Performance comparison of whole-genome sequencing platforms

被引：218

作者：

Lam, Hugo Y. K. ^{[1
]}

Clark, Michael J. ^{[1
]}

Chen, Rui ^{[1
]}

Chen, Rong ^{[2
]}

Natsoulis, Georges ^{[3
]}

O'Huallachain, Maeve ^{[1
]}

Dewey, Frederick E. ^{[4
]}

Habegger, Lukas ^{[5
]}

Ashley, Euan A. ^{[4
]}

Gerstein, Mark B. ^{[5
,6
,7
]}

Butte, Atul J. ^{[2
]}

Ji, Hanlee P. ^{[3
]}

Snyder, Michael ^{[1
]}

机构：

[1] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[2] Stanford Univ, Dept Pediat, Div Syst Med, Stanford, CA 94305 USA

[3] Stanford Univ, Dept Med, Stanford, CA 94305 USA

[4] Stanford Univ, Ctr Inherited Cardiovasc Dis, Div Cardiovasc Med, Stanford, CA 94305 USA

[5] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT USA

[6] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT USA

[7] Yale Univ, Dept Comp Sci, New Haven, CT 06520 USA

来源：

NATURE BIOTECHNOLOGY | 2012年 / 30卷 / 01期

基金：

美国国家卫生研究院;

关键词：

MACULAR DEGENERATION; STRUCTURAL VARIATION; PERSONAL GENOME; SHORT-READ; VARIANTS; GENE; ACCURATE; CFH;

D O I：

10.1038/nbt.2065

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Whole-genome sequencing is becoming commonplace, but the accuracy and completeness of variant calling by the most widely used platforms from Illumina and Complete Genomics have not been reported. Here we sequenced the genome of an individual with both technologies to a high average coverage of similar to 76x, and compared their performance with respect to sequence coverage and calling of single-nucleotide variants (SNVs), insertions and deletions (indels). Although 88.1% of the similar to 3.7 million unique SNVs were concordant between platforms, there were tens of thousands of platform-specific calls located in genes and other genomic regions. In contrast, 26.5% of indels were concordant between platforms. Target enrichment validated 92.7% of the concordant SNVs, whereas validation by genotyping array revealed a sensitivity of 99.3%. The validation experiments also suggested that >60% of the platform-specific variants were indeed present in the genome. Our results have important implications for understanding the accuracy and completeness of the genome sequencing platforms.

引用

页码：78 / U118

页数：6

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