A genome-wide scalable SNP genotyping assay using microarray technology


Oligonucleotide probe arrays have enabled massively parallel analysis of gene expression levels from a single cDNA sample. Application of microarray technology to analyzing genomic DNA has been stymied by the sequence complexity of the entire human genome. A robust, single base–resolution direct genomic assay would extend the reach of microarray technology. We developed an array-based whole-genome genotyping assay that does not require PCR and enables effectively unlimited multiplexing. The assay achieves a high signal-to-noise ratio by combining specific hybridization of picomolar concentrations of whole genome–amplified DNA to arrayed probes with allele-specific primer extension and signal amplification. As proof of principle, we genotyped several hundred previously characterized SNPs. The conversion rate, call rate and accuracy were comparable to those of high-performance PCR-based genotyping assays.

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Figure 1: WGG on DNA arrays.
Figure 2: WGA representation.
Figure 3: WGG on Sentrix array matrix using the WGG feasibility array.
Figure 4: Genotyping of HapMap quality control SNPs.


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We thank our Illumina colleagues in manufacturing for providing oligos and arrays and L. Zhou for generating the nonpolymorphic control sequences used in assay development. This work was supported in part by a US National Institutes of Health National Cancer Institute grant to K.L.G.

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Correspondence to Kevin L Gunderson.

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All authors are or were employees of Illumina, Inc. and may own stock or stock options in the company.

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Gunderson, K., Steemers, F., Lee, G. et al. A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet 37, 549–554 (2005) doi:10.1038/ng1547

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