Whole-Genome Genotyping on Microarrays

To map most of the genetic variation in the human genome, scientists need to look at several hundred thousand single nucleotide polymorphisms (SNPs) per individual.

Charles Choi
Jul 3, 2005

To map most of the genetic variation in the human genome, scientists need to look at several hundred thousand single nucleotide polymorphisms (SNPs) per individual. Most genotyping assays employ polymerase chain reaction (PCR) to make the genome's 3 billion base complexity manageable. But ideally these assays would mirror gene expression and employ a single-tube assay to readout all the loci in an array-based assay.

Kevin Gunderson and colleagues at Illumina in San Diego recently developed a whole-genome genotyping assay that bypasses PCR's multiplexing issues, using a single-tube amplification reaction combined with direct array readout via primer extension.1 The technique was 99.9% concordant with Illumina's PCR-based GoldenGate assay.

"There's a strong need for technologies that can do large-scale genotyping for hundreds of thousands to millions of SNPs accurately and at a low cost, and the technology that Gunderson developed appears to have all three," says Thomas Hudson of McGill University...

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