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From: "Steven C. Perkins" <>
Subject: Genome wide SNP testing
Date: Tue, 05 Jul 2005 14:37:41 -0500


I don't remeber this being discussed. Getting closer to full testing for SNPs.

Regards,

Steven C. Perkins


Nature Genetics 37, 549 - 554 (2005)
Published online: 17 April 2005; | doi:10.1038/ng1547

A genome-wide scalable SNP genotyping assay using microarray technology

Kevin L Gunderson1, Frank J Steemers1, 4, Grace Lee1, 4, Leo G Mendoza2 &
Mark S Chee3

1 Illumina, Inc., 9885 Towne Centre Dr., San Diego, California 92121, USA.

2 Ambion, Inc., 2130 Woodward, Austin, Texas 78744, USA.

3 Prognosys Biosciences, Inc., 4215 Sorrento Valley Blvd., Suite 105, San
Diego, California 92121, USA.

4 These authors contributed equally to this work.
Correspondence should be addressed to Kevin L Gunderson
<mailto:>
[]

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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