Sub-Saharan Africa

[HTML] from nih.gov

PJ Freidlin, D Goldblatt… – Journal of clinical …, 2009 – Am Soc Microbiol In addition, further CAS MIRU-VNTR types and associated spoligotypes were identified in …Spoligotyping.Spacer oligonucleotide typing (spoligotyping) for 43 spacers of the direct repeatregion (9 performed using a kit according to the manufacturer’s instructions (Isogen/Omicium

[HTML] Supervised learning for the automated transcription of spacer classification from spoligotype films

[HTML] from biomedcentral.com

D Jeffries, N Abernethy… – BMC bioinformatics, 2009 – biomedcentral.com a standardized method [4] using commercially prepared membranes from Isogen Biosciences (Maarsen Crawford JT: Transfer of a Mycobacterium tuberculosis genotyping method, Spoligotyping, from a AR, Tanaka MM: spolTools: online utilities for analyzing spoligotypes of

Potential challenges to the Stop TB Plan for humans in China; cattle maintain M. bovis and M. tuberculosis

[PDF] from yimg.com

Y Chen, Y Chao, Q Deng, T Liu, J Xiang, J Chen… – Tuberculosis, 2009 – Elsevier Spoligotyping was performed to define the genotype of Beijing family strains with a commercial kit (Isogen Bioscience BV, Maarssen, The Netherlands) according to the manufacturer’s instruction. The spoligotype that only contained

[PDF] Tuberculosis Control in Oman

[PDF] from ki.se A Al-Maniri – 2009 – diss.kib.ki.se Spoligotyping of 312 isolates of Mycobacterium tuberculosis from TB patientsdiagnosed during 2005-2007 was carried out in study IV. 25 6.5 Study IV: Biodiversity and clustering of M.tuberculosis isolates using spoligotyping …..

[HTML] Tuberculosis disparity between US-born blacks and whites, Houston, Texas, USA

[HTML] from nih.gov

JA Serpa, LD Teeter, JM Musser… – Emerging infectious …, 2009 – ncbi.nlm.nih.gov isolates underwent susceptibility and genotype testing (insertion sequence 6110 restriction fragment length polymorphism, spoligotyping, and genetic the spacer oligonucleotide type (spoligotype) was determined by using a commercially available kit (Isogen Bioscience BV

Molecular characterization of Mycobacterium Bovis isolates from selected slaughter houses in Kampala

[PDF] from mak.ac.ug

J Asiimwe – 2009 – dspace.mak.ac.ug Spoligotyping revealed that three of the M. bovis isolates had spoligopatterns that had previously been reported in Uganda while the seven Although a few clusters were identified on analysis of the spoligotypes and RFLP patterns, no geographical sub-structuring was observed

Predictors of poor treatment outcome in multi-and extensively drug-resistant pulmonary TB

[HTML] from ersj.org.uk

K Kliiman… – European Respiratory Journal, 2009 – ersj.org.uk The strains were spoligotyped as described by Kamerbeek et al. 17 using commercially available membranes (Isogen, Maarssen, The Netherlands) 17. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for

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[HTML] Tuberculosis Disparity between US-born Blacks and Whites, Houston, Texas, USA

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F Figures, I Capitalization, AS Guides… – Tuberculosis, 2009 – wwwnc.cdc.gov isolates underwent susceptibility and genotype testing (insertion sequence 6110 restriction fragment length polymorphism, spoligotyping, and genetic the spacer oligonucleotide type(spoligotype) was determined by using a commercially available kit (Isogen Bioscience BV

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2008

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Spoligotypes of< i> Mycobacterium tuberculosis</i> isolates of a high tuberculosis burden aboriginal township in Taiwan

PC Chuang, H Liu, C Sola, YMA Chen… – Infection, Genetics and …, 2008 – Elsevier A commercially available spoligotyping kit (Isogen Bioscience BV, Maarssen, The Netherlands) was used as All 138 isolates were successfully genotyped by spoligotyping, but only 122 were of A total of 27 spoligotypes were identified; 124 isolates (89.9%, 124/138) were

Genetic diversity of isoniazid-resistant Mycobacterium tuberculosis isolates collected in Poland and assessed by spoligotyping

[HTML] from nih.gov

E Augustynowicz-Kopeć, T Jagielski… – Journal of clinical …, 2008 – Am Soc Microbiol Spoligotyping was performed with a commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands), according to the manufacturer’s instructions and as All spoligotypes obtained were compared to those in the world spoligotyping database (SpolDB4) at

[HTML] Mycobacterium tuberculosis spoligotypes and drug susceptibility pattern of isolates from tuberculosis patients in peri-urban Kampala, Uganda

[HTML] from biomedcentral.com

B Asiimwe, S Ghebremichael… – BMC infectious …, 2008 – biomedcentral.com The obtained signatures were compared in binary format with the international spoligotyping\ database of the Pasteur Institute of Spoligotypes. To determine the strain lineages present in the sample, the 344 isolates were spoligotyped and binary outcomes compared with those

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Molecular typing of Mycobacterium tuberculosis isolates from a rural area of Kanpur by spoligotypingand mycobacterial interspersed repetitive units (MIRUs) typing

P Sharma, DS Chauhan, P Upadhyay… – Infection, Genetics and …, 2008 – Elsevier

2.3. Spoligotyping. Spoligotyping to detect 43 spacers was done with the help of commercially available kit (Isogen Biosciences, BV, Maarsen, The Netherlands). 3.1. Spoligotyping. A total of 46 distinct spoligotypes were obtained from this set of 97 M. tuberculosis isolates.

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Role of spoligotyping and IS6110-RFLP in assessing genetic diversity of< i> Mycobacterium tuberculosis</i> in India

JP Mathuria, P Sharma, P Prakash… – Infection, Genetics and …, 2008 – Elsevier spacers by using the standard method (Kamerbeek et al., 1997) with the help of commercially available kit (Isogen Biosciences, BV Spoligotyping. Presence of 19 orphan isolates indicates the need of conducting multicentric studies to know all the prevalent spoligotypes in Indian

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[PDF] Investigation of Cross-Contamination in a Mycobacterium tuberculosis Laboratory Using Epidemiological data and Spoligotyping

[PDF] from pjms.com.pk

F Al-Otaibi… – pjms.com.pk Spoligotyping was performed with a commer- cially available kit (Isogen Bioscience).6,7 RESULTS Culturing of phosphate buffer in MGIT tube was positive for MTB after seven-day inoculation. Ten different spoligotypes were identified among the 47 MTB isolates.

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Persistence and molecular evolution of Mycobacterium bovis population from cattle and wildlife in Doñana National Park revealed by genotype variation

[PDF] from cnrs.fr

B Romero, A Aranaz, Á Sandoval, J Álvarez… – Veterinary …, 2008 – Elsevier detected by hybridization of the biotin-labelled PCR product onto spoligotyping membrane (Isogen Bioscience BV The discriminatory capacity of spoligotyping was h = 0.38 The spoligotypes SB0950, SB1230 and SB1232 were shared between domestic and wildlife animals (red

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Spoligotyping of Mycobacterium tuberculosis in anthracotic bronchitis

K Najafizadeh, F Ghorbani, P Farnia… – … of Tuberculosis and …, 2008 – ingentaconnect.com use at −20°C. Spoligotyping Spoligotyping was performed, as previously described by Kamerbeek et al.,10 with a commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands). Analysis Information about the

Molecular analysis of drug‐resistant Mycobacterium tuberculosis isolates collected in central Poland

E Augustynowicz‐Kopeć, T Jagielski… – Clinical …, 2008 – Wiley Online Library DNA was prepared by the cetyl-trimethyl-ammonium bromide method [4]. Spoligotyping was performed using a commercially available kit (Isogen Bioscience BV was also performed as described previously [2]. Isolates with indistinguishable spoligotypes and IS6110

[HTML] Human tuberculosis caused by Mycobacterium bovis, Taiwan

[HTML] from nih.gov

R Jou, WL Huang… – Emerging infectious diseases, 2008 – ncbi.nlm.nih.gov Currently, 119 M. bovis spoligotypes are contained in the fourth international spoligotyping database (SpolDB 4) and strains, presence or absence of region of difference 1 was analyzed(5). Spoligotyping was performed with a commercial kit (Isogen Bioscience BV

A proposal for applying molecular markers as an aid to identifying potential cases of imported tuberculosis in immigrants

M Alonso, S Borrell, MM Lirola, E Bouza… – Tuberculosis, 2008 – Elsevier Spoligotyping was performed using primers of the spoligotyping kit (Isogen, Netherlands) andfollowing the manufacturer’s instructions. The spoligotypes were analyzed in the MIRU-VNTRplus application (www.miru-vntrplus.org) 19 in order to identify the genetic lineages

Characterization of extensively drug-resistant Mycobacterium tuberculosis clinical isolates in China

[HTML] from nih.gov

Z Sun, Y Chao, X Zhang, J Zhang… – Journal of clinical …, 2008 – Am Soc Microbiol repeat (MIRU-VNTR) analysis. Spoligotyping was performed with a commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands) according to the manufacturer’s protocols. PCR-based MIRU-VNTR analysis

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[HTML] Incidence of tuberculosis and the predictive value of ELISPOT and Mantoux tests in Gambian case contacts

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PC Hill, DJ Jackson-Sillah, A Fox, RH Brookes… – PLoS One, 2008 – dx.plos.org For molecular subtyping of index case isolates, we extracted mycobacterial DNA using CTAB and chloroform[18]. We performed spoligotyping using membranes from Isogen Biosciences (http:/www.isogen-lifescience.com), as previously described[19].

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[PDF] : Transmission from South American Sea Lion () to Bactrian Camel () and Malayan Tapirs ()

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I Moser, WM Prodinger, H Hotzel… – Veterinary …, 2008 – peer.ccsd.cnrs.fr by 30 cycles of 96°C for 15 sec, 67°C for 60 sec, 72°C for 60 sec, and a final extension at 18 72°C 300 sec. 19 Spoligotyping. Spoligotyping (9; Isogen Bioscience, The Netherlands) was performed using 20 DNA extracted from cultures. 21 MIRU typing.

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Use of PCR-based Mycobacterium tuberculosis genotyping to prioritize tuberculosis outbreak control activities

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M Ashworth, KL Horan, R Freeman… – Journal of clinical …, 2008 – Am Soc Microbiol Only one isolate per case was included in the analysis. Genotyping.Spoligotyping was performed according to previously published methods by using a spoligotypingkit (Isogen, IJsselstein, The Netherlands) (12). MIRU analysis

Mycobacteria causing human cervical lymphadenitis in pastoral communities in the Karamoja region of Uganda

[HTML] from nih.gov

J Oloya, J Opuda-Asibo, R Kazwala… – Epidemiology and …, 2008 – Cambridge Univ Press MTC were submitted for further differentiation by the spoligotyping kit ac- cording to the manufacturer’s instructions (Isogen, Life Science One of the spoligotypes (Hu-4 and Hu-5 in Fig. 1) is labelled LAM 3/S in the spoligotyping database SpolDB4, and has been isolated in 118

Cited by 23Related articlesBL DirectAll 12 versionsImport into BibTeX

Genotypic diversity of extensively drug-resistant tuberculosis (XDR-TB) in South Africa

CK Mlambo, RM Warren, X Poswa… – … of tuberculosis and …, 2008 – ingentaconnect.com Spoligotyping was performed ac- cording to the internationally standardised protocol11 using commercially of the genotyping data, serial isolates from 13 patients were randomly sampled and spoligotyped. was used to assign geno- type families to the spoligotypes obtained.12

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[HTML] Molecular epidemiology and evolutionary genetics of Mycobacterium tuberculosis in Taipei

[HTML] from biomedcentral.com

HY Dou, FC Tseng, CW Lin, JR Chang… – BMC infectious …, 2008 – biomedcentral.com Of 356 isolates spoligotyped, 290 (81.4%) displayed known spoligotypes and 66 were not …Spoligotyping was carried out according to the manufacturer’s instructions (Isogen Bioscience BV The resulting spoligotypes were documented under a binary code representing either a

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[HTML] Genotyping and drug resistance patterns of M. tuberculosis strains in Pakistan

[HTML] from biomedcentral.com

M Tanveer, Z Hasan, A Siddiqui, A Ali… – BMC Infectious …, 2008 – biomedcentral.com Spoligotyping of M. tuberculosis isolates. All M. tuberculosis strains were spoligotyped and their data analyzed using UPGMA calculation in the Bionumerics software. one (78%) isolates grouped into 59 different “shared types” while 205 (22%) isolates had ‘orphan’ spoligotypes.

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< i> Mycobacterium pinnipedii</i>: Transmission from South American sea lion (< i> Otaria byronia</i>) to Bactrian camel (< i> Camelus bactrianus bactrianus</i>) and …

[PDF] from tcd.ie

I Moser, WM Prodinger, H Hotzel, R Greenwald… – Veterinary …, 2008 – Elsevier 2.5. Spoligotyping. Spoligotyping (Kamerbeek et al., 1997; Isogen Bioscience, The Netherlands) was performed using DNA extracted from cultures. 2.6. MIRU typing. MIRU typing was performed targeting 12 chromosomal loci as given by Mazars et al.

