A genome-wide scalable SNP genotyping assay using microarray technology |
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Authors: | Gunderson Kevin L Steemers Frank J Lee Grace Mendoza Leo G Chee Mark S |
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Institution: | Illumina, Inc., 9885 Towne Centre Dr., San Diego, California 92121, USA. kgunderson@illumina.com |
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Abstract: | 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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