Whole-genome sequencing and variant discovery in C-elegans
Whole-genome sequencing and variant discovery in C-elegans
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DOI：
10.1038/nmeth.1179
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发表时间：
2008-02-01
期刊：
影响因子：
48
通讯作者：
Mardis, Elaine R.
中科院分区：
文献类型：
--
作者：
Hillier, LaDeana W.;Marth, Gabor T.;Mardis, Elaine R.
大规模并行测序仪器能够快速而廉价地产生DNA序列数据。由于这些仪器是新的，它们的数据需要在准确性和实用性方面进行描述。为了解决这个问题，我们使用Solexa Sequence Analyzer对Caernohabditis elegans N2Bristol菌株分离株进行了测序，并将读数与参考基因组进行了比较，以表征数据并评估覆盖率和代表性。大规模并行测序促进了全基因组序列变异发现的菌株与参比菌株的比较。由于产生了短读取长度的序列，我们开发了一种修订的方法来确定基因组中可以唯一定位短读取序列的区域。然后，我们将线虫菌株CB4858的Solexa读数与参考序列进行了比对，并筛选了单核苷酸多态(SNPs)和小Indels。这项研究证明了大规模并行短读测序对于全基因组重测序和准确发现全基因组多态的实用性。
Massively parallel sequencing instruments enable rapid and inexpensive DNA sequence data production. Because these instruments are new, their data require characterization with respect to accuracy and utility. To address this, we sequenced a Caernohabditis elegans N2 Bristol strain isolate using the Solexa Sequence Analyzer, and compared the reads to the reference genome to characterize the data and to evaluate coverage and representation. Massively parallel sequencing facilitates strain-to-reference comparison for genome-wide sequence variant discovery. Owing to the short-read-length sequences produced, we developed a revised approach to determine the regions of the genome to which short reads could be uniquely mapped. We then aligned Solexa reads from C. elegans strain CB4858 to the reference, and screened for single-nucleotide polymorphisms (SNPs) and small indels. This study demonstrates the utility of massively parallel short read sequencing for whole genome resequencing and for accurate discovery of genome-wide polymorphisms.