Mycobacterium tuberculosis population structures differ significantly on two Indonesian Islands

[HTML] from nih.gov

I Parwati, R Van Crevel, M Sudiro… – Journal of clinical …, 2008 – Am Soc Microbiol Therefore, we have spoligotyped M. tuberculosis isolates from a large cohort of patients Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for Global distribution of Mycobacterium tuberculosis

Development of multiplex assay for rapid characterization of Mycobacterium tuberculosis

[HTML] from nih.gov

IL Bergval, R Vijzelaar, ER Dalla Costa… – Journal of clinical …, 2008 – Am Soc Microbiol Strains 1 to 29 were selected for their specific spoligotypes and were used to determine the correlation between MLPA, the spoligotype, and the sequence of ogt codon 15 (a marker for theM Spoligotyping.Mycobacterium tuberculosis strains were spoligotyped by using a

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Mycobacterium bovis in wildlife in France

[HTML] from jwildlifedis.org

G Zanella, B Durand, J Hars… – Journal of wildlife …, 2008 – Wildlife Dis Assoc Biotin-labeled PCR products were detected on a spoligotyping membrane (Isogen Bioscience BV,Maarssen, The Netherlands). Purified sterile water and M. bovis and M. tuberculosis controlsincluded in the spoligomembrane kit were included in each batch of tests.

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Distribution of rpoB mutations among multidrug‐resistant Mycobacterium tuberculosis (MDRTB) strains from Thailand and development of a rapid method for mutation …

T Prammananan, W Cheunoy… – Clinical …, 2008 – Wiley Online Library In contrast, of 112 rifampicin-susceptible isolates that were spoligotyped, only 51 (45.5%) wererevealed to be a One additional MDRTB isolate was not available for spoligotyping. Association of specific mutations in katG, rpoB, rpsL and rrs genes with spoligotypes of multidrug

Molecular diversity of< i> Mycobacterium tuberculosis</i> isolates from patients with pulmonary tuberculosis in Sri Lanka

US Rajapaksa, TC Victor, AJ Perera… – Transactions of the …, 2008 – Elsevier Spoligotyping was performed using a commercially available kit (Isogen Bioscience BV, Maarssen,The Spoligotyping of 98 M. tuberculosis isolates revealed a total of 43 patterns, with six The finding of identical spoligotypes in geographically widely separated countries may be

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[PDF] Mutations in rpoB gene and genotypes of rifampin resistant Mycobacterium tuberculosis isolates in Iran

[PDF] from nritld.ac.ir

F Doustdar, AD Khosravi, P Farnia, AR Bahrmand… – Tanaffos, 2008 – nritld.ac.ir

tuberculosis isolates are defined on the basis of shared spoligotypes or closely related IS6110 …Spoligotyping was performed with a commercially available kit to detect 43 known spacers DR locus according to the instructions supplied by the manufacturer (Isogen Bioscience BV

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Molecular epidemiology of Mycobacterium bovis: usefulness in international trade

[PDF] from usda.gov

F Milian-Suazo, B Harris, CA Díaz… – Preventive veterinary …, 2008 – Elsevier Spoligotyping was performed following the protocol described by Kamerbeek et al Eighty-four M. bovis strains from Mexico and the US were spoligotyped under the same protocol in two When comparing spoligotypes from the two laboratories, 50 (59%) out of the 84 strains were

Attempts to revive Mycobacterium tuberculosis from 300‐year‐old human mummies

E Lemma, O Zimhony, CL Greenblatt… – FEMS microbiology …, 2008 – Wiley Online Library Spoligotyping was performed at day 250 following the instructions of the manufacturer of the ISOGEN Life Science Spoligotyping kit. Animal inoculations. Two sets of six female guinea pigs weighing an average of 250 g were used.

Mycobacterium tuberculosis Uganda genotype is the predominant cause of TB in Kampala, Uganda

[PDF] from mak.ac.ugBB Asiimwe, T Koivula, G Kallenius… – … of Tuberculosis and …, 2008 – ingentaconnect.com Data analysis Spoligotypes were analysed using BioNumerics soft- ware (version 4.6, Applied Maths, Kortrijk, Belgium) as a character type. Spoligotyping To determine the predominant strain lineages, the 344 isolates were spoligotyped and binary outcomes compared with

Pyrazinamide resistance among South African multidrug-resistant Mycobacterium tuberculosis isolates

[HTML] from nih.gov

M Mphahlele, H Syre, H Valvatne… – Journal of clinical …, 2008 – Am Soc Microbiol

(i) Spoligotyping.Spoligotyping was performed to further The resulting amplification products were then hybridized to a commercially available membrane (Isogen Bioscience BV, Bilthoven, The Netherlands), with covalently linked parallel rows of 43 synthetic oligonucleotides

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Genotyping North American animal Mycobacterium bovis isolates using multilocus variable number tandem repeat analysis

[HTML] from sagepub.com

LR Martinez, B Harris, WC Black… – Journal of Veterinary …, 2008 – vdi.sagepub.com The 6 isolates that comprised MLVA type N were divided into 3 spoligotypes: 1 isolate into SP2 A larger database of MLVA typed isolates, in combination with spoligotyping and conventional epidemiological investigations, can provide a n. Spacer sequences, Isogen Life Science

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[CITATION] First Insight Into Mycobacterium tuberculosis Biodiversity in Sri Lanka: Evidence for Predominance of Beijing Genotype and Ancestral Lineages Among …US Rajapaksa, AJ Perera, TC Victor… – International Journal of …, 2008 – Elsevier

[BOOK] Molecular characterization of Mycobacterium tuberculosis complex from Kampala, Uganda

[PDF] from mak.ac.ug

B Asiimwe – 2008 – dspace.mak.ac.ug and colleagues (69), which is commercially available as a kit (Isogen Bioscience BV the important lineages and sub-lineages in SpolDB4.0, the international spoligotyping database iii To investigate the association between the predominant spoligotypes, HIV sero- status and anti

IS6110 in oriC affects the morphology and growth of Mycobacterium tuberculosis and attenuates virulence in mice

Y Casart, L Turcios, I Florez, R Jaspe, E Guerrero… – Tuberculosis, 2008 – Elsevier DR locus was carried out as described earlier, 15 with membranes supplied by Isogen Bioscience BV to mention that all the clones isolated from 1C8 or 1D3 displayed identical spoligotyping and MIRU A1 insertion 12 (Figure 1B), (ii) The IS6110-RFLPs and spoligotypes did not

Intérêt du typage moléculaire pour l’épidémiologie de la tuberculose en Limousin (1998–2006)

[HTML] from em-consulte.com

H Bezanahary, MC Baclet, C Sola… – Médecine et Maladies …, 2008 – Elsevier Keywords: MIRU15 typing; Mycobacterium tuberculosis; Spoligotyping. L’hybridation (1H à 60°C) des amplicons a été réalisée sur une membrane Isogen ® (Bioscience BV sous forme d’uncode octal et comparés aux données de la banque de spoligotypes SpolDB4 (Institut

[PDF] TABLA 8.1 _ GEL DE CORRIMIENTO

[PDF] from ula.ve

TNN – Identificación y diagnóstico de Actinomicetales … – saber.ula.ve caontb. rivm. nl/Manuals/principl. html. Por su parte, Isogen Biosciences (http://www. isogen.nl) ofrece membranas con ADN inmobilizado de espaciadores, para utilizarse en pruebasde spoligotyping específicas para cepas de M. bovis/M. tuberculosis.

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Diversidade genética de estirpes de mycobacterium tuberculosis em pacientes com tuberculose nos distritos de Buzi e Manhiça, em Moçambique

[PDF] from utl.pt

CLS Mucavele – 2008 – repository.utl.pt number of spoligotypes were identical to profiles found in the region. The data reported showedthat migration and HIV might be factors of dissemination of TB in Humans in Mozambique. Factors that can compromise the performance of Spoligotyping technique and other

[BOOK] Molecular Characterisation of Antibiotic Resistance in Mycobacterium Tuberculosis

[PDF] from ki.se

P Juréen – 2008 – diss.kib.ki.se personnel (91). In order to overcome this, spoligotyping was evolved. This repeat) (91).MIRU-VNTR analyses copy-numbers of repeats, however, in contrast to spoligotyping,these have several sites scattered around the genome. Since

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Deletion-targeted multiplex PCR (DTM-PCR) for identification of Beijing/W genotypes of Mycobacterium tuberculosis

[PDF] from mvlab-fudan.cn

J Chen, AG Tsolaki, X Shen, X Jiang, J Mei… – Tuberculosis, 2007 – Elsevier Spoligotyping was performed by using an Isogen Bioscience spoligotyping kit (Isogen Life Science Figure 3. Beijing/W Spoligotypes observed in 182 isolates with deletion RD105. Comparison of the multiplex PCR with spoligotyping revealed 100% sensitivity and specificity for

Contribution of spoligotyping to the characterization of the population structure of Mycobacterium tuberculosis isolates in Portugal

[TXT] from min-saude.pt

S David, DR Ribeiro, A Antunes, C Portugal… – Infection, Genetics and …, 2007 – Elsevier Spoligotyping was carried out according to the manufacturer’s instructions (Isogen BioscienceBV, Maarsen, Netherlands). The resulting spoligotypes were documented under a binary coderepresenting either a positive or negative hybridization result (n and o) and analyzed

Spoligotyping of< i> Mycobacterium tuberculosis</i> DNA from Archival Ziehl–Neelsen-stained sputum smears

N Suresh, J Arora, H Pant, T Rana… – Journal of microbiological …, 2007 – Elsevier available kit, according to the instructions supplied by the manufacturer (Isogen Bioscience, BV a positive signal in spoligotyping, thus demonstrating the efficiency of spoligotyping in a analysisof DNA extracted from stored ZN slides identified tuberculosis spoligotypes in 41

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Improvement of spoligotyping with additional spacer sequences for characterization of Mycobacterium bovis and M. caprae isolates from Spain

MT Javed, A Aranaz, L De Juan, J Bezos… – Tuberculosis, 2007 – Elsevier using two membranes: a commercial membrane containing the 43 spacers described earlier23 (Isogen Bioscience BV Number of spoligotyping patterns of M. bovis and M. caprae.Thirty-one different spoligotypes were identified among the 308 M. bovis (26 patterns) and 88

Utility of mycobacterial interspersed repetitive unit typing for differentiating Mycobacterium tuberculosis isolates in Wuhan, China

[HTML] from sgmjournals.org

H Han, F Wang, Y Xiao, Y Ren… – Journal of medical …, 2007 – Soc General Microbiol To test the reproducibility of MIRU typing, we blindly typed 20 isolates in two independentexperiments. Spoligotyping. Spoligotyping was performed with a commercial spoligotyping kit(Isogen Bioscience), according to the instructions supplied by the manufacturer.

[PDF] … tuberculosis Beijingg family isolates from Hong Kong and comparisonn with 1S6110 restriction fragment lengthh polymorphism typing and spoligotyping

[PDF] from uva.nl K Kremer, BKY Au, PCW Yip, R Skuce, P Supply… – dare.uva.nl with a commercial membranee containing the standard set of 43 spacer oligonucleotides (Isogen Bio- sciencee BV The usee of spacers 56, 57, 66, 67, and 68 in spoligotyping increased the patterns among the Beijing lineage strains in this study from three to five spoligotypes..

Identification of Beijing lineage Mycobacterium tuberculosis with combined mycobacterial interspersed repetitive unit loci 26, 31, and ETR-A

[HTML] from nih.gov

PJ Chin, CC Chiu… – Journal of clinical microbiology, 2007 – Am Soc Microbiol These isolates were characterized by IS6110 RFLP following standard protocols (12) andspoligotyping with a commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands)(6). The characteristic All other spoligotypes are defined as non-Beijing genotypes.

