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

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...

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Bibliographic Details
Published inScience China. Life sciences Vol. 54; no. 10; pp. 945 - 952
Main Authors Jiang, Tao, Yang, Lei, Jiang, Hui, Tian, Geng, Zhang, XiuQing
Format Journal Article
LanguageEnglish
Published Beijing Science China Press 01.10.2011
Springer Nature B.V
Subjects
Analyzer
Biomedical and Life Sciences
Exons
Humans
Life Sciences
Oligonucleotide Array Sequence Analysis
Polymorphism, Single Nucleotide
Research Papers
全基因组扩增
单芯片
图书馆建设
外显子捕获
性能
探针阵列
测序方法
indel detection
SNP detection
high-throughput resequencing
whole exome sequencing
exon capture
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Summary: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.
Bibliography: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.
11-5841/Q
whole exome sequencing, exon capture, SNP detection, indel detection, high-throughput resequencing
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ISSN:1674-7305
1869-1889
DOI:10.1007/s11427-011-4232-4