Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays
Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays
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DOI：
10.1101/gr.8.5.435
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发表时间：
1998-05-01
期刊：
影响因子：
7
通讯作者：
Drenkow, J
中科院分区：
文献类型：
--
作者：
Gingeras, TR;Ghandour, G;Drenkow, J
高密度寡核苷酸阵列能够以高通量的方式快速检测大量的DNA序列。结核分枝杆菌rpoB基因705 bp特异核苷酸序列测定试剂盒准确检测出44株结核分枝杆菌临床分离株的利福平耐药突变。采用常规的rpoB和16S基因双脱氧核苷酸测序和rpoB寡核苷酸阵列杂交模式分析了121株分枝杆菌（包括10种）的核苷酸序列多样性。无论采用16S序列、rpoB序列还是rpoB杂交方式，每个分离株的鉴定结果都是相似的。然而，对于一些物种，16S和rpoB基因序列的等位基因数量提供了一个物种内遗传多样性的不一致估计。除了证实该阵列用于对结核分枝杆菌产生利福平耐药性的区域进行测序之外，这项工作还表明该阵列可以识别非结核分枝杆菌的种类。这证明了对重要基因组区域（如耐药性或致病性岛）进行测序的DNA微阵列可以同时识别物种并对生物体的种群结构提供一些见解。
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 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, 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.