The Mountain View, California-based company Perlegen recently made public the completion of its search for single nucleotide polymorphisms (SNPs) in the human genome. Following the November 2001 publication in Science of a SNP map of human chromosome 21, Perlegen scientists say they sequenced 50 complete haploid genomes, yielding more than 1.7 million SNPs.

More important, according to Perlegen CEO Brad Margus, was their demonstration that they could interrogate all 1.7 million SNPs in massively parallel fashion, opening the door for genome-wide association studies, which previously could not be attempted because of the prohibitive cost of genotyping.

Key to this work were high-density oligonucleotide arrays, which Perlegen scientists designed and had fabricated by Affymetrix, Perlegen's parent company. Amplifying the entire human genome required nearly 250,000 PCR assays, and more than 12 billion oligonucleotide probes were used to sequence the 50 haploid chromosomes. The company claims their system can complete a...

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