High-performance single-chip exon capture allows accurate whole exome sequencing using the Illumina Genome Analyzer  

作　　者：JIANG Tao YANG Lei JIANG Hui TIAN Geng ZHANG XiuQing 

机构地区：[1]Beijing Genomics Institute, Shenzhen 518000, China [2]Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China [3]Graduate University of Chinese Academy of Sciences, Beijing 100062, China

出　　处：《Science China(Life Sciences)》2011年第10期945-952,共8页中国科学（生命科学英文版）

基　　金：supported by the Chinese Academy of Sciences (Grant Nos.GJHZ0701-6 and KSCX-YWN-023);the National Natural Science Foundation of China (Grant Nos.30725008,90403130,90608010,30221004,90612019 and 30392130);the National Basic Research Program of China (Grant Nos.2007CB815701,2007CB815703 and 2007CB815705)

摘　　要：Here we present an adaptation of NimbleGen 2.1M-probe array sequence capture for whole exome sequencing using the Illumina Genome Analyzer (GA) platform.The protocol involves two-stage library construction.The specificity of exome enrichment was approximately 80% with 95.6% even coverage of the 34 Mb target region at an average sequencing depth of 33-fold.Comparison of our results with whole genome shot-gun resequencing results showed that the exome SNP calls gave only 0.97% false positive and 6.27% false negative variants.Our protocol is also well suited for use with whole genome amplified DNA.The results presented here indicate that there is a promising future for large-scale population genomics and medical studies using a whole exome sequencing approach.Here we present an adaptation of NimbleGen 2.1M-probe array sequence capture for whole exome sequencing using the Illumina Genome Analyzer （GA） platform. The protocol involves two-stage library construction. The specificity of exome enrichment was approximately 80% with 95.6% even coverage of the 34 Mb target region at an average sequencing depth of 33-fold. Comparison of our results with whole genome shot-gun resequencing results showed that the exome SNP calls gave only 0.97% false positive and 6.27% false negative variants. Our protocol is also well suited for use with whole genome amplified DNA. The results presented here indicate that there is a promising future for large-scale population genomics and medical studies using a whole exome sequencing approach.

关 键 词：whole exome sequencing exon capture SNP detection indel detection high-throughput resequencing 

分 类 号：Q78[生物学—分子生物学] Q75