Friday, 2 December 2011

HPCwire: Genomics Drowning in Data

The leap forward in genomics technology promises to change health care as we know it. Sequencing a human genome, which costs millions of dollars just a few years ago, now costs thousands. And the prospect of mapping a genome for under a thousand dollars is on the horizon.

But cheap gene sequencing, by itself, won't usher in a health care revolution. Anarticle in the New York Times  this week points out that turning those sequenced genomes into something useful is the true bottleneck. Doctors would like to be able to use their patients genome to determine their susceptibility to specific diseases or to devise personalized treatments for conditions they already have.

Sequencing all the DNA base pairs is really the easy part of the problem. It just reflects the ordering of these bases -- adenine (A) , thymine (T), guanine (G), cytosine (C) -- in the chromosomes. The bioinformatics software necessary to extract useful information from this low-level biomolecular alphabet is much more complex and therefore costly, and necessitates a fair amount of computing power.

According to David Haussler, director of the center for biomolecular science and engineering at the University of California, Santa Cruz, that's why it costs more to analyze a genome than to sequence it, and that discrepancy is expected to grow as the cost of sequencing falls.

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