Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing.
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.
Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.
Samuel
S
Myllykangas
Jason D
JD
Buenrostro
Georges
G
Natsoulis
John M
JM
Bell
Hanlee P
HP
Ji
D004273:DNA, Neoplasm / Q000235:genetics*; D005091:Exons; D052138:Genes, Neoplasm; D014644:Genetic Variation; D015894:Genome, Human / Q000235:genetics; D005854:Germ Cells / Q000737:chemistry*; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000737:chemistry / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011518:Proto-Oncogene Proteins / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras); D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods*; D018631:ras Proteins / Q000235:genetics
D004273:DNA, Neoplasm; C117307:KRAS protein, human; D011518:Proto-Oncogene Proteins; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins