Life Technologies Fires Latest Sequencing Salvo
Another week, another drop in the cost of whole-genome sequencing. The latest announcement comes from Life Technologies, which yesterday announced the launch of its SOLiD 4 sequencing system. The details of the announcement are well-covered by GenomeWeb and Matthew Herper of Forbes.com.
In brief, the SOLiD 4 generates 100 gigabases of data per run at a cost of $6,000 per genome, a cost that appears to account solely for the consumables and does not include the cost of the machine or of interpreting all of that sequence data. According to GenomeWeb, Life is also promising an upgrade to its system – SOLiD 4hq – in the second half of 2010 which it expects to triple the data output at half of the cost: 300 megabases per run, $3,000 per sequence.
As for the impact of Life’s SOLiD 4 announcement, Matthew Herper hits the nail on the head:
But although the news is good for Life and will keep it in the game as the price of decoding the genetic code continues to drop, the specs of this new machine don’t seem good enough to upset Illumina’s place as the first choice of geneticists. “It’s a solid improvement, but I don’t think this changes the game,” says Isaac Ro, an analyst at Leerink Swan who follows both companies.
Meet the New deCODE, Same as the Old deCODE?
When deCODE genetics declared bankruptcy last fall it made a big splash. Geneticists pondered the future of the Icelandic biotechnology company’s one-of-a-kind genetic database and research platform, while investors and creditors wondered if they were going to be left out in the cold.
The initial bankruptcy buzz gave way over the past several months to a steady but relatively unremarkable stream of filings in the United States Bankruptcy Court for the District of Delaware (the case is No. 09-14063). Last week, however, brought a noteworthy docket entry, with the bankruptcy court approving the sale of most of deCODE genetics Inc.’s assets to Saga Investments LLC (pdf) – an investment company whose owners include Polaris Venture Partners, ARCH Venture Partners and genomic sequencing giant (and DTC genomics dabbler) Illumina.
A Holiday Fire-Sale? The sale, as approved by the bankruptcy court, sends substantially all of deCODE genetics Inc.’s assets – including its valuable genetic research engine that is driven in part by its access to its large Icelandic population database – to Saga Investments. As we described back in November, the bankruptcy sale process required a Stalking Horse bidder (Saga Investments) and a sale and auction process that, at least in theory, allowed other interested parties a chance to step in and make a bid for deCODE’s assets. No other bidders came forward, and the sale to Saga Investments was approved in just under two months.
Back to the Future: NIH to Revisit Genomic Data-Sharing Policy
As first reported by GenomeWeb, last week the NIH issued a “Notice on Development of Data Sharing Policy for Sequence and Related Genomic Data.” Although the title doesn’t exactly trip off of the tongue, the NIH’s announcement provides an opportunity to review where we are and where we have already been when it comes to genomic data-sharing.
At the heart of the NIH’s announcement is a desire to increase the availability of genomic datasets. From last week’s notice:
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Consistent with the NIH mission to improve public health through research and the longstanding NIH policy to make data publicly available from the research activities that it funds, the NIH has concluded that the full value of sequence-based genomic data can best be realized by making the sequence, as well as other genomic and phenotype datasets derived from large-scale studies, available as broadly as possible to a wide range of scientific investigators.
For NIH-funded genomic researchers, this language should have a familiar ring. In 2007, the NIH published a policy covering data-sharing for genome-wide association studies (GWAS) that required all NIH-funded GWAS research be deposited in a central data repository. Here’s the mission statement from the 2007 policy:
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NCI’s New BRCA1 Test: Broader Utility and Another Challenge to Traditional Genetic Tests
Contributed by Allison Williams Dobson of the Center for Genomics and Society at the University of North Carolina at Chapel Hill.
As reported last week by GenomeWeb, on September 21, 2009, a team led by Shyam Sharan from the National Cancer Institute (NCI) published the development of a new BRCA1 test based on mouse embryonic stem cells. Potentially, the test could prove useful for a much broader range of patients than the controversial Myriad Genetics BRCA1 tests.
The NCI approach focuses more on protein production than DNA analysis. The BRCA1 gene serves as the blueprint for an important tumor suppressor protein. If BRCA1 protein is not produced in sufficient quality and/or quantity, a propensity to develop cancer in the breast tissue often results. The traditional genetic testing approach asks whether a subject carries any of the BRCA1 gene variants that have been associated with increased risk for breast cancer in studies of afflicted families. NCI’s approach asks a significantly different question—rather than focusing on an identified set of “bad” gene variants, NCI asks whether a subject carries BRCA1 variants that serve as adequate blueprints for a functional protein, whether those variants have been previously identified or not. It does this by testing the protein product of the gene.
Until now, women with a family history of breast cancer have been most likely to seek a BRCA genetic test and represent the principal source of BRCA genetic data. Thus Myriad’s patented tests are based on a set of culprit BRCA gene variants found by studying primarily families with a strong propensity toward breast cancer, despite the fact that only 5-7 % of breast cancers are familial. As a result, the Myriad tests only offer useful information about a subset of BRCA1 variants. But many people (both with and without family history) carry other BRCA1 variants of unknown significance (VUS). There just are not enough empirical data yet to support conclusions about the risk associated with VUS.