Znaczenie metody spoligotyping w epidemiologicznych dochodzeniach gruźlicy

[PDF] from viamedica.pl

E Augustynowicz-Kopeć… – Pneumonologia i …, 2007 – pneumonologia.viamedica.pl Autorzy dziękują Pani J. Scheenhart (Isogen Bioscience BV) za konsultację warunków repro IS6110 restriction fragment length polymor- phism patterns and spoligotypes determined by …Spoligotyping of Myco- bacterium tuberculosis isolates from patients with pulmo- nary

[HTML] Dedicated decontamination: A necessity to prevent cross contamination in high throughput mycobacteriology laboratories

[HTML] from jpgmonline.comC Rodrigues, D Almeida, S Shenai, N Goyal… – Indian Journal of …, 2007 – Medknow

Spoligotyping Spoligotyping was performed with a commercially available kit (Isogen Bioscience). Remaining two isolates grown from smear positive specimens had different spoligotypes hence were Since spoligotyping is known to be less refractory for differentiation of M

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Special Article-Dedicated decontamination: A necessity to prevent cross contamination in high throughput mycobacteriology laboratories

[PDF] from bioline.org.br

C Rodrigues, D Almeida, S Shenai… – Indian Journal of …, 2007 – bioline.org.br Spoligotyping was performed with a commercially available kit (Isogen Bioscience). Remainingtwo isolates grown from smear positive specimens had different spoligotypes hence were Sincespoligotyping is known to be less refractory for differentiation of M. tuberculosis, we

[HTML] Characterisation of mycobacteria isolated from slaughter cattle in pastoral regions of Uganda

[HTML] from biomedcentral.com

J Oloya, R Kazwala, A Lund… – BMC …, 2007 – biomedcentral.com in mid-central and mid-western areas of Uganda and detected new and specific spoligotypesnot reported Cultures belonging to the M. tuberculosis complex were submitted for furtherdifferentiation by Spoligotyping [20] as described by the producer (Isogen, Life science 

Genetic diversity of Mycobacterium tuberculosis isolates at the Military Medical Academy in Ankara, Turkey

O Kisa, A Albay, O Baylan, E Tozkoparan… – Research in …, 2007 – Elsevier

Spoligotyping was performed using a commercial kit (Isogen Bioscience BV, Maarssen, The

Netherlands) according to the 2.6. Comparison of spoligotypes with the international spoligotype

database. Spoligotyping results were entered in a binary format and octal code on Excel

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Evolution of the extensively drug-resistant F15/LAM4/KZN strain of Mycobacterium tuberculosis in KwaZulu-Natal, South Africa

[HTML] from oxfordjournals.org

M Pillay… – Clinical infectious diseases, 2007 – cid.oxfordjournals.org

Spoligotyping. Spoligotyping was performed using a kit from Isogen-Life Science in accordance with the manufacturer’s instructions. The presence or absence of 43 spacers in the direct-repeat region of isolates of M. tuberculosis

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[HTML] Longitudinal assessment of an ELISPOT test for Mycobacterium tuberculosis infection

[HTML] from plos.org

PC Hill, RH Brookes, A Fox, D Jackson-Sillah… – PLoS medicine, 2007 – dx.plos.org

We performed spoligotyping using membranes from Isogen Biosciences (http://www.isogen lifescience.com), as previously described [18] and analysed the results with software that we designed using Matlab software (MathWorks, http://www.mathworks.com).

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[HTML] M. tuberculosis genotypic diversity and drug susceptibility pattern in HIV-infected and non-HIV-infected patients in northern Tanzania

[HTML] from biomedcentral.comGS Kibiki, B Mulder, WMV Dolmans… – BMC …, 2007 – biomedcentral.com with samples which were INH-resistant, contained phenotypic rifampicin-resistant strains, or hadselected spoligotypes; phenotypic rifampicin Spoligotyping. 1 U/μl). Amplification and hybridizationwere performed according to the manufacturer’s manual (Isogen Bioscience BV

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Outbreak of Mycobacterium bovis infection in a wild animal park

SM Schmidbauer, P Wohlsein, G Kirpal… – Veterinary …, 2007 – veterinaryrecord.bmj.com and subtype of the MTC agent, 17 isolates from various organs were spoligotyped (Kamerbeekand FIG 2: Spoligotyping pattern of 17 mycobacterial isolates from various organs from seven in wild animals in Germany and in these cases the spoligotypes normally correspond to

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Molecular investigation of recurrent tuberculosis in patients from Rwanda

AN Umubyeyi, IC Shamputa… – … of Tuberculosis and …, 2007 – ingentaconnect.com DNA fingerprintingtechniques Spoligotyping was performed using a commercial kit (Isogen

Bioscience BV 4 of the 12 previously cured MDR-TB patients showed different spoligotypes,suggesting re of their recurrence (Figures 1 and 2). In contrast, the spoligotyping pat- terns of

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[HTML] Using ELISPOT to expose false positive skin test conversion in tuberculosis contacts

[HTML] from plos.org

PC Hill, DJ Jeffries, RH Brookes, A Fox… – PLoS One, 2007 – dx.plos.org spectrophotometry. We performed Spoligotyping using membranes (IsogenBiosciences), as previously described,[14] scanned the results and analysed themwith software designed in Matlab. Data management and analysis.

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[PDF] Usefulness of molecular techniques to identify ongoing tuberculosis transmission in Saudi Arabia

[PDF] from smj.org.sa

SA Al-Hajoj, VK Mohammed… – Saudi medical journal, 2007 – smj.org.sa The labeled PCR product was used as a probe to hybridize with 43 synthetic spacer oligonucleotides attached to a carrier membrane (Isogen Bioscience BV,Maarssen, TheNetherlands). The 2 isolates were identical by both RFLP and spoligotyping methods Figure

Molecular clues of a microepidemy among homeless tuberculosis patients in Budapest due to a new and local Mycobacterium tuberculosis clade

C Ködmön, S Niemann, MC Gutierrez… – Infection, Genetics and …, 2007 – Elsevier Spoligotyping was performed with a commercially available kit (Isogen BioscienceBV, Maarssen, The Netherlands) according to the instructions of the manufacturer(Kremer et al., 1999). Briefly, genomic mycobacterial DNA

Discovery of a novel Mycobacterium tuberculosis lineage that is a major cause of tuberculosis in Rio de Janeiro, Brazil

[HTML] from nih.govLCO Lazzarini, RC Huard, NL Boechat… – Journal of clinical …, 2007 – Am Soc Microbiol Spoligotyping.All M. tuberculosis strains were spoligotyped using a commercial kit (IsogenBioscience BV as an octal code (9). The person who performed the spoligotyping was blindedto information on the shared-type distributions of M. tuberculosis spoligotypes worldwide (N

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Genotype and phenotype relationships and transmission analysis of drug-resistant tuberculosis in Singapore

YJ Sun, ASG Lee, SY Wong… – … of Tuberculosis and …, 2007 – ingentaconnect.com

Spoligotyping Spoligotyping was performed using a commercial kit obtained from Isogen

Bioscience BV as previously described.21,22 IS6110 RFLP patterns and/or MIRU-VNTR patterns were used to determine genotypes for a few isolates with indeterminate spoligotypes.

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Evidence of ‘amplifier effect’in pulmonary multidrug-resistant tuberculosis: report of three casesA Umubyeyi, IC Shamputa, L Rigouts… – International Journal of …, 2007 – Elsevier Spoligotyping. Spoligotyping was performed with a commercial kit (Isogen Bioscience BV, Maarssen, The Netherlands) by the previously described method. 10 Briefly, 4 μl of the heat-killed bacterial suspension from each sample

[PDF] STUDY OF ISONIAZID-RESISTANT TUBERCULOSIS: MYCOBACTERIAL GENOTYPIC CHARACTERIZATION AND CLINICAL FEATURES IN HUMAN[PDF] from usc.edu

P Escalante – 2007 – digitallibrary.usc.edu BioImage Whole Band Analyzer™, version 3.2 software (BioImage, Ann Arbor, MI). Spoligotypingwas performed using the Isogen™ kit (Isogen, Bioscience, BV Maarseen, Netherlands) for allisolates according to the manufacturer instructions. In addition, all

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[BOOK] Study of isoniazid-resistant tuberculosis: Mycobacterial genotypic characterization and clinical features in human subjects

P Escalante – 2007 – books.google.com software (BioImage, Ann Arbor, MI). Spoligotyping was performed using the Isogen kit (Isogen, Bioscience, BV Maarseen, Netherlands) for all isolates according to the manufacturer instructions. In addition, all isolates also

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First insight into the population structure of Mycobacterium tuberculosis in Saudi Arabia

[HTML] from nih.govSAM Al-Hajoj, T Zozio, F Al-Rabiah… – Journal of clinical …, 2007 – Am Soc Microbiol to inter-DR spacer oligonucleotides covalently bound to a membrane (Isogen Life Science All spoligotypes were converted into octal format within Excel spreadsheets (8) and The individual spoligotyping patterns were compared with an updated SpolDB4 database named

Transmission of< i> Mycobacterium tuberculosis</i> in a Family Proved by Genotyping

CY Yang, R Jou, PC Chuang, JT Chang… – Journal of the Formosan …, 2007 – Elsevier Spoligotyping Spoligotyping is a polymerase chain reaction (PCR)-based analysis that uses commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands). The re-solved spoligotypes were M. tuberculosis complex strain-specific.

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[PDF] Molecular characterization of Mycobacterium tuberculosis isolates from Izmir, Turkey

[PDF] from microbiologica.net

C Bicmen, N Esen, EA Graviss… – … -Quarterly Journal of …, 2007 – microbiologica.net. were analyzed with the BioImage (Ann Arbor, Mich.,USA) Whole Band Analyzer, version 3.4.2.Spoligotyping was per- formed with a commercially available kit (Isogen Bioscience BV, Maarssen,

The Netherlands) in accordance with the manufacturer’s recom- mendations.

Instability of IS6110 patterns in multidrug-resistant strains of Mycobacterium tuberculosis

[HTML] from nih.gov

P Farnia, MR Masjedi, B Nasiri… – Epidemiology and …, 2007 – Cambridge Univ Press [12] with a commercially avail- able kit (Isogen Bioscience BV Stability of M. tuberculosis IS6110restriction fragment length polymorphism patterns and spoligotypes determined by expandingclones of M. tuberculosis and their global distribution assessed by spoligotyping in an

Identification of unique genetic markers in Rv0927c among< i> Mycobacterium tuberculosis</i> W-Beijing strainsX Jiang, Y Zhang, W Zhang, F Gao, J Jin… – Microbes and …, 2007 – Elsevier SDS) at 60 °C and then incubated in 1:4000 diluted streptavidin–peroxidase conjugate (IsogenBioscience) for This finding, which showed a spoligotyping pattern with hybridization only to thespacer 35 to 43 1. Spoligotypes of the 56 M. tuberculosis clinical isolates from China.

Laboratory diagnosis of pulmonary tuberculosis in TB and HIV endemic settings and the contribution of real time PCR for M. tuberculosis in bronchoalveolar lavage …

[PDF] from ru.nl

GS Kibiki, B Mulder… – Tropical Medicine & …, 2007 – Wiley Online Library

Spoligotyping patterns were analysed with Bionumerics 4.0 (Applied Maths, St-Martin-Latem,

Belgium). strains in 25 of the 28 BAL samples with positive MTB culture could be spoligotyped.

In all 25, the spoligotypes indicated that the isolates belonged to M. tuberculosis complex

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[PDF] MYCOBACTERIOSIS IN WILD BOAR: RESULTS OF 2000-2006 ACTIVITY IN NORTH-WESTERN ITALY

[PDF] from vet-alfort.fr

A Dondo, S Zoppi, F Rossi, L Chiavacci, A Barbaro… – aeema.vet-alfort.fr 37 a PCR based reverse line blot method covalently (Isogen, Netherland). M. bovis strains isolated were further characterized by VNTR typing (ETR A, B, C, D, E) according to Frothingham[Frothingham et al., 1998]. The strains unidentified by Spoligotyping were processed by a

Molecular epidemiology and prevalence of mutations conferring rifampicin and isoniazid resistance in Mycobacterium tuberculosis strains from the southern Ukraine

VV Nikolayevskyy, TJ Brown… – Clinical …, 2007 – Wiley Online Library[23] using commercially available membranes (Isogen, Maarssen, The binding to the corresponding targets, but an association between these specific spoligotypes and mutations in Spoligotyping results demonstrated a relative diversity in the genetic structure of M. tuberculosis

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Discrepant Results Between Pyrazinamide Susceptibility Testing by the Reference BACTEC 460TB Method and pncA DNA Sequencing in Patients Infected With …

J Dormandy, A Somoskovi, BN Kreiswirth… – Chest, 2007 – chestjournal.chestpubs.org Spoligotyping, a polymerase chain reaction-based genotyping method that detects 43 known spacer sequences that are interspersed between the direct repeats in the genomic repeat regionof M tuberculosis, was performed with a commercially available kit (Isogen Bioscience

Új Mycobacterium tuberculosis törzs okozta mikroepidémia budapesti hajléktalanokban C Ködmön, J Lukács, S Dávid, I Vadász… – Orvosi Hetilap, 2007 – akademiai.com A spoligotyping kevésbé érzékeny, mint az IS6110-RFLP fin- gerprint módszer, de kitûnôen elkülöníthetôk vele a világszer- te identifikáltuk [5, 6]. A mycobacteriális DNS kinyerését és a spoligotipizálást ke- reskedelmi forgalomban kapható teszttel (Isogen Bioscience BV

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A case of urinary tuberculosis due toMycobacterium bovissubspeciescaprae

V Sintchenko, P Jelfs, M Dally… – Pathology-Journal of …, 2006 – journals.lww.com Spoligotyping (Isogen Bioscience, The Netherlands), which involves PCR amplification of the MTBC direct repeat of reference laboratories to differentiate members of the MTBC by spoligotyping, 11 based on Several spoligotypes have been recognised among M. bovis subsp.

