Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Mapping duplicated sequences

Nature Biotechnology volume 27, pages 1001–1002 (2009)Cite this article

Duplicated genomic regions are accurately resolved using an optimized algorithm for mapping reads from next-generation sequencers.

Copy number variation (CNV), or differences in the number of copies of multi-kilobase segments of the genome, is a major source of genetic diversity, with several variants now conclusively linked to human disease. But existing methods for analyzing CNV tend to go astray at recently duplicated regions of the genome, where much of this variation arises. As described in Nature Genetics, Alkan et al.1 have developed a computational method for using next-generation sequencing to measure segmental copy number even in recently duplicated regions. Their approach opens a new avenue for exploring relationships between genetic and phenotypic variation.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Placement of multireads indicates copy number changes in duplicated genomic regions (blue boxes).

References

  1. Alkan, C. et al. Nat. Genet. 41, 1061–1067 (2009).

    Article  CAS  Google Scholar 

  2. Weiss, L.A. et al. N. Engl. J. Med. 358, 667–675 (2008).

    Article  CAS  Google Scholar 

  3. Stefansson, H. et al. Nature 455, 232–236 (2008).

    Article  CAS  Google Scholar 

  4. Stone, J.L. et al. Nature 455, 237–241 (2008).

    Article  CAS  Google Scholar 

  5. McCarroll, S.A. et al. Nat. Genet. 40, 1107–1112 (2008).

    Article  CAS  Google Scholar 

  6. Willer, C.J. et al. Nat. Genet. 41, 25–34 (2009).

    Article  CAS  Google Scholar 

  7. Perry, G.H. et al. Nat. Genet. 39, 1256–1260 (2007).

    Article  CAS  Google Scholar 

  8. Hollox, E.J. et al. Nat. Genet. 40, 23–25 (2008).

    Article  CAS  Google Scholar 

  9. Campbell, P.J. et al. Nat. Genet. 40, 722–729 (2008).

    Article  CAS  Google Scholar 

  10. Chiang, D.Y. et al. Nat. Methods 6, 99–103 (2009).

    Article  CAS  Google Scholar 

  11. Yoon, S. et al. Genome Res. 19, 1586–1592 (2009).

    Article  CAS  Google Scholar 

  12. Pushkarev, D. et al. Nat. Biotechnol. 27, 847–852 (2009).

    Article  CAS  Google Scholar 

  13. Eid, J. et al. Science 323, 133–138 (2009).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Derek Y. Chiang is at the University of North Carolina, Chapel Hill, North Carolina, USA.,

    Derek Y Chiang

  2. Steven A. McCarroll is at Harvard Medical School, Boston, Massachusetts, USA.,

    Steven A McCarroll

Authors
  1. Derek Y Chiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Steven A McCarroll
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Derek Y Chiang or Steven A McCarroll.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Chiang, D., McCarroll, S. Mapping duplicated sequences. Nat Biotechnol 27, 1001–1002 (2009). https://doi.org/10.1038/nbt1109-1001

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt1109-1001

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing