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Nat Biotechnol. 2011 Dec 18;30(1):78-82. doi: 10.1038/nbt.2065.

Performance comparison of whole-genome sequencing platforms.

Author information

  • 1Department of Genetics, Stanford University, Stanford, California, USA.

Erratum in

  • Nat Biotechnol. 2012 Jun;30(6):562.

Abstract

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.

PMID:
22178993
[PubMed - indexed for MEDLINE]
PMCID:
PMC4076012
Free PMC Article

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