Gary Patti was studying bacterial resistance when he realized that to understand what was going on, he was going to have to analyze a lot of metabolites. That led him to using NMR, but since that approach could only tackle a hundred or so metabolites at once, he started using mass spectrometry. That, in turn, led him to finding a fellowship in a metabolomics lab.
"It fit with the way that I thought about science really well so it's just accelerated even though I am no longer doing any work with bacterial resistance," Patti said. Instead, his lab at WashU is focusing on cancer and chronic pain.
A challenge of dealing with metabolomic data, as compared to genomic or proteomic data, is that metabolites are less well defined. Genes are made up of nucleotides and proteins of amino acids, but metabolites are much more diverse, Patti said.
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
Epic Sciences has appointed Greg Lucier as chairman of its board of directors. Lucier was previously chairman and CEO of Life Technologies.
Illumina said this week it has appointed Google Senior Vice President Jeff Huber to serve on its board of directors. Huber, who works with the Google X research branch, joined Google in 2003 and led development of Google Maps, Google Apps, and Google Ads. He also formerly was VP of architecture and systems development at eBay, and senior VP of engineering at Excite@Home.
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.
Conferences, Meetings & Deadlines
MSACL 2014 EU
September 2-5 / Salzburg, Austria
The Association for Mass Spectrometry Applications to the Clinical Lab
A study in the American Journal of Human Genetics suggests healthy individuals may pass on somatic mutations present in a small subset of their cells, playing a previously under-appreciated role in the risk of certain genetic conditions. Along with the new biological insights it provides, the work may eventually have clinical applications, the researchers noted, particularly for understanding how likely it is that a family that has one child with a rare genomic disorder will go on to have another.
PathoGenetix has filed for Chapter 7 bankruptcy in US Bankruptcy Court District of Massachusetts. The firm, formerly called US Genomics, had developed a genotyping technology called Genome Sequencing Scanning for detecting pathogens in environmental samples. Last year the company raised $10 million in a Series C financing round, and it was planning to launch its Resolution Microbial Genotyping System in the third quarter of this year with assays to identify and serotype Salmonella and pathogenic E. coli strains.
UK Prime Minster David Cameron has unveiled a £311 million ($523 million) investment package that includes a partnership between Genomics England and Illumina and will fund its national genome sequencing initiative, the 100,000 Genomes Project. As part of the plan Illumina will receive £78 million to support Genomics England with whole genome sequencing services, infrastructure, and expertise. In turn, Illumina has pledged to invest £162 million into the work in England over a four-year period.
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.