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New method of SNP discovery
By Bijal P. Trivedi

Researchers at the Whitehead Institute for Biomedical Research, in Cambridge, have been using a new technique called reduced representation shotgun (RRS) sequencing to discover SNPs.

RRS sequencing focuses on a portion of the genome that can simply and consistently be re-sampled. The researchers compared DNA sequences from 10 individuals at thousands of randomly selected sites scattered throughout the genome to find each SNP. The paper, published in this week's Nature, reports the discovery of 47,172 SNPs.

"The method is most valuable for finding SNPs in genomes where you don't have the complete sequence, like the dog or one of the major crop plants," says Eric Lander, of the Whitehead Institute.

David Bentley's group at the Sanger Centre, in Cambridge, UK, used the same strategy to find SNPs but focused their efforts on Chromosome 22. A map of the 2,730 SNPs discovered by the UK team is also published in this week's Nature.

Both these papers represent the pilot studies for RRS. But since their submission to the journal, much of the human genome has been sequenced. "With most of the sequence known, the most efficient method of SNP identification is the genomic-alignment strategy," says Lander. This method aligns individual shotgun sequences with the publicly available sequence to identify new SNPs.

Both the UK and US team are members of the SNP Consortium, an international mix of pharmaceutical companies, academic centers and a private foundation, whose goal has been to identify 300,000 SNPs. Using RRS and genome alignment the Consortium has now identified more that 350,00 SNPs.

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Altshuler, D. et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513-516 (September 28, 2000).
Mullikin, J.C. et al. An SNP map of human chromosome 22. Nature 407, 516-520 (September 28, 2000).

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