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Adam Bonislawski is the editor of GenomeWeb's ProteoMonitor. He covers proteomics and life science mass spectrometry. E-mail Adam Bonislawski and follow his GenomeWeb Twitter account at @ProteoMonitor.
PicoPLEX DNA-Seq: Single Cell Sequencing, Theory and Applications
In this archived webinar, recorded Feb. 19, 2014, two speakers outline applications of Rubicon Genomics' PicoPLEX DNA-seq single cell library preparation kit. Jeramiah Smith, assistant professor of biology at the University of Kentucky, discusses the use of PicoPLEX DNA-seq for de novo sequencing of single amphibian chromosomes, while John Langmore, co-founder and chief scientific officer of Rubicon, details the use of PicoPLEX DNA-seq for aneuploidy, CNV, and STR testing of single human cancer and reproductive cells.
Speakers: Jeramiah Smith, Assistant Professor of Biology, University of Kentucky; and John Langmore, Co-Founder and Chief Scientific Officer, Rubicon Genomics
Sponsor: Rubicon Genomics
Recording Date: 2/19/2014
Recording Time: 1 hour
Young Investigator Profile
Pennsylvania State University
Connecting Phenotypes to SNPs
Bioinformatics, Sarah Pendergrass said, is a perfect match between her experience in engineering and her desire to be able to solve biological problems.
Pendergrass and her colleagues are working on what's been dubbed phenome-wide association studies, in which they study links between a number of SNPs and a range of phenotypes. She noted that they work with a number of different outcomes, both different types of datasets and different types of diseases or conditions, ranging from autism to lipid levels to cancer and to HIV.
"We're phenotype agnostic," Pendergrass said.
For example, one project she and her colleagues are currently working on is an electronic medical record-based PheWAS. This involves searching through electronic medical records — their source of phenotypes — to find variants linked to immune response. Another one, which she said is more pharmacogenomics-centered, draws on an HIV dataset as part of a clinical trial.
Researchers from Stanford University and Illumina publish details of a method for whole-genome haplotyping using a statistical algorithm to take advantage of the partially phased information contained in long genomic fragments analyzed by short-read sequencing. For a human sample, they report that as little as 30 gigabase pairs of additional sequencing data are needed to phase genotypes identified by 50x coverage whole-genome sequencing, and the team used the method to phase 99 percent of single-nucleotide variants in three human genomes into long haplotype blocks between 0.2 megabase pairs and 1 megabase pairs in length. "Our analysis yielded a base-resolution map of DNA methylation across a human genome, which is a valuable resource for understanding mechanisms involving allele-specific DNA methylation," they add.
The processes of cattle domestication and breed formation have left signs of selective sweeps in the genomes of modern-day cattle, according to a study by researchers in Germany and the US. Using millions of SNPs found through re-sequencing of 43 animals from a German cattle breed called Fleckvieh, the team narrowed in on more than 100 regions suspected of being subject to past selection. To that, the group added association mapping information gleaned from more than 3,000 cattle, identifying genes related to coat color and other cattle traits that overlapped with some apparent sites of selection.
People on the Move
Sequenom announced this week that CEO Harry Hixson plans to retire from that position in June, at the time of the company's stockholder meeting. Current President and Chief Operating Officer William Welch will assume Hixson's position upon his retirement. Hixson will continue to serve as chairman of the firm's board of directors, a title he has held since 2003. Welch also will be nominated to serve on the board at the annual meeting, Sequenom said. Also, CFO Paul Maier also will retire from his job in June, but will continue to work with the company as a consultant. Current VP and Chief Accounting Officer Carolyn Beaver will replace Maier as CFO upon his retirement. She previously was corporate VP and controller of Beckman Coulter. In addition, Dirk van den Boom will be promoted to be chief scientific and strategy officer. He has been with Sequenom since 1998, and he recently was the company's executive VP of R&D and chief technology officer.
Former Life Technologies executive Paul Grossman has joined Telegraph Hill Partners as a venture partner. Grossman previously was head of global strategy and corporate development at Life Tech, and he also held the same position at Invitrogen. Before he joined Invitrogen, Grossman held a variety of leadership roles at Applied Biosystems, including as a research scientist and patent attorney, VP of intellectual property, and VP of strategy and business development.
Becton Dickinson has appointed Amit Bhalla to be VP of global strategy and development. In the role, Bhalla will work with the senior management team to develop BD's overall strategy. Bhalla joins BD from Citi, where he has been director of equity research for life science tools and medical technology since 2006. Before joining Citi, he was VP of equity research for emerging medical technology at Morgan Stanley, and a technical operations R&D associate at Johnson and Johnson.
A pair of studies published in Science is providing a look at the genetic variants influencing the innate immune system's response to bacterial or viral pathogens. Along with variants influencing the expression of neighboring genes, the study helped define sets of more distant variants that orchestrate the broader immune response. The researchers also saw clues that at least some eQTLs mediating immune response early on during a bacterial infection are distinct from those at play later in the infectious process.
A new company called Human Longevity was launched this week by J. Craig Venter that will combine human genome, microbiome, and metabolome data coupled with clinical information to fuel development of new diagnostics, therapeutics, and stem cell treatments for diseases related to aging. Using $70 million in Series A financing, the firm plans to conduct genome, microbiome, and tumor sequencing on patients from the UCSD Moores Cancer Center and use their clinical phenotype and metabolomics data to create a massive database.
The 2015 federal budget proposal from the Obama Administration is seeking a marginal increase in funding for the National Institutes of Health — an increase of nearly one percent — to $30.36 billion from $30.15 billion in FY 2014. Under the proposed budget, the National Human Genome Research Institute would receive a $1 million increase to $498 million, while NCI would receive $8 million more this year, or $4.93 billion in total. United for Medical Research said the budget "falls short of reversing the damage done by a decade of flat funding ... and sequestration."