A month ago, Science magazine named the study of human genetic variation as the breakthrough of the year in 2007. Speaking at the JPMorgan Healthcare Conference, being held this week is San Francisco, Dr Stephen Fodor, CEO of Affymetrix outlined new products the firm plans to launch in the next year.
Studying human genetic variation can help explain the complex roots of many diseases and guide drug development and diagnostics. The concept of personalised medicine is reliant on our understanding of our genetic code. According to Fodor, the newest technology is "clearly driving the marketplace."
Fodor said that in several landmark studies which helped Science to its conclusion, Affymetrix "played a critical role". In particular he highlighted the Wellcome Trust Case Control Consortium project and a copy number variation map being published by the International Genome Structural Variation Consortium.
The firm believes one of the next challenges is to identify more rare DNA sequence variations. Another is that current copy number approaches are based on around one million markers across the genome. However, a higher density of markers is needed to yield higher resolution data on structural variation.
However, any advance needs to be cost-effective as studies could potentially have hundreds of thousands of samples to analyse.
The first area Affymetrix has been focussing on is new chemistry techniques, such as a new higher yield synthesis technique - up to 75 bases long and in both directions. This is being used to fabricate high-density whole-genome targeted arrays - arrays that will capture portions of the genome.
The first product that will be launched - around the first half of 2008 - is an ultra-high resolution number copy tool.
"This product will allow us to analyse the genome at around 30 times the resolution of the current state-of-the-art technology in the marketplace," claimed Fodor.
The product consists of a set of three chips that contain 30 million 50-mers that span the genome, 10 million on each chip across the non-repetitive working parts of the genome.
Affymetrix's second plan is to incorporate enzymatic sequence reactions directly onto microarray chips. Fodor explained that both polymerase and ligase labelling reactions can be applied to target any or all of the genome.
In order to validate the tool, the firm is screening the entire human variation database - some 12.5 million polymorphisms - against the extended diversity panel of 1,100 individuals. The data gained can then be used "to design next-generation products" that can, for example, look at up to 10 million assays per chip, said Fodor.