comprehensive comparison of three commercial human whole-exome capture platforms综合比较三种商业载人whole-exome捕获平台.pdfVIP

Asan et al. Genome Biology 2011, 12:R95 /2011/12/9/R95 RESEARCH Open Access Comprehensive comparison of three commercial human whole-exome capture platforms 2,3*† 1† 1† 4† 4 1 1 1 1 Asan , Yu Xu , Hui Jiang , Chris Tyler-Smith , Yali Xue , Tao Jiang , Jiawei Wang , Mingzhi Wu , Xiao Liu , 1 1 1 1* 1* Geng Tian , Jun Wang , Jian Wang , Huangming Yang and Xiuqing Zhang Abstract Background: Exome sequencing, which allows the global analysis of protein coding sequences in the human genome, has become an effective and affordable approach to detecting causative genetic mutations in diseases. Currently, there are several commercial human exome capture platforms; however, the relative performances of these have not been characterized sufficiently to know which is best for a particular study. Results: We comprehensively compared three platforms: NimbleGen’s Sequence Capture Array and SeqCap EZ, and Agilent’s SureSelect. We assessed their performance in a variety of ways, including number of genes covered and capture efficacy. Differences that may impact on the choice of platform were that Agilent SureSelect covered approximately 1,100 more genes, while NimbleGen provided better flanking sequence capture. Although all three platforms achieved similar capture specificity of targeted regions, the NimbleGen platforms showed better uniformity of coverage and greater genotype sensitivity at 30- to 100-fold sequencing depth. All three platforms showed similar power in exome SNP calling, including medically relevant SNPs. Compared with genotyping and whole-genome sequencing data, the th