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… tandem-repeat genotyping of Mycobacterium bovis and comparison of the method with IS6110 restriction fragment length polymorphism analysis and spoligotyping

[HTML] from nih.gov

C Allix, K Walravens, C Saegerman… – Journal of clinical …, 2006 – Am Soc Microbiol PCR products were detected by hybridization onto a spoligotyping membrane (Isogen Bioscience BV IS6110 RFLP, spoligotyping, and MIRU-VNTR patterns of isolates obtained from animals based on MIRU-VNTR types and IS6110 fingerprints and spoligotypes was evaluated

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Spoligotyping of Mycobacterium tuberculosis isolates from Pakistan reveals predominance of Central Asian Strain 1 and Beijing isolates

[HTML] from nih.gov

Z Hasan, M Tanveer, A Kanji, Q Hasan… – Journal of clinical …, 2006 – Am Soc Microbiol positive. Spoligotyping.All 314 isolates were spoligotyped and analyzed (Fig. 1). A total of 197 (63%) isolates were grouped into 22 different clusters, while119 (37%) isolates had unique spoligotypes. Previously

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Molecular epidemiology of multidrug-resistant Mycobacterium bovis isolates with the samespoligotyping profile as isolates from animals

[HTML] from nih.gov

B Romero, A Aranaz, L de Juan… – Journal of clinical …, 2006 – Am Soc Microbiol Spoligotyping was performed on a commercial membrane (Isogen Bioscience BV, Maarssen,The of techniques is required for appropriate discrimination, even for those spoligotypes that have a Furthermore, the design of a new spoligotyping membrane that complements the

< i> rpoB</i> gene sequencing and spoligotyping of multidrug-resistant< i> Mycobacterium tuberculosis</i> isolates from India

N Suresh, UB Singh, J Arora, H Pant… – Infection, Genetics and …, 2006 – Elsevier to the AIIMS hospital, 149 MDR TB strains and 38 drug-susceptible strains were sequenced to identify mutations associated with RIF r in the rpoB gene and spoligotyped. 2.2. Spoligotyping. A total of 80 distinct spoligotypes were obtained from 149 MDR M. tuberculosis isolates.

Usefulness of restriction fragment length polymorphism and spoligotyping for epidemiological studies of< i> Mycobacterium bovis</i> in Madagascar: Description of …

V Rasolofo Razanamparany, R Quirin… – Veterinary …, 2006 – Elsevier

containing 43 oligonucleotides derived from spacer DNA sequences (obtained from Isogen Bioscience BV, Utrecht, The Netherlands). PCR and hybridization were performed as described by Kamerbeek et al. (1997). Spoligotyping patterns or spoligotypes were confirmed by

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[HTML] Variantes genéticas de Mycobacterium tuberculosis aisladas de pacientes de la Xª Región de Chile

[HTML] from scielo.cl

M Mancilla E, A Martínez H… – Revista chilena de …, 2006 – SciELO Chile A significant number of spoligotypes were identical to profiles found in Brazil followed by Argentina and Spain. utilizando los partidores biotinilados DRa (5′-GGTTTTGGGTCTGACGAC) y DRb (5′- CCGAGA GGGGACGGAAAC), incluidos en el sistema de spoligotyping (ISOGEN.

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Mycobacterium africanum elicits an attenuated T cell response to early secreted antigenic target, 6 kDa, in patients with tuberculosis and their household contacts

[HTML] from oxfordjournals.org

BC de Jong, PC Hill, RH Brookes… – Journal of Infectious …, 2006 – jid.oxfordjournals.org

were assessed by spectrophotometry (Eppendorf BioPhotometer). Spoligotypingwas performed using membranes (Isogen Biosciences), in accordance withstandardized methods [19]. Spoligotyping results were scanned and

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rpoB gene mutations and molecular characterization of rifampin-resistant Mycobacterium tuberculosis isolates from Shandong Province, China

[HTML] from nih.gov

X Ma, H Wang, Y Deng, Z Liu, Y Xu… – Journal of clinical …, 2006 – Am Soc Microbiol (20), with data analyzed by Whole Band Analysis software (version 3.2; BioImage,Ann Arbor, MI). Spoligotyping was carried out by using commercial kits from Isogen Bioscience BV (Maarssen, The Netherlands). Mycobacterial

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[HTML] Tuberculosis associated with Mycobacterium tuberculosis Beijing and non-Beijing genotypes: a clinical and immunological comparison

[HTML] from biomedcentral.com

YJ Sun, TK Lim, A Ong, B Ho… – BMC infectious …, 2006 – biomedcentral.com Spoligotyping was performed using a commercial kit (Isogen Bioscience BV, Maarssen, theNetherlands The remaining one isolate (N07) was not detected by spoligotyping, but MIRU-VNTR Based on spoligotypes and/or MIRU-VNTR patterns, the remaining 20 isolates were

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Prevalence of Haarlem I and Beijing types of Mycobacterium tuberculosis strains in Iranian and Afghan MDR-TB patients

[PDF] from mrc.ac.ir

P Farnia, MR Masjedi, M Mirsaeidi, F Mohammadi… – Journal of Infection, 2006 – Elsevier Spoligotyping. Spoligotyping was performed as described by Kamerbeek et al. 5 with acommercially available kit, according to the instructions supplied by the manufacturer (IsogenBioscience BV, Maarsen, The Netherlands). Distribution of the 263 MDR-TB spoligotypes.

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Molecular epidemiology of drug-resistant tuberculosis in Hungary

[HTML] from nih.gov

C Ködmön, S Niemann, J Lukács… – Journal of clinical …, 2006 – Am Soc Microbiol described previously (3, 14, 17). Spoligotyping was performed with a commerciallyavailable kit (Isogen Bioscience BV, Maarssen, The Netherlands) according to theinstructions of the manufacturer (10). The IS6110 fingerprint and

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Tuberculosis in mandrills at the Lisbon zooA Amado, T Albuquerque, A Gonçalves… – Veterinary …, 2006 – veterinaryrecord.bmj.com In order to investigate the infection source, spoligotyping was performed using conventional 43oligonucleotide Isogen membranes as described by Kamerbeek and others (1997). The twoisolates shared the same spoligotype described as type 237 (Anon 2006).

[HTML] Molecular characterisation of Mycobacterium tuberculosis isolates in the First National Survey of Anti-tuberculosis Drug Resistance from Venezuela

[HTML] from biomedcentral.com

L Aristimuño, R Armengol, A Cebollada… – BMC …, 2006 – biomedcentral.com to a set of 43 oligonucleotides covalently bound to the spoligo-membrane (Isogen BiosciencesBV of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in anInternational study Global distribution of Mycobacterium tuberculosis spoligotypes.

[PDF] 2. Lipoarabinomannans—structurally diverse and functionally enigmatic macroamphiphiles of mycobacteria and related actinomycetes•

[PDF] from pasteur.ac.ir

I Sutcliffe, T Matsumoto, H Ano, T Nagai, K Danno… – 2006 – journals2005.pasteur.ac.ir

Spoligotyping The clones of M. tuberculosis with less than five IS6110 RFLP bands were subjectedto the second typing, spoligotyping. Spoligotyping membranes were purchased from Isogenbioscience BV (Biltho- ven, The Netherlands). The procedures were

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Beijing genotype of Mycobacterium tuberculosis is significantly associated with human immunodeficiency virus infection and multidrug resistance in cases of …

[HTML] from nih.gov

M Caws, G Thwaites, K Stepniewska… – Journal of clinical …, 2006 – Am Soc Microbiol Spoligotyping.Spoligotyping of isolates was performed according to the standard protocol (6).Briefly, DNA Dra (biotin labeled) and DRb, hybridized to the spoligotype membrane (IsogenBioscience BV Spoligotypes were available for isolates from 35 HIV-positive patients (Fig.

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The most prevalent Mycobacterium tuberculosis superfamilies among Iranian and Afghan TB cases

[PDF] from mrc.ac.ir

AA Velayati, P Farnia, M Mirsaeidi… – … journal of infectious …, 2006 – informahealthcare.com [7] with a commercially available kit, according to the instructions supplied by the manufacturer(Isogen Bioscience BV, Maarsen, The Netherlands). Spoligotyping Figure 1. Shows thepredominant spoligotypes which are prevalent among Iranian and Afghan-born immigrants.

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Extensively drug-resistant tuberculosis: 2 years of surveillance in Iran

[HTML] from oxfordjournals.org

MR Masjedi, P Farnia, S Sorooch… – Clinical infectious …, 2006 – cid.oxfordjournals.org[13] with a commercially available kit (Isogen Bioscience). On the basis of spoligotyping results, these strains were determined to belong to the East African Indian 3 M. tuberculosis superfamily.Table 1. Table 1 Distribution of the 12 XDR TB spoligotypes.

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[HTML] Predominance of ancestral lineages of Mycobacterium tuberculosis in India

[HTML] from 9med.net

MC Gutierrez, N Ahmed, E Willery… – Emerg Infect …, 2006 – journal.9med.net Spoligotyping was performed by using a commercial kit (Isogen Bioscience BV, Maarsen, the Netherlands) according to was built based on spoligotypes alone or on a combination of VNTR and spoligotypes, although the resolution was lower when spoligotyping was used

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High resolution typing system for pathogenic Mycobaterium tuberculosum

PS Keim, RS Spurgiesz, JM Schupp – US Patent 7,026,467, 2006 – Google Patents

7:390-6. 2001. Sola, C. et al., “Mycobacterium tuberculosis phylogeny reconstruction based on combined numerical analysis with IS1081, IS6110, VNTR, and DR-based spoligotyping sug- gests the existence of two new phlyogeographical clades”. J Molecr Ev. 53:680-9. 2001.

Mycobacterium tuberculosis genotypes and their relationships with clinical and immunological phenotypes in Singapore

[PDF] from 137.132.14.55

SUN YONGJIANG – 2006 – 137.132.14.55

Furthermore, this method is highly reproducible and easy to perform (Kremer et al., 1999); particularly spoligotypes can be digitized into binary or octal code formats (Dale et al., 2001) which greatly facilitate the management and interlaboratory comparison of spoligotyping data.

Recent transmission of tuberculosis involving retired patients

PI Cafrune, LW Riley, LG Possuelo, ARM Valim… – Journal of Infection, 2006 – Elsevier Spoligotyping. Spoligotyping was performed as described by Kamerbeek et al. 19

probed. Hybridization was performed with a commercial kit, according to the manufacturer instructions (Isogen Biosciences BV, The Netherlands).

[PDF] INFORME FINAL DE PROYECTO DE INVESTIGACIÓN

[PDF] from ins.gob.pe

EN MULTIDROGORESISTENCIA… – bvs.ins.gob.pe

Salud e interpretadas en el software ALFWin TM Sequence Analyser 2.0 1998. Ensayode genotipificación mediante Spoligotyping Fue usado un kit comercialmentedisponible (Isogen Bioscience BV, Maarssen, The Netherlands

Assessment of diagnostic tools for eradication of bovine tuberculosis in cattle co-infected with Mycobacterium bovis and M. avium subsp. paratuberculosis

[PDF] from vetres-archive.org

A Aranaz, L De Juan, J Bezos, J Álvarez… – Veterinary …, 2006 – vetres.org

Thirty-six M. bovis isolates were char- acterised by spoligotyping and MIRU- VNTR: the 23 M The biotin-labelled amplified product was hybridised onto a membrane (Isogen Bio- science BV,

Maarssen Four spoligotypes were found, and three of them, numbered spb-7, spb-9

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INTÉRÊT DU TYPAGE MOLÉCULAIRE POUR L’ÉPIDÉMIOLOGIE DE LA TUBERCULOSE EN LIMOUSIN (1998–2006)

[HTML] from em-consulte.com

H Bezanahary, MC Baclet, C Sola… – Médecine et Maladies …, 2008 – Elsevier Keywords: MIRU15 typing; Mycobacterium tuberculosis; Spoligotyping. L’hybridation (1H à 60°C) des amplicons a été réalisée sur une membrane Isogen ® (Bioscience BV sous forme d’uncode octal et comparés aux données de la banque de spoligotypes SpolDB4 (Institut

… TANDEM-REPEAT GENOTYPING OF MYCOBACTERIUM BOVIS AND COMPARISON OF THE METHOD WITH IS6110 RESTRICTION FRAGMENT LENGTH POLYMORPHISM ANALYSIS AND SPOLIGOTYPING

[HTML] from nih.gov

C Allix, K Walravens, C Saegerman… – Journal of clinical …, 2006 – Am Soc Microbiol PCR products were detected by hybridization onto a spoligotyping membrane (Isogen BioscienceBV IS6110 RFLP, spoligotyping, and MIRU-VNTR patterns of isolates obtained from animals based on MIRU-VNTR types and IS6110 fingerprints and spoligotypes was evaluated

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A CASE OF URINARY TUBERCULOSIS DUE TOMYCOBACTERIUM BOVISSUBSPECIESCAPRAE

V Sintchenko, P Jelfs, M Dally… – Pathology-Journal of …, 2006 – journals.lww.com Spoligotyping (Isogen Bioscience, The Netherlands), which involves PCR amplification of the MTBC direct repeat of reference laboratories to differentiate members of the MTBC by spoligotyping, 11 based on Several spoligotypes have been recognised among M. bovis subsp.

