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Variagenics Gambles on SNP Function

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In the great gene debacle, half the industry went into hiding when both sequencing groups agreed on an estimate of roughly 30,000 genes — one-third to one-half of what most people predicted. So you’d think companies would hesitate before announcing estimates of anything else.

Not Variagenics, whose recently published study by Daniel Chasman and R. Mark Adams says about 26 to 32 percent of all SNPs in coding regions that change amino acid sequence have an effect on function — which could mean an effect on drug response rather than a direct effect on the protein itself, says Colin Dykes, vice president of research.

Variagenics uses a method that analyzes various parameters, some of which are considered especially important in function prediction; for instance, depth within molecule, conservation across species, flexibility in an evolutionary context, and changes between positive and negative charges.

The company has already applied these methods to its database of more than 20,000 SNPs. The goal is to select pivotal SNPs that are relatively common in the population and eventually to track down markers for drug response, Dykes says. But as far as more specifics on SNPs or potential profits from this — even Variagenics won’t put numbers on that.

— Meredith Salisbury

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