Full-text access for premium subscribers only.
Existing premium subscribers login here.
New to GenomeWeb? Register here quickly.
Julia Karow tracks trends in next-generation sequencing for research and clinical applications for GenomeWeb's In Sequence and Clinical Sequencing News. E-mail Julia Karow or follow her GenomeWeb Twitter accounts at @InSequence and @ClinSeqNews.
When she was growing up in Australia, Felicity Jones' family spent a lot of time outdoors, going on hikes or camping, and Jones became fascinated with the biodiversity that she saw.
"I got very interested in that when I was really young and knew that I would be really interested to try and understand, 'Where did that come from and how did that happen?' And try to understand general principles about how species evolve," Jones said.
To study those evolutionary processes, she has focused on the stickleback fish as her model organism. It, she noted, has diverged repeatedly and in parallel, making it a good natural system to study since it has those built-in replicates.
Currently, her lab is using genomic tools to examine the molecular mechanisms underlying species divergence and adaptation to new environments.
University of Virginia researchers describe an algorithm for finding new structural variants in whole-genome sequencing data. The breakpoint prediction approach, called LUMPY, integrates several types of structural variant information in read data — from split reads and read pairs in alignment data to read depth — in multiple sample datasets, the study's authors say. Their comparison suggests LUMPY compares favorably with other structural variant detection methods. In a previously sequenced human genome, for example, the method identified more than 4,500 new or known structural variant breakpoints.
A team from the University of North Carolina, Chapel Hill, presents details of a new method for RNA motif discovery. Their approach, known as selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling, or SHAPE-MaP, enables de novo and large-scale identification of RNA functional motifs. In their paper, the researchers used the method to define a new model for the HIV-1 RNA genome, which contains all known structured motifs and previously unknown elements, including experimentally validated pseudoknots.
People on the Move
Peter Dansky, formerly the president of the molecular and cell biology division at Life Technologies, has joined Agena Bioscience as its CEO and a member of its board of directors. He will lead Agena's expansion of its genetic analysis business into new application areas including clinical diagnostics. Previously, he held management positions at Arcturus Bioscience, Affymetrix, Molecular Dynamics, PerSeptive BioSystems and Millipore.
Mark Guyer has retired from his post as deputy director of the National Human Genome Research Institute. Guyer joined the Office of Human Genome Research, the institute's precursor, in 1998, and he helped guide NHGRI's research activities from the earliest days of the Human Genome Project. He became director of the NHGRI Division of Extramural Research, now the Extramural Research Program, and he has had a hand in establishing programs such as the 1,000 Genomes Project; the Large-Scale Genome Sequencing and Analysis Centers; the Ethical, Legal and Social Implications research program; and The Cancer Genome Atlas project, among others.
Omicia has appointed Heidi Rehm, Geoffrey Ginsberg, Thomas Quertermous, and Mark Yandell to its scientific advisory board. Rehm is director of the Laboratory for Molecular Medicine at Partners Healthcare Personalized Medicine and associate professor of pathology at Harvard Medical School. Ginsberg is director of genomic medicine at the Duke Institute for Genome Sciences & Policy, executive director of Duke's Center for Personalized Medicine and Precision, and a professor of medicine and biomedical engineering. Quertermous is the William G. Irwin professor of medicine and director of research for the division of cardiovascular medicine at Stanford University. Yandell is co-director of the University of Utah's USTAR Center for Genetic Discovery and a professor of human genetics, and a co-inventor of Omicia's VAAST and Phevor algorithms.
Adaptive Biotechnologies has tapped Dean Schorno to be chief financial officer. Schorno held leadership positions at Genomic Health over a 13-year period, including most recently as CFO, where he helped manage the launch and operations of the company's clinical lab.
Conferences, Meetings & Deadlines
MSACL 2014 EU
September 2-5 / Salzburg, Austria
The Association for Mass Spectrometry Applications to the Clinical Lab
In a study appearing in Nature, researchers from China, France, and the UK described a gut microbiome signature for identifying individuals with liver cirrhosis. After tossing out gut microbial community members that seemed to be shared between individuals with liver cirrhosis and other conditions such as type 2 diabetes and inflammatory bowel disease, the investigators were left with 15 bacterial species suspected of being specific to liver cirrhosis. They noted that the overall diversity and gene richness was higher in the gut microbial communities from healthy individuals studied.
Saying that it does not believe its Chemical and Applied Markets division can achieve "acceptable financial performance" in the next two years, Bruker said that it plans to sell and/or restructure certain parts of the CAM business, resulting in an expected 200 to 250 layoffs. Bruker said the planned actions would result in a reduction in annual run-rate revenues of between $50 million and $70 million, while profits are estimated to improve by $15 million to $20 million per year upon the completion of the reorganization. CAM was formed in 2010 following Bruker's purchase of certain Varian businesses.
US Senator Tom Harkin (D – Iowa) plans to introduce the Accelerating Biomedical Research Act sometime later this month in an effort to let NIH restore some of the funding it has lost in recent years due to flat budgets and sequestration. The legislation would free up appropriators in the Senate and House of Representatives and target NIH for funding boosts while other agencies would remain stuck under hard spending caps imposed last year. If the legislation, currently still in draft form, passes, NIH could see an increase of nearly $3 billion next year. By 2021, NIH would receive as much as $46.2 billion.
This online seminar will discuss the discovery and evaluation of gene expression signatures associated with cancer treatment outcomes. These presentations will provide an overview of the promise of tumor microenvironment profiling in the radiation oncology setting, as well as the challenges in applying genomic methods to biomarker discovery.