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Genome-wide in situ exon capture for selective resequencing

Nature Genetics volume 39, pages 1522–1527 (2007)Cite this article

Abstract

Increasingly powerful sequencing technologies are ushering in an era of personal genome sequences and raising the possibility of using such information to guide medical decisions. Genome resequencing also promises to accelerate the identification of disease-associated mutations. Roughly 98% of the human genome is composed of repeats and intergenic or non–protein-coding sequences. Thus, it is crucial to focus resequencing on high-value genomic regions. Protein-coding exons represent one such type of high-value target. We have developed a method of using flexible, high-density microarrays to capture any desired fraction of the human genome, in this case corresponding to more than 200,000 protein-coding exons. Depending on the precise protocol, up to 55–85% of the captured fragments are associated with targeted regions and up to 98% of intended exons can be recovered. This methodology provides an adaptable route toward rapid and efficient resequencing of any sizeable, non-repeat portion of the human genome.

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Figure 1: Array-based exon selection scheme followed by Illumina 1G sequencing.
Figure 2: Read-exon distance distributions.
Figure 3: Pairwise comparisons of exon-capture specificity.
Figure 4: Exon coverage versus Illumina 1G read depth.
Figure 5: Effect of a variant input DNA preparation on capture efficiency and read depth.

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Acknowledgements

The authors thank M.Q. Zhang and A. Smith for their help in the read mapping and analysis, J. Silva for providing the MCF10A cell line DNA, and M. Rooks, S. McCarthy and members of the McCombie and Hannon laboratories for helpful discussion. G.J.H. is an Investigator of the Howard Hughes Medical Institute and is supported in part by a kind gift from Kathryn W. Davis and major support from the Stanley Foundation. Purchase of instrumentation and this work were supported in part by grants from the US National Science Foundation and National Institutes of Health (M.Q. Zhang, G.J.H. and W.R.M.).

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Author notes

  1. Emily Hodges and Zhenyu Xuan: These authors contributed equally to this work.

Authors and Affiliations

  1. Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, 11724, New York, USA

    Emily Hodges, Zhenyu Xuan & Gregory J Hannon

  2. Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, 11724, New York, USA

    Zhenyu Xuan, Vivekanand Balija, Melissa Kramer & W Richard McCombie

  3. NimbleGen Systems, Inc., 1 Science Court, Madison, 53711, Wisconsin, USA

    Michael N Molla, Steven W Smith, Christina M Middle, Matthew J Rodesch & Thomas J Albert

Authors
  1. Emily Hodges
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  2. Zhenyu Xuan
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  3. Vivekanand Balija
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  4. Melissa Kramer
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  5. Michael N Molla
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  6. Steven W Smith
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  7. Christina M Middle
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  8. Matthew J Rodesch
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  9. Thomas J Albert
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  10. Gregory J Hannon
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  11. W Richard McCombie
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Corresponding authors

Correspondence to Gregory J Hannon or W Richard McCombie.

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Competing interests

T.J.A., M.N.M., S.W.S., C.M.M. and M.J.R. are employees of Nimblegen, Inc.

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Hodges, E., Xuan, Z., Balija, V. et al. Genome-wide in situ exon capture for selective resequencing. Nat Genet 39, 1522–1527 (2007). https://doi.org/10.1038/ng.2007.42

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