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 ∼76×, 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 ∼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.
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Sequence Read Archive
Ajay, S.S., Parker, S.C., Ozel Abaan, H., Fuentes Fajardo, K.V. & Margulies, E.H. Accurate and comprehensive sequencing of personal genomes. Genome Research 21, 1498–1505 (2011).
Ashley, E.A. et al. Clinical assessment incorporating a personal genome. Lancet 375, 1525–1535 (2010).
Wheeler, D.A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872–876 (2008).
McKernan, K.J. et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 19, 1527–1541 (2009).
Roach, J.C. et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636–639 (2010).
Pushkarev, D., Neff, N. & Quake, S. Single-molecule sequencing of an individual human genome. Nat. Biotechnol. 27, 847–852 (2009).
Korbel, J.O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420–426 (2007).
Snyder, M., Du, J. & Gerstein, M. Personal genome sequencing: current approaches and challenges. Genes Dev. 24, 423–431 (2010).
Rios, J., Stein, E., Shendure, J., Hobbs, H.H. & Cohen, J.C. Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Hum. Mol. Genet. 19, 4313–4318 (2010).
Lee, W. et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465, 473–477 (2010).
The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).
Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
Sherry, S.T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311 (2001).
Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
Chen, R., Davydov, E.V., Sirota, M. & Butte, A.J. Non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association. PLoS ONE 5, e13574 (2010).
Kaur, I. et al. Variants in the 10q26 gene cluster (LOC387715 and HTRA1) exhibit enhanced risk of age-related macular degeneration along with CFH in Indian patients. Invest. Ophthalmol. Vis. Sci. 49, 1771–1776 (2008).
Tam, P.O. et al. HTRA1 variants in exudative age-related macular degeneration and interactions with smoking and CFH. Invest. Ophthalmol. Vis. Sci. 49, 2357–2365 (2008).
Yamaguchi, H. et al. Mutations in TERT, the gene for telomerase reverse transcriptase, in aplastic anemia. N. Engl. J. Med. 352, 1413–1424 (2005).
Albers, C.A. et al. Dindel: Accurate indel calls from short-read data. Genome Res. 21, 961–973 (2011).
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
Clark, M.J. et al. Performance comparison of exome DNA sequencing technologies. Nat. Biotechnol. 29, 908–914 (2011).
This work is supported by the Stanford Department of Genetics and the US National Institutes of Health.
M.S. is a scientific advisory board member for Genapsys, Inc.; a scientific advisory board member and cofounder of Personalis, Inc.; and a consultant for Illumina.
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Lam, H., Clark, M., Chen, R. et al. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol 30, 78–82 (2012) doi:10.1038/nbt.2065
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