Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays

Gingeras, T. R., Ghandour, G., Wang, E., Berno, A., Small, P. M., Drobniewski, F., Alland, D., Desmond, E., Holodniy, M., Drenkow, J. (1998) Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Research, 8 (5). pp. 435-448. ISSN 10889051 (ISSN) (Public Dataset)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/9582189
DOI: 10.1101/gr.8.5.435

Abstract

High-density oligonucleotide arrays can be used to rapidly examine large amounts of DNA sequence in a high throughput manner. An array designed to determine the specific nucleotide sequence of 705 bp of the rpoB gene of Mycobacterium tuberculosis accurately detected rifampin resistance associated with mutations of 44 clinical isolates of M. tuberculosis. The nucleotide sequence diversity in 121 Mycobacterial isolates (comprised of 10 species) was examined by both conventional dideoxynucleotide sequencing of the rpoB and 165 genes and by analysis of the rpoB oligonucleotide array hybridization patterns. Species identification for each of the isolates was similar irrespective of whether 16S sequence, rpoB sequence, or the pattern of rpoB hybridization was used. However, for several species, the number of alleles in the 16S and rpoB gene sequences provided discordant estimates of the genetic diversity within a species. In addition to confirming the array's intended utility for sequencing the region of M. tuberculosis that confers rifampin resistance, this work demonstrates that this array can identify the species of nontuberculous Mycobacteria. This demonstrates the general point that DNA microarrays that sequence important genomic regions (such as drug resistance or pathogenicity islands) can simultaneously identify species and provide some insight into the organism's population structure.

Item Type: Paper
Uncontrolled Keywords: bacterial dna oligonucleotide rifampicin antibiotic resistance article biodiversity dna hybridization dna sequence gene frequency gene mutation gene sequence genetic polymorphism genotype molecular cloning mycobacterium mycobacterium tuberculosis nonhuman nucleotide sequence polymerase chain reaction priority journal species differentiation Alleles DNA, Bacterial DNA-Directed RNA Polymerases Drug Resistance, Microbial Genes, Bacterial Molecular Sequence Data Mutagenesis Nucleic Acid Hybridization Oligonucleotides Polymorphism Genetic Rifampin RNA, Ribosomal 16S Sequence Analysis, DNA Species Specificity Actinobacteria class Bacteria (microorganisms) Corynebacterineae Prokaryota uncultured actinomycete
Subjects: bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
bioinformatics > genomics and proteomics > annotation > sequence annotation
organism description > bacteria
CSHL Authors:
Communities: CSHL labs > Gingeras lab
Depositing User: CSHL Librarian
Date: 1998
Date Deposited: 13 Mar 2012 16:13
Last Modified: 28 Mar 2014 19:49
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Dataset ID:
URI: http://repository.cshl.edu/id/eprint/25264

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