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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.

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


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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).

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Correspondence to Kevin L Gunderson.

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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)

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

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