RT Journal
A1 Gingeras, Thomas R.
A1 Ghandour, Ghassan
A1 Wang, Eugene
A1 Berno, Anthony
A1 Small, Peter M.
A1 Drobniewski, Francis
A1 Alland, David
A1 Desmond, Edward
A1 Holodniy, Mark
A1 Drenkow, Jorg
T1 Simultaneous Genotyping and Species Identification Using Hybridization Pattern Recognition Analysis of Generic Mycobacterium DNA Arrays
JF Genome Research 
JO Genome Research 
YR 1998 
FD May 01 
VO 8 
IS 5 
SP 435 
OP 448 
DO 10.1101/gr.8.5.435 
UL http://genome.cshlp.org/content/8/5/435.abstract 
AB 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 therpoB 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 16S 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, rpoBsequence, or the pattern of rpoB hybridization was used. However, for several species, the number of alleles in the 16S andrpoB 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.[The sequence data described in this paper have been submitted to GenBank under accession nos. AF09766–AF059853 and AF060279–AF060367.]