SPOLIGOTYPING OF MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM PAKISTAN REVEALS PREDOMINANCE OF CENTRAL ASIAN STRAIN 1 AND BEIJING ISOLATES

[HTML] from nih.gov

Z Hasan, M Tanveer, A Kanji, Q Hasan… – Journal of clinical …, 2006 – Am Soc Microbiol

positive. Spoligotyping.All 314 isolates were spoligotyped and analyzed (Fig.1). A total of 197 (63%) isolates were grouped into 22 different clusters, while119 (37%) isolates had unique spoligotypes. Previously

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MOLECULAR EPIDEMIOLOGY OF MULTIDRUG-RESISTANT MYCOBACTERIUM BOVIS ISOLATES WITH THE SAMESPOLIGOTYPING PROFILE AS ISOLATES FROM ANIMALS

[HTML] from nih.gov

B Romero, A Aranaz, L de Juan… – Journal of clinical …, 2006 – Am Soc Microbiol Spoligotyping was performed on a commercial membrane (Isogen Bioscience BV, Maarssen,The of techniques is required for appropriate discrimination, even for those spoligotypes that havea Furthermore, the design of a new spoligotyping membrane that complements the

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< I> RPOB</I> GENE SEQUENCING AND SPOLIGOTYPING OF MULTIDRUG-RESISTANT< I> MYCOBACTERIUM TUBERCULOSIS</I> ISOLATES FROM INDIA

N Suresh, UB Singh, J Arora, H Pant… – Infection, Genetics and …, 2006 – Elsevier

to the AIIMS hospital, 149 MDR TB strains and 38 drug-susceptible strains were sequenced to

identify mutations associated with RIF r in the rpoB gene and spoligotyped. 2.2. Spoligotyping.

A total of 80 distinct spoligotypes were obtained from 149 MDR M. tuberculosis isolates.

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[HTML] Spoligotyping of Mycobacterium bovis isolates found in Manitoba

[HTML] from nih.gov

C Lutze-Wallace, C Turcotte… – Canadian journal of …, 2005 – ncbi.nlm.nih.gov Table I. Table I Summary of spoligotyped isolates by year, species, and location. types are 656573377603600 (MB-1) and 656473377603600 (MB-2). These spoligotypes have not … Spoligotyping is particularly useful for differentiating isolates harbouring only a single copy of

Characterization of Mycobacterium tuberculosis complex isolates from Greek patients with sarcoidosis by spoligotyping

[HTML] from nih.gov

M Gazouli, J Ikonomopoulos… – Journal of clinical …, 2005 – Am Soc Microbiol hybridization with membrane-bound spacer oligonucleotides and a spoligotyping kit (ISOGEN Bioscience, Maarsen The spoligotyping results were entered in a binary format as Excel spreadsheets All of the identified spoligotypes have been submitted to the World Spoligotype

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… Mycobacterium tuberculosis Beijing family isolates from Hong Kong and comparison with IS6110 restriction fragment length polymorphism typing and spoligotyping

[HTML] from nih.gov

K Kremer, BKY Au, PCW Yip, R Skuce… – Journal of clinical …, 2005 – Am Soc Microbiol In addition to spoligotyping with a commercial membrane containing the standard set of 43 spaceroligonucleotides (Isogen Bioscience BV, Maarssen, The (35), who also subjected Beijing strains to spoligotyping with novel spacers, at least seven spoligotypes can be

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Characterization of clonal complexity in tuberculosis by mycobacterial interspersed repetitive unit-variable-number tandem repeat typing

[HTML] from nih.gov

DG de Viedma, NA Rodriguez, S Andrés… – Journal of clinical …, 2005 – Am Soc Microbiol Spoligotyping.Spoligotyping was performed using primers of a spoligotyping kit (Isogen, The Netherlands with the loci showing different alleles within a box) and spoligotypes for the The two clones with different MIRU types were indistinguishable by spoligotyping and RFLP (Fig

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Discrimination of isolates of Mycobacterium bovis in Northern Ireland on the basis of variable numbers of tandem repeats (VNTRs)

RA Skuce, SW McDowell, TR Mallon… – Veterinary …, 2005 – veterinaryrecord.bmj.com

The isolates were spoligotyped according to the instructions of the manu- facturer (Isogen). the

inclusion of more than one isolate per herd (VNTR D=0·90, spoligotyping D=0 The difference

between years in the prevalence of VNTR pro- files and spoligotypes was not statistically

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[HTML] Molecular genotyping of Mycobacterium tuberculosis isolates from Turkey

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B Gencer… – Am J Infect Dis, 2005 – biomedsearch.com

Of the 374 isolates spoligotyped, 87 (23%) displayed unique spoligotypes and 287 (77 …Spoligotyping: Spoligotyping was performed using a commercial kit (Isogen Bioscience BV, Maarssen Spoligotyping: Spoligotypes were obtained for 374 isolates (Table 2): 87 isolates (23 Cited by 5Related articlesCachedAll 6 versionsImport into BibTeX

[CITATION] Epidemiologische Studie bei 109 Tuberkulosefällen im Regierungsbezirk Oberfalz basierend auf Spoligotyping

B Werner, C Ellermeier, L Naumann… – Pneumologie, 2005

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Inter-laboratory validation of PCR-based detection of Mycobacterium tuberculosis in formalin-fixed, paraffin-embedded tissues

[PDF] from charite.de

C Schewe, T Goldmann, M Grosser, A Zink… – Virchows Archiv, 2005 – Springer All samples with positive amplification of IS6110 were subjected to further analysis by spoligotyping. The method was performed as described previously [22, 32, 44]. We used a commercial Spoligotyping Kit (Isogen, Maarsen, The Netherlands, http://www.isogen.nl/).

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[CITATION] Case-Report: Lungentuberkulose einer MTA–Nachweis von 3 Neuinfektionen durchSpoligotyping B Werner, C Ellermeier, L Naumann… – Pneumologie, 2005

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Molecular characterization of< i> Mycobacterium tuberculosis</i> isolates in a region of Brazil with a high incidence of tuberculosis

S Borsuk, MM Dellagostin, SG Madeira, C Lima… – Microbes and …, 2005 – Elsevier

Hybridization of the PCR product to the spoligo-membrane (Isogen Life Sciences) was The strains

clustered by spoligotyping were analyzed by IS6110-RFLP to confirm any The spoligotypes were

compared to SpoligoDatabase3 (http://www.pasteur-guadeloupe.fr/tb/spoldb3

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S< i> 6110</i> DNA fingerprinting analysis of individually separated colonies of< i> Mycobacterium tuberculosis</i>

T Matsumoto, H Ano, T Nagai, K Danno… – Tuberculosis, 2005 – Elsevier

to the second typing, spoligotyping. Spoligotyping membranes were purchasedfrom Isogen bioscience BV (Bilthoven, The Netherlands). The procedures werecarried out according to the manufacturer’s instructions. Results.

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Distribution of the Beijing family genotypes of Mycobacterium tuberculosis in Taiwan

[HTML] from nih.govR Jou, CY Chiang… – Journal of clinical microbiology, 2005 – Am Soc Microbiol Genotyping method.Spoligotyping was used to identify and differentiate the M. tuberculosiscomplex isolates in A commercially available kit (Isogen Bioscience BV, Maarssen, The

Netherlands) was used as The spoligotypes resolved were M. tuberculosis complex strain specific

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Characterization of Mycobacterium caprae isolates from Europe by mycobacterial interspersed repetitive unit genotyping

[HTML] from nih.gov

WM Prodinger, A Brandstätter… – Journal of clinical …, 2005 – Am Soc Microbiol

Spoligotyping and IS6110 RFLP analysis.Spoligotyping was carried out as described previously (23) by using membranes (Isogen Bioscience BV, Maarsen, The Netherlands). The octal codes for spoligotypes were determined as proposed previously (14).

Novos dados sobre os Spoligotypes de estirpes do complexo Mycobacterium tuberculosis isoladas no Hospital Fernando Fonseca (Amadora-Sintra, Portugal)

[TXT] from min-saude.pt

S Davis, V Barros, C Portugal… – Rev Port …, 2005 – repositorio.hff.min-saude.pt out in accordance with the recommendations of the mem- brane Kit manufacturer (IsogenBioscience BV contributed the most in this field, seeing that it allows the Spoligotypes to be …Spoligotyping make it easier to differentiate between the species of the M. tuberculosis complex

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Efficient discrimination within a Corynebacterium diphtheriae epidemic clonal group by a novel macroarray-based method

[HTML] from nih.gov

I Mokrousov, O Narvskaya… – Journal of clinical …, 2005 – Am Soc Microbiol .. in parallel slots (channels) by using an MN45 miniblotter apparatus (Isogen Biosciences,Maarssen both ribotypes of the epidemic clone, while the other 33 spoligotypes included strains had unique profiles (Table 2). The discriminatory power of the spoligotyping assessed with

Place du spoligotypage lors d’une enquête épidémiologique devant un cas de suspicion de tuberculose pulmonaire nosocomiale F Jauréguy, MC Gutierez, CJ Marie, C Poirier… – Pathologie Biologie, 2005 – Elsevier Keywords: Nosocomial tuberculosis; Epidemiology; Spoligotyping. inter-DR ou spacers ont été synthétisées et immobilisées sur une membrane de nylon commercialisée (Isogen Bioscience BV, BT Les résultats des différents spoligotypes obtenus sont présentés dans la Fig.

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[CITATION] 波兰肺结核患者耐药结核分枝杆菌分子流行病学研究A Sajduda, A Brzostek, M PopXawska, N Rastogi… – 结核与肺部疾病杂志, 2005

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[HTML] SPOLIGOTYPING OF MYCOBACTERIUM BOVIS ISOLATES FOUND IN MANITOBA

[HTML] from nih.govC Lutze-Wallace, C Turcotte… – Canadian journal of …, 2005 – ncbi.nlm.nih.gov Table I. Table I Summary of spoligotyped isolates by year, species, and location. types are656573377603600 (MB-1) and 656473377603600 (MB-2). These spoligotypes have not

Spoligotyping is particularly useful for differentiating isolates harbouring only a single copy of

CHARACTERIZATION OF MYCOBACTERIUM TUBERCULOSIS COMPLEX ISOLATES FROM GREEK PATIENTS WITH SARCOIDOSIS BY SPOLIGOTYPING

[HTML] from nih.gov

M Gazouli, J Ikonomopoulos… – Journal of clinical …, 2005 – Am Soc Microbiol hybridization with membrane-bound spacer oligonucleotides and a spoligotyping kit (ISOGENBioscience, Maarsen The spoligotyping results were entered in a binary format as Excelspreadsheets All of the identified spoligotypes have been submitted to the World Spoligotype

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… MYCOBACTERIUM TUBERCULOSIS BEIJING FAMILY ISOLATES FROM HONG KONG AND COMPARISON WITH IS6110 RESTRICTION FRAGMENT LENGTH POLYMORPHISM TYPING AND SPOLIGOTYPING

[HTML] from nih.gov

K Kremer, BKY Au, PCW Yip, R Skuce… – Journal of clinical …, 2005 – Am Soc Microbiol

In addition to spoligotyping with a commercial membrane containing the standard set of 43 spacer

oligonucleotides (Isogen Bioscience BV, Maarssen, The (35), who also subjected Beijing strains

to spoligotyping with novel spacers, at least seven spoligotypes can be

Cited by 64Related articlesAll 17 versionsImport into BibTeX

RECHERCHE DE MARQUEURS GÉNÉTIQUES DE SOUCHES DE MYCOBACTÉRIUM TURBERCULOSIS MULTIRÉSISTANTES AUX ANTIBIOTIQUES EN RÉPUBLIQUE CENTRAFRICAINE

[PDF] from univ-toulouse.fr

LX Nouvel – 2005 – oatao.univ-toulouse.fr 61 FIGURE 14 : CARTE DES 41 LOCI MIRU SUR LE CHROMOSOME DE M.TUBERCULOSIS H37RV ….. 63 FIGURE 15 : DENDROGRAMME DES 79 PROFILSDE SPOLIGOTYPES DIFFERENTS DES 284 SOUCHES TYPEES.

[CITATION] CASE-REPORT: LUNGENTUBERKULOSE EINER MTA–NACHWEIS VON 3 NEUINFEKTIONEN DURCHSPOLIGOTYPING

B Werner, C Ellermeier, L Naumann… – Pneumologie, 2005

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[PDF] EDITORIAL BOARD• EDITORIAL BOARD

[PDF] from pasteur.ac.ir

T Bhatnagar, S Boutaiba… – FEMS …, 2005 – journals2005.pasteur.ac.irFEMS MICROBIOLOGY LETTERS Volume 248, Issue 2, Pages 133-274 (15 July 2005) 1. Editorialboard• EDITORIAL BOARD Pages iii-vi Research Letters 2. Lipolytic activity from Halobacteria:Screening and hydrolase production• SHORT COMMUNICATION Pages 133-140 Related articlesAll 2 versionsImport into BibTeX

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PCR-based genotyping of Mycobacterium tuberculosis with new GC-rich repeated sequences and IS6110 inverted repeats used as primers

[HTML] from nih.gov

R Kotłowski, IC Shamputa, NA El Aila… – Journal of clinical …, 2004 – Am Soc Microbiol In experimental studies, 27 M. tuberculosis isolates were analyzed. Ten colonies isolated from one sputum sample were subjected to spoligotyping (Isogen; Bioscience, Maarssen, The Netherlands) and IS6110-restriction fragment length polymorphism (RFLP) assay (13).

