New Chips with Rare Variants to Drive Growth in SNP Market

A setback in the scientific basis for single nucleotide polymorphisms (SNPs) analysis may turn out to be a blessing in disguise for makers of genotyping equipment, reagents, and software, according to recent market research.

The medical market research publisher, Kalorama Information (New York, NY, USA), foresees double-digit growth in equipment sales, chemicals, and software as more sophisticated chips enter the market with the ability to measure rarer variants.

SNP analysis has become an attractive method for identifying variations in DNA sequences for several reasons--SNPs are numerous, they account for over 80% of genetic variation in terms of quantity, they are stable through the generations, and they are easy to score. Moreover, the prices and the amount of content provided in SNP products have continued to improve, with the cost per genotype dropping on the order of 10-fold every two years since 2000.

While it was anticipated that the first round of genome-wide association studies would result in the discovery of many disease associations for common ailments, the results were disappointing, according to Kalorama Information. The scientific community had relied on the supposition that common diseases were caused by common variants, which would be elucidated with SNP chips containing variants having 5% frequency. In the end, it appears that such studies need to look at rare variants occurring at around 1% frequency or less.

SNP genotyping can only analyze the variants that have been provided on the chips. Therefore, if only 5 to 10 variants were required for a given disease, as initially believed, fewer samples would need to be run per study. However, if 100 rare variants are cumulatively responsible for a given complex disease, as seems to be the case, then it is necessary to study more people to get enough data for statistical significance. This situation is an opportunity for new products that provide new capabilities.

"Despite the recent challenges, there is still money to be made in this market,” noted Bruce Carlson, publisher of Kalorama Information. "The need to find rarer variants will require new chips and more samples, which means greater use of the machines and chemicals involved in the analysis process.”

New microarray chips with more DNA probes capable of measuring more variants are just making their way onto the market. Kalorama anticipates they will lead to a new surge in projects, with growth approaching historic levels. The same instruments can still function with these chips.

Kalorama estimates annual growth of the SNP analysis technologies market at 10.1%, from US$735 million in 2008 to approximately $1.3 billion in 2014. This growth will be driven mainly by whole-genome SNP analysis products in the near term. Longer term, the lower multiplexing products used in clinical trials will begin to account for more of the growth, as will the development of a side market in agriculture. Prices are expected to drop continuously, offsetting some of the growth from increased adoption.

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