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Strides in cancer research, NIH consulting, and Lynx


One year ago this month, Genome Technology’s cover story attacked cancer from a handful of systems biology standpoints, from bioinformatics to RNAi. We spoke with Colin Hill, co-founder of Gene Network Sciences, who introduced us to his company’s approaches to modeling the mechanisms of cancer drugs. These days, the biosimulation firm’s technology is being used to classify patient subgroups and identify biomarkers in clinical settings thanks to a partnership with the Mary Crowley Medical Research Center.

In last year’s cancer special, Maciek Sasinowski also shared details on the genesis of Incogen’s modular mass spec version of the company’s VIBE software tool. Since talking with us, Sasinowski has been appointed to Virginia Governor Tim Kaine’s Technology Transition Committee, while the company has gone on to release a beta version of its bioinformatics education software, VIBE-Ed.

The NIH was the focus of a column in last year’s issue, back when emotions ran high in the wake of the release of guidelines prohibiting government researchers from consulting for pharma, biotech, and some public-sector institutions. At the time, some forecasted an exodus of researchers to academia or the private sector as a result of the policy. The sound and fury turned out to signify very little, as most government researchers remain at their posts one year later.

Five years ago, our cover story featured profiles of five DNA analysis facilities, some of which were the largest sequencing and genotyping operations in the world. The Beijing Genome Institute was one of the powerhouses covered. At the time, the institute mentioned its plans to sequence genomes of the indica rice strain, pig, and human chromosome 3. One year after our article ran, researchers at BGI published a draft sequence of the rice genome in Science. By spring of 2003, one of BGI’s research teams was among the first to sequence a strain of the SARS coronavirus. Later that year, BGI’s Hangzhou branch, in collaboration with Zhejiang University, founded a new research institute, the James D. Watson Institute of Genome Sciences. This spring, BGI will host the Post Genomics Summit 2006 meeting, which will focus on the influence of genomics on medicine.

In April 2001, our feature story looked at Lynx Therapeutics and its powerful bead-based sequencing tool. The MPSS technology fueling the Lynx product came from Sydney Brenner, who picked up a Nobel prize a year after our story ran. Last spring, Brenner devised a method to obtain sequence data from thousands of genomes simultaneously, and co-founded a company called Population Genetics Technologies to develop the platform. In the meantime, Lynx joined forces with Solexa, which made its debut on the Nasdaq National Market in February.

In lighter news, our Blunt End humor page five years ago featured Rick Wilson back when his center had just signed on to sequence the Y chromosome. Wilson regaled us with virile tales of tae kwon do, rock bands, and home-brewed beer. Upon being asked why the human X chromosome is so much longer than the Y, he replied, “Good things come in small packages.” To be fair, Wilson did add that he doesn’t “discriminate against any chromosomes.” Apparently not. In the last five years, Wilson has helped sequence a slew of genomes, including chromosomes 2, 4, and, of course, X.

— Jen Crebs


Don’t miss these upcoming features in the May issue:

Biomarkers approach the clinic

Research using biomarkers has grown tremendously over the past few years, but when will the fruits of these efforts reach the clinic? We’ll examine the different kinds of biomarkers — SNPs, protein expression, epigenetic marks, and more — and talk to experts to find out how close these tools are to being useful in a clinical setting.

Sequencing technology

For the past several years, scientists at companies and in academic institutions have been locked in a race to develop technology capable of sequencing a human genome for $1,000. The first of these tools has finally hit the market, and a handful more are getting close to commercialization as well. We’ll check in on how the available tools are faring, as well as on upcoming low-cost and high-throughput sequencing technologies.

The Scan

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.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.