Tuesday, January 13, 2015

Weekly Links January 19,2015

“MUST READ”
o    Traditional forensic methods can’t differentiate between DNA belonging to identical twins
o    Using what’s known as ultra-deep, next-generation sequencing, a team in Germany has developed a test that claims to reliably identify which twin a biological sample belongs to
DISRUPTION, REVOLUTION
tags: NIPT
o    The first NIPT was released in October 2011 by Sequenom. Subsequently, six other companies globally have released their own NIPTs: Verinata Health, Ariosa Diagnostics and Natera in the United States, Berry Genomics and Beijing Genomics Institute (BGI) in China, and Premaitha Health in the UK. As an indication of how valuable this space is, genomics powerhouse Illumina purchased Verinata in January 2013 for USD$450 million and has publicly stated its plans to develop the first diagnostic version of the NIPT
o    In Europe payers have not been as responsive. Although the test is currently distributed in over 16 countries throughout Western and Eastern Europe, most patients will need to pay for the test out of pocket. Few nationalized health systems and private insurers in these regions currently reimburse for the test. In the UK, the National Health Service (NHS) is performing a five-year evaluation program, known as the RAPID project, to generate its own data and make a more informed decision about future reimbursement policies.
TOOLS/TECHNIQUES
o    Making a Next Generation Sequencing (NGS) library can seem a bit daunting to the new user, as failures can be expensive. But don’t be put off, as NGS library preparation is relatively simple molecular biology, and can be very easy if you choose to use a commercial kit from one of the many suppliers.
o    I’ve included some handy hints in this article to get you going on your way to preparing an awesome NGS library.

HEALTH/MEDECINE
tags: antibiotic
o    The discovery of teixobactin, the antibiotic, was published in the prestigious journal Nature, and at a time when most of the news in this area relates to scary drug-resistant superbugs, journalists pounced on the positive finding.   
Researchers who work on the problem of antibiotic resistance, however, were much less excited. To put it plainly, they think the media over-hyped the new "miracle drug" and had several important reservations about teixobactin and whether it would actually be helpful in humans. Here's what they said.
o    A team from Northeastern University/Bonn/Novobiotic (and Selcia) has published a very worthwhile paper in Nature on a new antibiotic, with a new mechanism of action, via a new discovery technology. The compound itself is not the world-changing new last line of defense that everyone's hoping for, but it's nothing to sneeze at, either. And the platform used to find it is worth keeping an eye on.
COMPANIES
o    In a deal that shakes up the full-steam-ahead world of cancer diagnostics, the world’s top oncology drug company, Roche, said today it’s spending more than $1 billion for a majority stake in Foundation Medicine and creating a powerful drug-diagnostic collaboration.
It’s a significant gamble on the as-yet-unrealized potential of tests that aim for broad genetic profiles of cancer patients’ tumors, one that Roche hopes can not only accelerate the impact of its broad range of cancer-fighting drug programs, but also extend the reach of its global diagnostics business.
tags: NIPT france                          
SAN DIEGO and SAINT-OUEN-L'AUMONE, France, Dec. 10, 2013 /PRNewswire/ -- Sequenom, Inc. (NASDAQ: SQNM), a life sciences company providing innovative testing and genetic analysis solutions, announced that Laboratoire Cerba has launched its validated noninvasive prenatal test (NIPT) to health care providers and their patients in France, Belgium, Luxembourg and portions of the Middle East and Africa. Laboratoire Cerba's test utilizes patented technology licensed from Sequenom to analyze the relative amounts of chromosomes 21, 18 and 13 in cell-free fetal DNA obtained from a maternal blood sample.
o    The San Diego-based DNA sequencing technology company (NASDAQ: ILMN) plans to consolidate most of its Bay Area operations — now spread between San Francisco's Mission Bay, Redwood City, Hayward and Santa Clara — at the 19-acre site off Highway 92 near the base of the San Mateo Bridge.
o    For the highest paid CEO in this group, John Martin at Gilead Sciences, the biggest portion of pay came from the $159 million in option profits he made in 2013, the latest year for which figures are available. While Gilead’s stock is up more than 350% in the last five years, that level of growth is dwarfed by the share price increase at Regeneron of more than 2,000% in the same period.
SOMETHING DIFFERENT
The Atlantic article tackles Hofstadter’s belief that, contrary to the machine learning approach, developing AI programmes can be a way of testing out ideas about the components of thought itself. This idea may be now starting to re-emerge.
tags: weeklylinks                                                                           
o    Douglas Hofstadter, the Pulitzer Prize–winning author of Gödel, Escher, Bach, thinks we've lost sight of what artificial intelligence really means. His stubborn quest to replicate the human mind.


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