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[HTML] PCR-based genotyping of Mycobacterium tuberculosis with new GC-rich repeated sequences and IS6110 inverted repeats used as primers

[HTML] from ukpmc.ac.uk

R Kotlowski, IC Shamputa, NA El Aila… – JOURNAL OF …, 2004 – ukpmc.ac.uk In experimental studies, 27 M. tuberculosis isolates were analyzed. Ten colonies isolated from one sputum sample were subjected to spoligotyping (Isogen; Bioscience, Maarssen, The Netherlands) and IS6110-restriction fragment length polymorphism (RFLP) assay (13).

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Molecular fingerprinting of Mycobacterium bovis subsp. caprae isolates from Central Europe

[HTML] from nih.gov

W Erler, G Martin, K Sachse… – Journal of clinical …, 2004 – Am Soc Microbiol method (12) and subjected to direct-repeat-specific PCR and hybridization with membrane-boundspacer oligonucleotides and a spoligotyping kit (ISOGEN Bioscience, Maarsen, The Spoligotypingof the 79 isolates revealed 11 different spoligotypes (designated C1 to

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Analysis of clonal composition of Mycobacterium tuberculosis isolates in primary infections in children

[HTML] from nih.gov

DG de Viedma, M Marín, MJ Ruiz… – Journal of clinical …, 2004 – Am Soc Microbiol The PCR for amplification of the DR region was performed with the primers in thespoligotyping kit (Isogen, Maarsen, The Netherlands) and according to the instructions ofthe manufacturer. All spoligotypes were confirmed by repeating the assay.

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Spoligotyping profile change caused by deletion of a direct variable repeat in a Mycobacterium tuberculosis isogenic laboratory strain

[HTML] from nih.gov

A Aranaz, B Romero, N Montero… – Journal of clinical …, 2004 – Am Soc Microbiol The test was carried out with membranes obtained from Isogen Bioscience BV, Maarssen, The associated with the DR locus and their influence on the interpretation of spoligotyping. corresponding to relapses or infections at different sites showed identical spoligotypes (6, 10,

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Bovine tuberculosis (Mycobacterium bovis) in wildlife in Spain

[HTML] from nih.gov

A Aranaz, L De Juan, N Montero… – Journal of Clinical …, 2004 – Am Soc Microbiol of the biotin-labeled PCR product onto a spoligotyping membrane (Isogen Bioscience BV Schematic representation of spoligotyping patterns identified among wildlife and areas where the patterns Six spoligotypes were identified among the isolates from Doñana National Park.

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[PDF] Simultaneous detection and typing of Mycobacterium tuberculosis complex bacteria

[PDF] from cli-online.com

M de Boer, A van der Zanden… – cli-online.com of the mem- brane or by specific imaging systems developed by Isogen Life Science in thelaboratory, because different M. tuberculosis strains or DNA can yield different spoligotypes. Thusspoligotyping can be used for quality control of microscopy of AFB, cultures or nucleic

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Transmission of tuberculosis from smear negative patients: a molecular epidemiology study

[HTML] from highwire.org

E Hernandez-Garduno, V Cook, D Kunimoto… – Thorax, 2004 – thorax.highwire.org A spoligotyping kit (Isogen Bioscience, Maarssen) was used as a secondary typingtechnique for strains with five copies or less of IS6110. 13 Smear specimens werestained with Auramine O and confirmed by Ziehl Neelsen staining.

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Characterization of ancestral Mycobacterium tuberculosis by multiple genetic markers and proposal of genotyping strategy

[HTML] from nih.gov

YJ Sun, ASG Lee, ST Ng, S Ravindran… – Journal of clinical …, 2004 – Am Soc Microbiol Spoligotyping.Spoligotyping was performed using a commercial kit (Isogen Bioscience BV,Maarssen, The Netherlands) according to the instructions of the manufacturer. The spoligotypeswere presented by using pseudo-original patterns or 15 octal codes, as described by

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Genotypic and phenotypic heterogeneity among Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients

[HTML] from nih.gov

IC Shamputa, L Rigouts, LA Eyongeta… – Journal of clinical …, 2004 – Am Soc Microbiol Spoligotyping.Spoligotyping was performed with a commercial kit (Isogen Bioscience BV,Maarssen, The All 10 clones from each of the 97 patients were tested by spoligotyping. of the 97patients tested, including the 7 Beijing genotype strains, showed identical spoligotypes.

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Relating the size of molecularly defined clusters of tuberculosis to the duration of symptoms

[HTML] from oxfordjournals.org

TP Giordano, H Soini, LD Teeter… – Clinical infectious …, 2004 – cid.oxfordjournals.org BioImage). Isolates containing <5 IS6110 elements were spoligotyped [27] with acommercially available kit (Isogen Bioscience BV). Spoligotyping is an alternativemethod for molecular characterization of M. tuberculosis isolates.

Molecular epidemiology of drug-resistant Mycobacterium tuberculosis strains isolated from patients with pulmonary tuberculosis in Poland: a 1-year study

A Sajduda, A Brzostek, M Poplawska… – … of Tuberculosis and …, 2004 – ingentaconnect.com

Spoligotyping was per- formed using a commercially available kit (Isogen Bioscience BV, Maarssen,The Netherlands) accord- ing to the In accordance with previous findings, spoligotyping was lessdiscrimina- tory than IS6110 RFLP.8,9 A total of 91 spoligotypes

Transmission characteristics of tuberculosis in the foreign-born and the Canadian-born populations of Alberta, Canada

D Kunimoto, K Sutherland… – … of Tuberculosis and …, 2004 – ingentaconnect.com Two or more isolates with the same DNA fingerprint were called a cluster. A spoligotyping kit (Isogen Bioscience, Maarssen, The Netherlands) was used for secondary analysis of all strains with five copies or less of IS6110.6

Species differentiation and antibiotic susceptibility testing with DNA microarrays

[PDF] from aseanbiotechnology.info

G Vernet, C Jay, M Rodrigue… – Journal of applied …, 2004 – Wiley Online Library (Please refer to Fig. 3a.). 4.2.1 Reference spoligotyping. (Please refer to Fig. (1997). Reagents were provided by Isogen Life Science (The Netherlands). 4.2.2 Comparison of spoligotypes obtained by dot-blot and by the microarray with a strain of M. bovis. (Please refer to Fig.

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High rates of clustering of strains causing tuberculosis in Harare, Zimbabwe: a molecular epidemiological study

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PJ Easterbrook, A Gibson, S Murad… – Journal of clinical …, 2004 – Am Soc Microbiol primer 5′-CCAAGAGGGGACGGAAAC-3′ and biotinylated primer 5′-GGTTTTGGGTCTGACGAC-3′). The PCR products were then hybridized to a Biodyne C membrane (Isogen Bioscience, Maarsen By using spoligotyping alone, 54 distinct spoligotypes were identified

Identification of MDR-TB Beijing/W and other Mycobacterium tuberculosis genotypes in Nairobi, Kenya

WA Githui, AM Jordaan, ES Juma… – … of Tuberculosis and …, 2004 – ingentaconnect.com Spoligotyping and analysis The method is based on in vitro PCR amplification of the Membranes and primers were obtained from Isogen, Bioscience BV, Utrecht, The Netherlands. were scanned and added to an existing spoligotype data- base containing spoligotypes from all

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First isolation of< i> Mycobacterium microti</i>(Llama-type) from a dog

L Deforges, HJ Boulouis, JL Thibaud… – Veterinary …, 2004 – Elsevier

Definitive subspecies identification was established by spoligotyping (for “Spacer Oligotyping Easthill, NY, USA) sensitised with 43 aminolink–oligonucleotides, according to the procedures recommended by the manufacturer of the oligonucleotides (Isogen Bioscience, Maarssen

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Impact of drug resistance on fitness of Mycobacterium tuberculosis strains of the W‐Beijing genotype

OS Toungoussova, DA Caugant… – FEMS Immunology …, 2004 – Wiley Online Library 20,21]. Spoligotyping was performed by using a commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands) according to the instructions supplied by the manufacturer, as previously described [22]. M. tuberculosis

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6 Molecular Epidemiology of Mycobacterium bow’s

RA SKUCE… – Tuberculosis, 2004 – books.google.com

e Spoligotyping result of M. tuberculosis H37Rv and M. bovis field isolates (rows), A membrane Courtesy of Isogen Bioscience BV representative panels of M. tuberculosis complex bac- teria(van 2000) and relatively large databases of spoligotypes are being curated (Sola et al.

Genomic characterization of an endemic Mycobacterium tuberculosis strain: evolutionary and epidemiologic implications

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D Nguyen, P Brassard, D Menzies… – Journal of clinical …, 2004 – Am Soc Microbiol Spoligotyping (or spacer oligonucleotide typing) was done by using a PCR-based technique which detects the presence or absence of 43 unique sequence spacers in the direct repeat (DR) locus (Isogen Bioscience BV, Maarssen, The Netherlands) (20).

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[HTML] Drug susceptibility of Brazilian strains of Mycobacterium bovis using traditional and molecular techniques

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PM Parreiras, FCF Lobato, AP Alencar… – Memórias do Instituto …, 2004 – SciELO Brasil 2002), applied on the membrane using a Miniblotter MN45 (Isogen, the Netherlands) and after 1 min incubation at RT, the membrane was This observation was confirmed by the generation of M. bovis genotypes after submitting the isolates to spoligotyping (data not shown).

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[PDF] Antimicrobial resistance among Campylobacter strains, United States, 1997–2001

[PDF] from cdc.gov

A Gupta, JM Nelson, TJ Barrett, RV Tauxe… – Emerg Infect …, 2004 – wwwnc.cdc.gov Page 130. We summarize antimicrobial resistance surveillance data in human andchicken isolates of Campylobacter. Isolates were from a sentinel county study from1989 through 1990 and from nine state health departments

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Multicenter evaluation of reverse line blot assay for detection of drug resistance in Mycobacterium tuberculosis clinical isolates

[PDF] from rivm.nl

I Mokrousov, NV Bhanu, PN Suffys… – Journal of …, 2004 – Elsevier Furthermore, the proposed method requires the same simple equipment as that used forspoligotyping and permits simultaneous analysis of Biodyne ®C membrane (Pall GelmanLaboratory, Ann Arbor, MI, USA) using the MN45 miniblotter apparatus (Isogen Biosci., Maarssen

PCR-BASED GENOTYPING OF MYCOBACTERIUM TUBERCULOSIS WITH NEW GC-RICH REPEATED SEQUENCES AND IS6110 INVERTED REPEATS USED AS PRIMERS

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R Kotłowski, IC Shamputa, NA El Aila… – Journal of clinical …, 2004 – Am Soc Microbiol In experimental studies, 27 M. tuberculosis isolates were analyzed. Ten colonies isolated from one sputum sample were subjected to spoligotyping (Isogen; Bioscience, Maarssen, The Netherlands) and IS6110-restriction fragment length polymorphism (RFLP) assay (13).

ANALYSIS OF CLONAL COMPOSITION OF MYCOBACTERIUM TUBERCULOSIS ISOLATES IN PRIMARY INFECTIONS IN CHILDREN

[HTML] from nih.gov

DG de Viedma, M Marín, MJ Ruiz… – Journal of clinical …, 2004 – Am Soc Microbiol The PCR for amplification of the DR region was performed with the primers in thespoligotyping kit (Isogen, Maarsen, The Netherlands) and according to the instructions ofthe manufacturer. All spoligotypes were confirmed by repeating the assay. Cited by 20Related articlesBL DirectAll 11 versionsImport into BibTeX

[HTML] PCR-BASED GENOTYPING OF MYCOBACTERIUM TUBERCULOSIS WITH NEW GC-RICH REPEATED SEQUENCES AND IS6110 INVERTED REPEATS USED AS PRIMERS

[HTML] from ukpmc.ac.uk

R Kotlowski, IC Shamputa, NA El Aila… – JOURNAL OF …, 2004 – ukpmc.ac.uk In experimental studies, 27 M. tuberculosis isolates were analyzed. Ten colonies isolated fro one sputum sample were subjected to spoligotyping (Isogen; Bioscience, Maarssen, The Netherlands) and IS6110-restriction fragment length polymorphism (RFLP) assay (13).

