Skip to main content

Thank you for visiting 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.

  • Brief Communication
  • Published:

Whole-genome genotyping with the single-base extension assay


We describe an efficient, accurate and robust whole-genome genotyping (WGG) assay based on a two-color, single-base extension (SBE), single-nucleotide polymorphism (SNP)-scoring step. We report genotyping results for biallelic International HapMap quality control (QC) SNPs using a single probe per locus. We show scalability, throughput and accuracy of the system by resequencing homozygous loci from our 100k Human-1 Genotyping BeadChip.

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

Access options

Buy this article

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

Figure 1: WGG with SBE.
Figure 2: Combined SBE resequencing and ASPE genotyping on the Sentrix Human-1 Genotyping BeadChip (100k exon-centric).

Similar content being viewed by others


  1. Syvanen, A.C. Nat. Genet. 37 (Suppl.), S5–10 (2005).

    Article  Google Scholar 

  2. Craig, D.W. & Stephan, D.A. Expert Rev. Mol. Diagn. 5, 159–170 (2005).

    Article  CAS  Google Scholar 

  3. Matsuzaki, H. et al. Nat. Methods 1, 109–111 (2004).

    Article  CAS  Google Scholar 

  4. Carlson, C.S., Eberle, M.A., Kruglyak, L. & Nickerson, D.A. Nature 429, 446–452 (2004).

    Article  CAS  Google Scholar 

  5. Gunderson, K.L., Steemers, F.J., Lee, G., Mendoza, L.G. & Chee, M.S. Nat. Genet. 37, 549–554 (2005).

    Article  CAS  Google Scholar 

  6. Gunderson, K.L. et al. In Genetic variance detection: technologies for pharmacogenomics (ed. Hecker, K.H.) 221–235 (DNA Press, Eagleville, Pennsylvania, 2005).

    Google Scholar 

  7. Pastinen, T. et al. Genome Res. 10, 1031–1042 (2000).

    Article  CAS  Google Scholar 

  8. Kuppuswamy, M.N. et al. Proc. Natl. Acad. Sci. USA 88, 1143–1147 (1991).

    Article  CAS  Google Scholar 

  9. Pastinen, T., Kurg, A., Metspalu, A., Peltonen, L. & Syvanen, A.C. Genome Res. 7, 606–614 (1997).

    Article  CAS  Google Scholar 

  10. Hirschhorn, J.N. et al. Proc. Natl. Acad. Sci. USA 97, 12164–12169 (2000).

    Article  CAS  Google Scholar 

  11. Wang, H.Y. et al. Genome Res. 15, 276–283 (2005).

    Article  CAS  Google Scholar 

  12. Gunderson, K.L. et al. Genome Res. 14, 870–877 (2004).

    Article  CAS  Google Scholar 

  13. Pinkel, D., Straume, T. & Gray, J.W. Proc. Natl. Acad. Sci. USA 83, 2934–2938 (1986).

    Article  CAS  Google Scholar 

  14. Fan, J.B. et al. Cold Spring Harb. Symp. Quant. Biol. LXVIII, 69–78 (2003).

    Article  Google Scholar 

Download references


We thank C. Allred for help with the grant applications and administration, M. Hansen for assistance in data analysis, E. Johnson, M. Graige and manufacturing department for bead pools and arrays, N. Espinosa and J. Stuelpnagel for manuscript suggestions. This work was supported in part by grants from the US National Institutes of Health (2R44CA103406-02) and National Cancer Institute (1R43CA108391-01).

Author information

Authors and Affiliations


Corresponding author

Correspondence to Kevin L Gunderson.

Ethics declarations

Competing interests

All authors have a financial interest in Illumina either via employment and/or stock ownership.

Supplementary information

Supplementary Fig. 1

Effect of SSB in the extension reaction. (PDF 71 kb)

Supplementary Table 1

Allele count and distribution over the SNP classes. (PDF 29 kb)

Supplementary Methods (PDF 85 kb)

Supplementary Discussion (PDF 77 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Steemers, F., Chang, W., Lee, G. et al. Whole-genome genotyping with the single-base extension assay. Nat Methods 3, 31–33 (2006).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


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