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

Nature Biotechnology
Samuel MyllykangasHanlee P Ji

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.

References

May 15, 2012·Nucleic Acids Research·René BöttcherP J van der Zaag
Feb 1, 2012·Genome Medicine·Hanlee P Ji
May 31, 2013·Genome Medicine·Peidong ShenCurt Scharfe
Oct 12, 2013·PloS One·Michael S AkhrasNader Pourmand
May 2, 2014·Nucleic Acids Research·Erik S HopmansHanlee P Ji
Dec 16, 2011·BMC Biotechnology·Samuel MyllykangasHanlee P Ji
Feb 2, 2016·Nature Biotechnology·Grace X Y ZhengHanlee P Ji
Dec 17, 2014·BMC Medical Genomics·Dorin ManaseSeema Mital
Feb 19, 2015·American Journal of Medical Genetics. Part a·Anita HiippalaTero-Pekka Alastalo
Aug 8, 2015·Molecular Genetics & Genomic Medicine·Sanna VattulainenSamuel Myllykangas
Jun 19, 2015·European Heart Journal·Oyediran AkinrinadeTiina Heliö
Jul 18, 2014·Genomics & Informatics·Eun-Hye KimByung Chul Kim
Oct 27, 2015·Journal of Cardiovascular Magnetic Resonance : Official Journal of the Society for Cardiovascular Magnetic Resonance·Pauli PöyhönenMiia Holmström
Jun 22, 2016·Nucleic Acids Research·Li C XiaNancy R Zhang

Citations

Jan 28, 2005·Nature·E HoskinsonThomas M Haard
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Aug 6, 2005·Science·Jay ShendureGeorge M Church
Aug 12, 2005·Cytogenetic and Genome Research·J JurkaJ Walichiewicz
Dec 31, 2005·Nucleic Acids Research·Erich M SchwarzPaul W Sternberg
Oct 16, 2007·Nature Methods·Thomas J AlbertRichard A Gibbs
Oct 16, 2007·Nature Methods·Gregory J PorrecaJay Shendure
Oct 16, 2007·Nature Methods·David T OkouMichael E Zwick
Nov 6, 2007·Nature Genetics·Emily HodgesW Richard McCombie
Nov 7, 2008·Nature·David R BentleyAnthony J Smith
Apr 8, 2009·Nature Methods·Emily H TurnerJay Shendure
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jan 30, 2010·Nature Methods·Lira MamanovaDaniel J Turner

Related Concepts

Exons
Genome
Tumor Tissue Sample
Colorectal Neoplasms
DNA, Neoplasm
DNA Resequencing
Sequencing
Gametes
Oligonucleotide Primers
Colorectal Cancer Pathway

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