SPOLIGOTYPING PROFILE CHANGE CAUSED BY DELETION OF A DIRECT VARIABLE REPEAT IN A MYCOBACTERIUM TUBERCULOSIS ISOGENIC LABORATORY STRAIN

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A Aranaz, B Romero, N Montero… – Journal of clinical …, 2004 – Am Soc Microbiol The test was carried out with membranes obtained from Isogen Bioscience BV, Maarssen, The associated with the DR locus and their influence on the interpretation of spoligotyping. corresponding to relapses or infections at different sites showed identical spoligotypes (6, 10,

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BOVINE TUBERCULOSIS (MYCOBACTERIUM BOVIS) IN WILDLIFE IN SPAIN

[HTML] from nih.gov

A Aranaz, L De Juan, N Montero… – Journal of Clinical …, 2004 – Am Soc Microbiol of the biotin-labeled PCR product onto a spoligotyping membrane (Isogen Bioscience BV Schematic representation of spoligotyping patterns identified among wildlife and areas wherethe patterns Six spoligotypes were identified among the isolates from Doñana National Park.

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TRANSMISSION OF TUBERCULOSIS FROM SMEAR NEGATIVE PATIENTS: A MOLECULAR EPIDEMIOLOGY STUDY

[HTML] from highwire.org

E Hernandez-Garduno, V Cook, D Kunimoto… – Thorax, 2004 – thorax.highwire.org A spoligotyping kit (Isogen Bioscience, Maarssen) was used as a secondary typingtechnique for strains with five copies or less of IS6110. 13 Smear specimens were stained with Auramine O and confirmed by Ziehl Neelsen staining.

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CHARACTERIZATION OF ANCESTRAL MYCOBACTERIUM TUBERCULOSIS BY MULTIPLE GENETIC MARKERS AND PROPOSAL OF GENOTYPING STRATEGY

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YJ Sun, ASG Lee, ST Ng, S Ravindran… – Journal of clinical …, 2004 – Am Soc Microbiol Spoligotyping.Spoligotyping was performed using a commercial kit (Isogen Bioscience BV,Maarssen, The Netherlands) according to the instructions of the manufacturer. The spoligotypes were presented by using pseudo-original patterns or 15 octal codes, as described by

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GENOTYPIC AND PHENOTYPIC HETEROGENEITY AMONG MYCOBACTERIUM TUBERCULOSIS ISOLATES FROM PULMONARY TUBERCULOSIS PATIENTS

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IC Shamputa, L Rigouts, LA Eyongeta… – Journal of clinical …, 2004 – Am Soc Microbiol Spoligotyping.Spoligotyping was performed with a commercial kit (Isogen Bioscience BV,Maarssen, The All 10 clones from each of the 97 patients were tested by spoligotyping. of the 97patients tested, including the 7 Beijing genotype strains, showed identical spoligotypes.

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HIGH RATES OF CLUSTERING OF STRAINS CAUSING TUBERCULOSIS IN HARARE, ZIMBABWE: A MOLECULAR EPIDEMIOLOGICAL STUDY

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PJ Easterbrook, A Gibson, S Murad… – Journal of clinical …, 2004 – Am Soc Microbiol primer 5′-CCAAGAGGGGACGGAAAC-3′ and biotinylated primer 5′-GGTTTTGGGTCTGACGAC-3′). The PCR products were then hybridized to a Biodyne C membrane (IsogenBioscience, Maarsen By using spoligotyping alone, 54 distinct spoligotypes were identified Cited by 37Related articlesBL DirectAll 12 versionsImport into BibTeX

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Evaluation of the epidemiologic utility of secondary typing methods for differentiation of Mycobacterium tuberculosis isolates

[HTML] from nih.gov

A Kwara, R Schiro, LS Cowan… – Journal of clinical …, 2003 – Am Soc Microbiol

Spoligotyping (Isogen Bioscience BV, Maarssen, The Netherlands) was performed in accordance with previously published methods (8). Results were recorded as an octal code (4). MIRU loci (10) were amplified with primers specific for sequences flanking each locus (Table 1

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Characterization of Mycobacterium tuberculosis complex DNAs from Egyptian mummies byspoligotyping

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AR Zink, C Sola, U Reischl, W Grabner… – Journal of clinical …, 2003 – Am Soc Microbiol

For this analysis, we used a commercial spoligotyping kit (Isogen, Maarsen, The Netherlands it has been shown that the absence of spacers 33 to 36 in the spoligotyping signatures of absence of spacers 33 to 36 (Table 4), most of the M. tuberculosis spoligotypes obtained from

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Characterization of Finnish Mycobacterium tuberculosis isolates by spoligotyping

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K Puustinen, M Marjamäki, N Rastogi… – Journal of clinical …, 2003 – Am Soc Microbiol Spoligotyping was performed with a commercially available kit (Isogen Bioscience BV, Maarssen,The Netherlands) according to the instructions of the manufacturer. We analyzed 380 M. tuberculosis isolates by spoligotyping and obtained a total of 138 spoligotypes.

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Widespread pyrazinamide-resistant Mycobacterium tuberculosis family in a low-incidence setting

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D Nguyen, P Brassard, J Westley… – Journal of clinical …, 2003 – Am Soc Microbiol IS6110 RFLP by Southern blotting (38) and spoligotyping (Isogen Bioscience BV) (26) were performed using the observation that the DNA fingerprints by both IS6110 RFLP and spoligotyping are similar approximately 2 to 3.2 years (13, 42) and that of spoligotypes is believed to

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Molecular epidemiology and drug resistance of Mycobacterium tuberculosis isolates in the Archangel prison in Russia: predominance of the W-Beijing clone family

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OS Toungoussova, A Mariandyshev… – Clinical infectious …, 2003 – cid.oxfordjournals.org Spoligotyping was performed using a commercially available spoligotyping kit (Isogen BioscienceBV) in were represented by 6 and 3 isolates each, and 4 spoligotypes comprised 2 All isolateswith identical IS6110 RFLP patterns were found to be identical by spoligotyping. Cited by 62Related articlesBL DirectAll 12 versionsImport into BibTeX

Molecular typing of Mycobacterium tuberculosis by using nine novel variable-number tandem repeats across the Beijing family and low-copy-number IS6110 isolates

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RS Spurgiesz, TN Quitugua, KL Smith… – Journal of clinical …, 2003 – Am Soc Microbiol In a database of 3,319 spoligotypes from isolates collected in geographically distinct areas, seven spoligotype Advanced Nucleic Acids Technology Core Facility, San Antonio, Tex.) and commercially available spoligotyping membranes (Isogen, Maarssen, The

The molecular epidemiology of tuberculosis in western CanadaJM FitzGerald, A Fanning… – … of Tuberculosis and …, 2003 – ingentaconnect.com All isolates matched as identical by computer were manually confirmed by visually comparingthe original autoradiographs. A spoligotyping kit (Isogen Bioscience, Maarssen, The Netherlands)was used for secondary analysis of 90 strains with five copies or less of IS6110.

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Genetic biodiversity of Mycobacterium tuberculosis complex strains from patients with pulmonary tuberculosis in Cameroon

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SN Niobe-Eyangoh, C Kuaban, P Sorlin… – Journal of clinical …, 2003 – Am Soc Microbiol

(i) Spoligotyping.Spoligotyping was performed as a probe to hybridize with 43 synthetic spacer oligonucleotides covalently bound to a membrane (Isogen Biosciences BV Spoligotypes were analyzed with the Bionumerics program version 2.5 (Applied Maths, Kortrijk, Belgium).

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Detection of pathogenic mycobacteria of veterinary importance

RA Skuce, MS Hughes, MJ Taylor… – METHODS IN MOLECULAR …, 2003 – Springer 2.5.3. Membrane-Based Analysis 1. Spoligotyping Kit (Isogen Bioscience BV, Maarssen,Netherlands). 2. SSPE buffer (2X): 1X SSPE is 0.18 M HCl, 10 mM NaH2PO4, 1 mM EDTA.To be supplemented with 0.1 % sodium dodecyl sulfate (SDS).

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Analysis of multidrug-resistant Mycobacterium bovis from three clinical samples from Scotland

VM Hughes, R Skuce, C Doig… – … of Tuberculosis and …, 2003 – ingentaconnect.com from each isolate was subjected to spoligotyping,11 exactly as specified by the kit manufacturers(Isogen Bioscience BV linked as they shared spoligotyping and DRr-RFLP profiles. The DRr-RFLPprofiles and spoligotypes shared by Cases I/94 and II/98 have never previously Cited by 8Related articlesBL DirectAll 5 versionsImport into BibTeX

[PDF] ÇOĞUL DİRENÇLİ MYCOBACTERİUM TUBERCULOSİS İZOLATLARINDA SEKONDER İLAÇLARA DİRENÇ VE

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E TAKİP – 2003 – uvt.ulakbim.gov.tr Spoligotyping için ticari kit kullanılmıştır (Isogen Bioscience BV, Maarssen, The Netherlands inCuba outside of Havana, July 1994- June 1995: utility of spoligotyping versus IS6110 BN, KremerK., Valetudie G. et al, Global distribution of Mycobacterium tuberculosis spoligotypes.

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Investigations into an outbreak of tuberculosis in a flock of sheep in contact with tuberculous cattle

FE Malone, EC Wilson, JM Pollock… – Journal of Veterinary …, 2003 – Wiley Online Library Molecular strain typing was undertaken on 39 cattle and three sheep M. bovis isolates usingspoligotyping (Kamerbeek et al., 1997) exactly as directed by the manufacturer (Isogen Bioscience,Netherlands) and a selection of six VNTR markers (Skuce and Neill, 2001).

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IS6110-mediated deletion polymorphism in the direct repeat region of clinical isolates of Mycobacterium tuberculosis

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SL Sampson, RM Warren, M Richardson… – Journal of …, 2003 – Am Soc Microbiol These isolates were chosen on the basis of spoligotypes, which indicated a deletion of …Spoligotyping.DNA polymorphism in the DR locus was detected by spoligotyping according toa products were then hybridized to a commercially available membrane (Isogen Biosciences

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Heterogeneity of Mycobacterium tuberculosis isolates in Yangon, Myanmar

S Phyu, R Jureen, T Ti, UR Dahle… – Journal of clinical …, 2003 – Am Soc Microbiol susceptibility test, niacin accumulation test, nitrate reduction test, and pyrazinamidase activity)were performed for phenotyping (4). Spoligotyping was performed with a commercial kit asrecommended by the manufacturer (Isogen Bioscience BV, Maarssen, The Netherlands).

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Single nucleotide polymorphisms in genes associated with isoniazid resistance in Mycobacterium tuberculosis

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SV Ramaswamy, R Reich, SJ Dou… – Antimicrobial agents …, 2003 – Am Soc Microbiol

Spoligotyping and major genetic group assignment.Low-copy-number isolates were subjected to a secondary typing method by use of spoligotyping. This method was performed with a commercially available kit (Isogen Bioscience BV, Maarssen, The Netherlands) according to

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Apport épidémiologique du typage moléculaire des bacilles de la tuberculose

V Vincent… – Médecine et Maladies Infectieuses, 2003 – Elsevier à partir d’un lysat cellulaire utilisé comme source d’ADN, puis hybridée à une membrane sur laquelle sont fixés les 43 séquences inter DR les plus fréquentes (la membrane est commercialisée par Isogen Bioscience BV, Maarsen, Hollande) (Fig. 2). Le spoligotyping est

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[CITATION] Multicenter Evaluation of Reverse Line Blot Assay to Predict Drug Resistance in Mycobacterium tuberculosis Clinical IsolatesI Mokrousov, NV Bhanu, PN Suffys, GV Kadival…

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EVALUATION OF THE EPIDEMIOLOGIC UTILITY OF SECONDARY TYPING METHODS FOR DIFFERENTIATION OF MYCOBACTERIUM TUBERCULOSIS ISOLATES

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A Kwara, R Schiro, LS Cowan… – Journal of clinical …, 2003 – Am Soc Microbiol

Spoligotyping (Isogen Bioscience BV, Maarssen, The Netherlands) was performed in accordance with previously published methods (8). Results were recorded as an octal code (4). MIRU loci (10) were amplified with primers specific for sequences flanking each locus (Table 1

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CHARACTERIZATION OF FINNISH MYCOBACTERIUM TUBERCULOSIS ISOLATES BY SPOLIGOTYPING

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K Puustinen, M Marjamäki, N Rastogi… – Journal of clinical …, 2003 – Am Soc Microbiol Spoligotyping was performed with a commercially available kit (Isogen Bioscience BV, Maarssen,The Netherlands) according to the instructions of the manufacturer. We analyzed 380 M.tuberculosis isolates by spoligotyping and obtained a total of 138 spoligotypes.

