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PGx in the Recent and Distant Past, Next-Gen Sequencers, and Nanotech

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In Genome Technology’s May 2006 cover story, we talked about biomarkers being “on the horizon.” Well, it looks like the sun has finally risen. At the time, experts spoke about the challenges behind discovery and, more importantly, verification. Today, Metabolon, one of the story’s featured companies, has emerged as a leader in the field of metabolomics, which uses the metabolome to find novel biomarkers in the early stages of drug development. Over the course of the second half of 2006, Metabolon launched a three-product series of metabolomic drug safety and efficacy testing solutions: mSelect, mProveClinical, and mVivo.

Also on the fast track, next-gen sequencing has seen a major growth spurt since we reported on it last May. Then, 454 Life Sciences was the only manufacturer to have placed instruments in the market, and users were invited to talk shop. Concerns then, as now, revolved around read length and how to best reconcile precision with the robust and high-throughput reads of the traditional Sanger method. Competitors Agencourt Biosciences, Helicos BioSciences, and Solexa had yet to launch their respective instruments. Fast forward one year, and the market looks very different: Helicos stands to be the only publicly traded pure-play next-gen company after announcing plans for an IPO early this year. The landscape of scrappy startups has shifted considerably with the purchases of Agencourt Personal Genomics by Applied Biosystems in May 2006, Solexa by Illumina in January 2007, and 454 by Roche in March 2007.

Five years ago, our May 2002 cover story made pharmacogenomics a punching bag, asking experts and an invited roundtable of panelists to talk about whether the “pharmacogenomics payback is years to come.” Not only was George Poste’s hunch correct — Poste signed the first multimillion-dollar deal between SmithKline Beecham and Human Genome Sciences in 1993 — but it was prophetic. The goal of PGx, he said, was to get “higher quality targets and an understanding of how they function in various populations.” Five years later, many pharma companies are warming up to PGx when it helps them run clinical trials more efficiently and save precious R&D dollars. More than 200 companies are starting to employ PGx strategies in their early R&D, and the FDA has updated a number of drug labels with information regarding genetic testing.

Finally, a feature story in 2002 checked out many of the “first practical applications” of nanotechnology for genomics and proteomics, since at the time it was unclear whether they would offer real value. The field has exploded, with nanotechnology research and development in the US having grown into a $2 billion industry. The NSF-funded National Nanotechnology Infrastructure Network launched in 2004, and will operate a network of 13 university research sites led by Cornell over the next five years. Invitrogen purchased Quantum Dot, one of the startups we profiled, in October 2005. It hopes to put to use Quantum Dot’s semiconductor nanocrystals in gene expression and high-throughput drug screening assays.

The Scan

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Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.