Skip to main content

Advertisement

SpringerLink
Log in

Direct selection of human genomic loci by microarray hybridization

  • Brief Communication
  • Published:

From Nature Methods

View current issue Submit your manuscript

This article has been updated

Abstract

We applied high-density microarrays to the enrichment of specific sequences from the human genome for high-throughput sequencing. After capture of 6,726 approximately 500-base 'exon' segments, and of 'locus-specific' regions ranging in size from 200 kb to 5 Mb, followed by sequencing on a 454 Life Sciences FLX sequencer, most sequence reads represented selection targets. These direct selection methods supersede multiplex PCR for the large-scale analysis of genomic regions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1: Schematic of the microarray direct genomic selection scheme.
Figure 2: Captured sequences.
Figure 3: Sequence coverage depth.

Similar content being viewed by others

Change history

  • 21 October 2007

    In the version of this article initially published online, e-mail address of the corresponding author was incorrect. The correct address should be talbert@nimblegen.com. The error has been corrected for all versions of the article.

References

  1. Mullis, K.B. & Faloona, F.A. Methods Enzymol. 155, 335–350 (1987).

    Article  CAS  Google Scholar 

  2. Nuwaysir, E.F. et al. Genome Res. 12, 1749–1755 (2002).

    Article  CAS  Google Scholar 

  3. Albert, T.J. et al. Nucleic Acids Res. 31, e35 (2003).

    Article  Google Scholar 

  4. Margulies, M. et al. Nature 437, 376–380 (2005).

    Article  CAS  Google Scholar 

  5. Bashiardes, S. et al. Nat. Methods 2, 63–69 (2005).

    Article  CAS  Google Scholar 

  6. Dahl, F. et al. Proc. Natl. Acad. Sci. USA 104, 9387–9392 (2007).

    Article  CAS  Google Scholar 

  7. Porreca, G.J. et al. Nat. Methods advance online publication 14 October 2007 (doi:10.1038/nmeth1110).

    Article  CAS  Google Scholar 

  8. Okou, D.T. et al. Nat. Methods advance online publication 14 October 2007 (doi:10.1038/nmeth1109).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank M. Zwick and D. Okou for helpful conversations, and the US National Human Genome Research Institute (grant U54 HG003273) and the US National Cancer Institute (grant R21HG004553) for support for this effort.

Author information

Authors and Affiliations

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

    Thomas J Albert, Michael N Molla, Todd A Richmond, Chris M Middle, Matthew J Rodesch & Charles J Packard

  2. Human Genome Sequencing Center, One Baylor Plaza, Houston, 77030, Texas, USA

    Donna M Muzny, Lynne Nazareth, David Wheeler, Xingzhi Song, George M Weinstock & Richard A Gibbs

Authors
  1. Thomas J Albert
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michael N Molla
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Donna M Muzny
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lynne Nazareth
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. David Wheeler
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xingzhi Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Todd A Richmond
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Chris M Middle
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Matthew J Rodesch
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Charles J Packard
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. George M Weinstock
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Richard A Gibbs
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

T.J.A., G.M.W. and R.A.G., experimental design, analysis and interpretation; M.N.M. and T.A.R., experimental design and data analysis; D.M.M. and L.N., sequencing; D.W. and X.S., data analysis; C.M.M. and C.J.P., laboratory experimentation (arrays); M.J.R., experimental design and laboratory experimentation (arrays).

Corresponding authors

Correspondence to Thomas J Albert or Richard A Gibbs.

Ethics declarations

Competing interests

T.J.A., M.N.M, T.A.R., C.M.M., M.J.R. and C.J.P are employed by NimbleGen Systems.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–3, Supplementary Methods (PDF 146 kb)

Supplementary Table 4

Exon target regions. (XLS 398 kb)

Supplementary Data 1

Selection microarray probe Sequences. (ZIP 57089 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Albert, T., Molla, M., Muzny, D. et al. Direct selection of human genomic loci by microarray hybridization. Nat Methods 4, 903–905 (2007). https://doi.org/10.1038/nmeth1111

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth1111

  • Springer Nature America, Inc.

This article is cited by

Search

Navigation