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WIDESPREAD PYRAZINAMIDE-RESISTANT MYCOBACTERIUM TUBERCULOSIS FAMILY IN A LOW-INCIDENCE SETTING

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D Nguyen, P Brassard, J Westley… – Journal of clinical …, 2003 – Am Soc Microbiol IS6110 RFLP by Southern blotting (38) and spoligotyping (Isogen Bioscience BV) (26) wereperformed using the observation that the DNA fingerprints by both IS6110 RFLP and spoligotypingare similar approximately 2 to 3.2 years (13, 42) and that of spoligotypes is believed to

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CHARACTERIZATION OF MYCOBACTERIUM TUBERCULOSIS COMPLEX DNAS FROM EGYPTIAN MUMMIES BYSPOLIGOTYPING

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AR Zink, C Sola, U Reischl, W Grabner… – Journal of clinical …, 2003 – Am Soc Microbiol For this analysis, we used a commercial spoligotyping kit (Isogen, Maarsen, The Netherlands it has been shown that the absence of spacers 33 to 36 in the spoligotyping signatures of absenceof spacers 33 to 36 (Table 4), most of the M. tuberculosis spoligotypes obtained from

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Tuberculosis recurrences: reinfection plays a role in a population whose clinical/epidemiological characteristics do not favor reinfection

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DG de Viedma, M Marin, S Hernangomez… – Archives of internal …, 2002 – Am Med Assoc The polymerase chain reaction (PCR) for amplifying the directed repeats region was performedusing primers of the spoligotyping kit (Isogen Bioscience, Maarssen, the Netherlands), followingthe manufacturer’s instructions. All spoligotypes showing differences for the strains

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[HTML] Molecular differentiation of Mycobacterium tuberculosis strains without IS6110 insertions

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KH Lok, WH Benjamin Jr, ME Kimerling… – Emerging infectious …, 2002 – ncbi.nlm.nih.gov Spoligotyping membranes were purchased from Isogen Bioscience BV (Isogen, Bilthoven, theNetherlands). repeats results of three zero-copy IS6110 isolates with identical spoligotyping andpolymorphic Fourteen of 32 spoligotyped strains are similar and have the same CDC

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Variable-number tandem repeat typing of Mycobacterium tuberculosis isolates with low copy numbers of IS6110 by using mycobacterial interspersed repetitive units

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LS Cowan, L Mosher, L Diem… – Journal of clinical …, 2002 – Am Soc Microbiol Spoligotyping.Spoligotyping was performed using a commercial kit (Isogen Bioscience BV,Maarssen, The Q could also be divided by IS6110 RFLP and spoligotyping into subclusters characterized by different insertion sites and divergent spoligotypes, as described

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Infection of red deer, cattle, and humans with Mycobacterium bovis subsp. caprae in western Austria

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WM Prodinger, A Eigentler… – Journal of clinical …, 2002 – Am Soc Microbiol on membranes with covalently bound, spacer sequence-specific oligonucleotides purchased from Isogen Bioscience BV region I isolates (3 cattle, 1 deer); lanes 5 to 9, spoligotypes from four wax-embedded tissue from that animal yielded the region II spoligotyping pattern (Fig.

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Transmission of drug-resistant tuberculosis in Texas and Mexico

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TN Quitugua, BJ Seaworth, SE Weis… – Journal of clinical …, 2002 – Am Soc Microbiol Locally synthesized and biotinylated PCR primers (Advanced Nucleic Acids TechnologyCore Facility, UTHSCSA) were used with commercially available spoligotyping membranes (Isogen, Maarssen, The Netherlands). Spoligotyping

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Spread of drug-resistant Mycobacterium tuberculosis strains of the Beijing genotype in the Archangel Oblast, Russia

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OS Toungoussova, P Sandven… – Journal of clinical …, 2002 – Am Soc Microbiol Spoligotyping was performed by using a commercially available kit (Isogen Bioscience BV …Spoligotyping.The spoligotyping method was used as an additional tool to further to the Beijing genotype by their IS6110 RFLP patterns showed identical spoligotypes, lacking spacers 1

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[HTML] Molecular typing of Mycobacterium tuberculosis strains with a common two-band IS6110 pattern

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KH Lok, WH Benjamin Jr, ME Kimerling… – Emerging infectious …, 2002 – ncbi.nlm.nih.gov Spoligotyping membranes were used according to manufacturer’s recommendations (Isogen Bioscience BV, Bilthoven well between these sizes, which could result in different spoligotypes of a Using VNTR and spoligotyping techniques to reexamine some of these clusters, we

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Sputum induction problems identified through genetic fingerprinting

B Nivin, T O’Flaherty, E Leibert, BY Zhao… – Infection control and …, 2002 – JSTOR Because spoligotyping is less discriminatory than IS6110-based analysis, identical spoligotypesmay indi- cate the need for further confirmation using the latter method. The spoligotyping analysiswas performed using a commercially available kit (Isogen Bioscience BV

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Isoniazid resistance, mycobacterial genotype and outcome in Vietnamese adults with tuberculous meningitis

GE Thwaites, TTH Chau, M Caws… – … of Tuberculosis and …, 2002 – ingentaconnect.com was car- ried out in accordance with a standardised protocol for spoligotyping.16 Briefly were heat-denatured and hybridised to the spoligotype membrane (Isogen Biosciences, Asmaars Patterns were compared against the Beijing and ‘Vietnam’ spoligotypes described by Anh et

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Biochemical and genetic evidence for the transfer of Mycobacterium tuberculosis subsp. caprae Aranaz et al. 1999 to the species Mycobacterium bovis Karlson and …

[PDF] from sgmjournals.org

S Niemann, E Richter… – International journal of …, 2002 – Soc General Microbiol Spoligotyping, which is based on the detection of various non- repetitive spacer sequences located between small repetitive units (direct blotting technique, was performed as described previously (Kamerbeek et al., 1997) by using a commercially available membrane (Isogen).

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Molecular epidemiology and drug resistance of Mycobacterium tuberculosis isolates from Ethiopian pulmonary tuberculosis patients with and without human …

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J Bruchfeld, G Aderaye, IB Palme… – Journal of clinical …, 2002 – Am Soc Microbiol synthetic spacer oligonucleotides which are covalently bound to a membrane (Isogen Bioscience BV 24, 41); and they all lacked the typical M. canetti spoligotyping patterns (presence of 3. Schematic representation of the spoligotypes of M. tuberculosis isolates belonging to four

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[HTML] Genotyping analyses of tuberculosis cases in US-and foreign-born Massachusetts residents

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S Sharnprapai, AC Miller, R Suruki… – Emerging infectious …, 2002 – ncbi.nlm.nih.gov with the molecular weight standards provided by CDC. Spoligotyping was performed with a commercially available kit, in accordance with the manufacturer’s instructions(Isogen Bioscience BV, Maarseen, the Netherlands).

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[HTML] Statewide Molecular Epidemiology of Mycobacterium tuberculosis Transmission in a Moderate-to Low-Incidence State: Are Contact Investigations Enough?

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WA Cronin, JE Golub, MJ Lathan… – Emerging Infectious …, 2002 – ncbi.nlm.nih.gov Spoligotyping was performed for all matching strains that had six or more IS6110copies by using a commercially available kit, according to the manufacturer’sinstructions (Isogen Bioscience BV, Maarssen, the Netherlands) (13).

Tuberculosis

[PDF] from ascpjournals.org

Q Eichbaum… – American Journal of Clinical …, 2002 – ajcp.ascpjournals.org Quentin Eichbaum, MD, PhD, MPH,1 and Eric J. Rubin, MD, PhD2 Key Words: Susceptibility;Rapid culture; Molecular beacons; Nested PCR; Ligation; Spoligotyping; Strains DOI:

10.1309/XX1NBANX8JKMTUQN Page 2. Eichbaum and Rubin / TUBERCULOSIS

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[HTML] STATEWIDE MOLECULAR EPIDEMIOLOGY OF MYCOBACTERIUM TUBERCULOSIS TRANSMISSION IN A MODERATE-TO LOW-INCIDENCE STATE: ARE CONTACT INVESTIGATIONS ENOUGH?

[HTML] from nih.gov

WA Cronin, JE Golub, MJ Lathan… – Emerging Infectious …, 2002 – ncbi.nlm.nih.gov Spoligotyping was performed for all matching strains that had six or more IS6110copies by using a commercially available kit, according to the manufacturer’sinstructions (Isogen Bioscience BV, Maarssen, the Netherlands) (13).

BIOCHEMICAL AND GENETIC EVIDENCE FOR THE TRANSFER OF MYCOBACTERIUM TUBERCULOSIS SUBSP. CAPRAE ARANAZ ET AL. 1999 TO THE SPECIES MYCOBACTERIUM BOVIS KARLSON AND …

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S Niemann, E Richter… – International journal of …, 2002 – Soc General Microbiol Spoligotyping, which is based on the detection of various non- repetitive spacer sequences locatedbetween small repetitive units (direct blotting technique, was performed as described previously(Kamerbeek et al., 1997) by using a commercially available membrane (Isogen).

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Transmission of Mycobacterium tuberculosis to a Funeral Director During Routine Embalming*

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M Lauzardo, P Lee, H Duncan… – Chest, 2001 – chestjournal.chestpubs.org Secondary strain typing of M tuberculosis was performed by spoligotyping (IsogenBioscience, BV; Maarssen, The Netherlands) as described by Kamerbeek et al. 10Spacer regions within the direct repeat locus of the chromosome Cited by 9Related articlesBL DirectAll 5 versionsImport into BibTeX

Epidemiologic Usefulness of Spoligotyping for Secondary Typing ofMycobacterium tuberculosis Isolates with Low Copy Numbers of IS6110

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WA Cronin, JE Golub, LS Magder… – Journal of clinical …, 2001 – Am Soc Microbiol Maryland culture-positive tuberculosis (TB) patients with low-copy IS6110-spoligotyped clustered strains investigation of low-copy clusters to those with rare spoligotypes may also In conclusion, spoligotyping did not appreciably improve strain differentiation among isolates with

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Mycobacterium tuberculosis complex DNA from an extinct bison dated 17,000 years before the present

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BM Rothschild, LD Martin, G Lev… – Clinical Infectious …, 2001 – cid.oxfordjournals.org The sequence was analyzed in an ABI PRISM 310 automated sequencer (PE Applied Biosystems).Spoligotyping. To determine the species of Mycobacterium within the M. tuberculosis complex,the spoligotyping system (Isogen) was applied in the Jerusalem laboratory.

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Spread of drug-resistant pulmonary tuberculosis in Estonia

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A Krüüner, SE Hoffner, H Sillastu… – Journal of clinical …, 2001 – Am Soc Microbiol Membranes for spoligotyping were obtained from Isogen, Bioscience BV, Utrecht, The Netherlands. Genetic homogenity of family A confirmed by spoligotyping.The 12 strains from family A showedan The spoligotypes of the non-Beijing family strains were highly diverse (Table 2

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Transmission dynamics and molecular characterization of Mycobacterium tuberculosis isolates with low copy numbers of IS6110

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H Soini, X Pan, L Teeter, JM Musser… – Journal of clinical …, 2001 – Am Soc Microbiol Spoligotyping was performed with a commercially available kit (Isogen Bioscience BV,Maarssen, The Netherlands) according to the instructions of the manufacturer. …Spoligotyping.A total of 72 spoligotypes was identified among the 377 isolates

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Identification of a contaminating Mycobacterium tuberculosis strain with a transposition of an IS6110insertion element resulting in an altered spoligotype

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WH Benjamin Jr, KH Lok, R Harris… – Journal of clinical …, 2001 – Am Soc Microbiol 36-bp direct repeats of M. tuberculosis, was done using membranes from Isogen BiosciencesBV of direct repeat regions and thus loss of spacers on spoligotyping have been The second report explains differences between two common spoligotypes found in the IS6110 Harlem

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Spoligotype diversity of Mycobacterium bovis strains isolated in France from 1979 to 2000

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N Haddad, A Ostyn, C Karoui… – Journal of clinical …, 2001 – Am Soc Microbiol “None” corresponds to departments where two or more spoligotypes were codominant (6), was used for the spoligotyping of M of 43 aminolink oligonucleotides by following the procedures recommended by the manufacturer of the oligonucleotides (Isogen Bioscience, Maarssen

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Risk of Mycobacterium tuberculosis transmission in a low-incidence country due to immigration from high-incidence areas

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T Lillebaek, ÅB Andersen, J Bauer… – Journal of clinical …, 2001 – Am Soc Microbiol For spoligotyping, DNA extraction was performed by mechanical disruption of the cells with glass beads by vortexing either a few colonies from solid media or 100 μl of the frozen culture stock(27). The membranes used (Isogen; Bioscience BV, Utrecht, The Netherlands

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TRANSMISSION OF MYCOBACTERIUM TUBERCULOSIS TO A FUNERAL DIRECTOR DURING ROUTINE EMBALMING*

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M Lauzardo, P Lee, H Duncan… – Chest, 2001 – chestjournal.chestpubs.org Secondary strain typing of M tuberculosis was performed by spoligotyping (Isogen Bioscience, BV; Maarssen, The Netherlands) as described by Kamerbeek et al. 10 Spacer regions within the direct repeat locus of the chromosome

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EPIDEMIOLOGIC USEFULNESS OF SPOLIGOTYPING FOR SECONDARY TYPING OFMYCOBACTERIUM TUBERCULOSIS ISOLATES WITH LOW COPY NUMBERS OF IS6110

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WA Cronin, JE Golub, LS Magder… – Journal of clinical …, 2001 – Am Soc Microbiol Maryland culture-positive tuberculosis (TB) patients with low-copy IS6110-spoligotyped clustered strains investigation of low-copy clusters to those with rare spoligotypes may also In conclusion, spoligotyping did not appreciably improve strain differentiation among isolates with

Cited by 29Related articles