Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing

Nat Biotechnol. 2011 Oct 23;29(11):1024-7. doi: 10.1038/nbt.1996.

Abstract

We describe an approach for targeted genome resequencing, called oligonucleotide-selective sequencing (OS-Seq), in which we modify the immobilized lawn of oligonucleotide primers of a next-generation DNA sequencer to function as both a capture and sequencing substrate. We apply OS-Seq to resequence the exons of either 10 or 344 cancer genes from human DNA samples. In our assessment of capture performance, >87% of the captured sequence originated from the intended target region with sequencing coverage falling within a tenfold range for a majority of all targets. Single nucleotide variants (SNVs) called from OS-Seq data agreed with >95% of variants obtained from whole-genome sequencing of the same individual. We also demonstrate mutation discovery from a colorectal cancer tumor sample matched with normal tissue. Overall, we show the robust performance and utility of OS-Seq for the resequencing analysis of human germline and cancer genomes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Neoplasm / genetics*
  • Exons
  • Genes, Neoplasm*
  • Genetic Variation
  • Genome, Human / genetics
  • Germ Cells / chemistry*
  • Humans
  • Mutation
  • Neoplasms / chemistry
  • Neoplasms / genetics*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Proto-Oncogene Proteins / genetics
  • Proto-Oncogene Proteins p21(ras)
  • Sequence Analysis, DNA / instrumentation
  • Sequence Analysis, DNA / methods*
  • ras Proteins / genetics

Substances

  • DNA, Neoplasm
  • KRAS protein, human
  • Proto-Oncogene Proteins
  • Proto-Oncogene Proteins p21(ras)
  • ras Proteins