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Drugs, proteomics, and next-gen sequencing


One year ago in Genome Technology, our cover story looked into the roles played by genomics and its cousins — think toxicogenomics, pharmacogenomics, and RNAi — in the realm of drug development. It was obvious then that pharma companies were making ample use of technologies and methods afforded by integrated biology, as evidenced by pushes to move systems biology downstream at Abbott, Millennium Pharmaceuticals, and Bristol-Myers Squibb.

These days, pharma appears more eager than ever to use such tools for the discovery and validation of both drug targets and biomarkers. Check out our feature story on p. 21 to see how a handful of proteomics-based biotech firms are helping pharma hit their targets, whether they be of the protein or fiscal variety.

This time last year, Roche Diagnostics signed a pact with 454 Life Sciences to distribute its next-gen sequencing instruments. By January of this year, Roche had sold a Genome Sequencer 20 system to Keygene, making it the first European customer to snatch up the device. Soon after, at the Plant and Animal Genome meeting, Keygene launched its CRoPS technology, a SNP discovery and detection tool developed with the 454 platform. Most recently, Roche and 454 introduced an updated version of the GS20, and the companies have further disclosed plans to release beta versions of a new sequencer later this year. The companies plan to formally launch that platform, to be called the Genome Sequencer 100, sometime in 2007.

Last year’s issue also featured a news item on Helicos, back when the company was ironing out details on the third incarnation of its sequencing device. At the time, the plan was to have beta instruments out this year, with a commercial system poised to hit the market in 2007. CEO Stan Lapidus is still talking about getting an instrument on the market next year, but no word yet on beta machines. In the meantime, Solexa officially launched its sequencer at the HUGO meeting in June, and Agencourt Personal Genomics, which was just acquired by Applied Biosystems, said it aims to have an instrument ready to go next year as well.

Five years ago, the July issue celebrated its first batch of “All-Stars” — that is, scientists with the most outstanding accomplishments in 2001, as chosen by readers. In those first heady months following the publication of the draft human genome, Eric Lander and Craig Venter pulled in the most votes in their respective categories.

The past five years have been busy for both men. Venter stepped down from Celera in January 2002, after which he founded the J. Craig Venter Institute, a nonprofit genomics research center. In 2004, Venter published results from his round-the-world sailing expedition during which he collected samples with which to conduct sequencing for metagenomic analysis. Eric Lander, meanwhile, may not have logged as many nautical miles but did manage to secure the promise of as much as $200 million from philanthropists Eli and Edythe Broad. That milestone in 2003 helped turn Lander's sequencing center into the Broad Institute, which just this year moved into a new building in Cambridge, Mass.

Jen Crebs



Next Month in GT

Don’t miss these features in the September issue:

New applications for microarrays

The tried-and-true gene expression technology has been commandeered for a host of new applications, from comparative genomic hybridization to molecular pathology. GT will canvass the sector to alert readers to the latest uses for chips.

Pathway modeling and analysis

Thanks to databases full of sequence, protein, and other systems biology information, scientists are finally able to start pulling data together to better understand how entire pathways function. We’ll talk to field leaders about what’s involved in pathway modeling and technology options for readers working in pathway analysis.


The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.