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

Nature Biotechnology volume 29, pages 10241027 (2011) | Download Citation

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.

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Acknowledgements

This work was supported by the US National Institutes of Health grants K08CA96879 (H.P.J.), DK56339 (H.P.J.), P01HG000205 (J.D.B., J.M.B. and H.P.J.), RC2HG005570 (G.N., J.M.B. and H.P.J.), R21CA140089 (G.N., J.M.B. and H.P.J.), the Sigrid Jusélius Foundation Fellowship (S.M.), the Academy of Finland Grant (S.M.), Doris Duke Clinical Foundation Clinical Scientist Development Award (H.P.J.), the Howard Hughes Medical Foundation Early Career Grant (H.P.J.), the Reddere Foundation Award (H.P.J.), the Liu Bie Ju Cha and Family Fellowship in Cancer (H.P.J.), and the Wang Family Foundation Research Grant (G.N. and H.P.J.).

Author information

Author notes

    • Samuel Myllykangas
    •  & Jason D Buenrostro

    These authors contributed equally to this work.

Affiliations

  1. Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.

    • Samuel Myllykangas
    • , Georges Natsoulis
    •  & Hanlee P Ji
  2. Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA.

    • Jason D Buenrostro
    • , John M Bell
    •  & Hanlee P Ji

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Contributions

The project was conceived and experiments planned by S.M., J.D.B. and H.P.J. S.M. and J.D.B. carried out all experiments. J.D.B., S.M., J.M.B., G.N. and H.P.J. performed data analysis. J.D.B., S.M., J.M.B. and H.P.J. wrote the manuscript, and all authors reviewed it. All aspects of the study were supervised by H.P.J.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Hanlee P Ji.

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    Supplementary Tables 1–3, Supplementary Methods and Supplementary Figures 1–8

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DOI

https://doi.org/10.1038/nbt.1996

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