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Next Generation Sequencing and Beyond

Methods to sequence DNA have been used in labs for 30 years. Why is there suddenly so much interest in sequencing technology and what is driving the growth of this market segment?

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Biotech / Biomedical Spotlight10

Whitehouse Releases Guidelines for the Bioeconomy

Saturday April 28, 2012

The White House just released a National Bioeconomy Blueprint which outlines initiatives and policies for Federal government agencies to advance and promote development of a broad range of biology-related industries from biofuels through environmental sciences. Of course, a large portion of the report the report focuses on the largest segment of the bioeconomy, biomedical research.  Two of the six outlined objectives target the major challenges with developing and launching new drugs, diagnostic tests, and medical devices.

In an effort to speed up the discovery of new drugs and disease markers, the blueprint talks about increasing support for translational research. Activities supporting this objective includes the National Center for Advancing Translational Sciences (NCATS) started the end of last year. NCATS is a publicly funded enterprise within the NIH that provides research support to identify and validate new drugs and drug targets.  This initiative addresses difficulties at the start of the drug development pipeline by expanding the potential validated drug candidates and finding additional druggable targets beyond the several hundred GPCRs, proteases, and kinases that are the focus of most current drug screening.  However, the blueprint also focuses on the regulatory challenges that limit the approval and launch of new therapeutics.

The same translational research objective that includes the above initiative also mentions the NIH/FDA collaborative Regulatory Science program.  Implemented to speed up development and adoption of advanced technology, such as nanotechnology and microdevices, in regulatory evaluations, this program aim to "more effectively evaluate product safety, efficacy and quality" of new drugs and diagnostics.  Another objective in the plan specifically targets regulations reform "to reduce barriers, increase the speed and predictability of regulatory processes, and reduce costs...." and include several activities targeted toward streamlining and improving FDA regulatory procedures.  It seems these actions might be very timely given recent criticism from some sectors that the FDA approval process is having a negative effect on drug development.

Read the National Bioeconomy Blueprint.

Researchers Find Age-Related Gene Regulators

Saturday April 28, 2012

Researchers in the UK appear to have found a set of epigenetically regulated genes that influence aging. The study published in the on-line journal PLoS Genetics associated chemical modifications in DNA (i.e., epigenetic marks) with age and aging characteristics, such as lung function, bone mineral density, blood pressure, of 172 female identical twins between 32 and 80 years old. They found 490 genes with that had changes in epigenetic marks that correlated with the age, but just 4 that correlated with differences in age-related traits, specifically LDL cholesterol levels, lung function, and maternal longevity (mother's lifespan).

The findings indicate that, with few exceptions, such as the examples related to cholesterol and lung function found in this study, most epigenetic changes related with aging do not appear regulate health conditions associated with old age.   However, some of the age-related epigenetic marks do appear to occur very early in life so it is still unclear what lifestyle and environmental factors might influence these, or even if they are inherited.

For more details, you can also read the announcement from King's College in London.

Roche Abandons Takeover of Illumina

Thursday April 26, 2012

Roche's $46.8 billion bid to take over Illumina fell through when Roche allowed it to expire last week after Illumina's shareholders rejected Roche's attempt to appoint its own directors to Illumina's board. Although Roche has been actively pursuing this deal since December last year and agreed to sweeten the offer from $44.50 per share in cash to $51.00 per in the end of March, Roche declined to pursue the company further after the latest rebuff.

Given the trend toward personalized medicine and continued growth of high-throughput next-generation sequencing market, it is likely Roche remains strategically very interested in advanced sequencing. However, in light of new systems recently coming on-line by other next-generation sequencing companies, like Life Technologies' Personal Genome Machine and Oxford Nanopore's MiniOn System in the last few months, perhaps Roche's confidence in the continued dominance of the Illumina platform has slipped a bit. Early reviews of Illumina's new MiSeq sequencer do seem to be quite positive though.  It will be interesting to see what Roche's next move will be.

For more details on the failed takeover, check out the articles on Bloomberg and the Wall Street Journal.

Supreme Court's Ruling against Prometheus Shakes Up Personalized Medicine

Thursday April 26, 2012

The Supreme Court's unanimous ruling last month that a Prometheus Laboratories' patents on a PCR-based blood test that looks at variations of a particular gene to determine an individual's dosage for a particular drug were not valid created somewhat of a sensation in the biotech sphere. Prometheus, part of Nestle Health Science, sued the Mayo Clinic when the clinic substituted its own in-house developed procedure for the $260 test that Prometheus sold to determine a patient's starting dose of the drug thiopurine, which is often used to treat inflammatory bowel diseases such as Crohn's disease or ulcerative colitis. Prometheus lost and the Court invalidated claims in two of its patents in a ruling that rippled in companies involved with personalized medicine.

The diagnostic test at the center of the dispute uses PCR to identify variations of the gene thiopurine methyltransferase (TPMT). Different variants of TPMT metabolize the drug at different rates so a doctor can infer which dosage of the drug to give a patient by identifying which genetic variation of TPMT that a patient has. The Supreme Court sided with the original ruling of the local district court that the test was unpatentable because it is an observation of a natural correlation between the gene and the metabolism rate of the drug.  In other words, the Court felt it is simply an observation not a patentable invention.

As evidenced by the range of coverage in biotech trade publications (e.g., GEN , GenomeWeb, The Scientist, and ScienceInsider), the ruling certainly stimulated significant discussion. At issue, it creates a lot of uncertainty for companies trying to protect their right to commercialize discoveries that relate clinical treatments with specific genetic variations. This the basis of emerging personalized medicine approaches.

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