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Uduak Grace Thomas is the editor of GenomeWeb's BioInform. She covers bioinformatics, computational biology, and life science informatics. E-mail Uduak Grace Thomas or follow her GenomeWeb Twitter account at @BioInformGW.
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
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.
Ardy Arianpour has joined Pathway Genomics as chief strategy officer, the company said this week.
Arianpour most recently was senior VP of business development at Ambry Genetics, and during his 13-year career in the biotech sector he also has worked in senior sales and business development roles at Clinical Data, Cogenics, and Eurogentec North America. In his new post, Arianpour will lead the San Diego-based company's global strategy, strategic planning, and partnership activities.
Kevin Shianna has left the New York Genome Center, where he was most recently deputy scientific director of sequencing operations. His role has been taken over by Soren Germer and Dayna Oschwald, who both joined the NYGC in early 2012 as sequencing program managers.
A multi-center study performed by researchers from Tufts Medical Center, Illumina, and elsewhere suggests fetal aneuploidy screening based on cell-free DNA sequencing from pregnant women's blood finds fewer false-positive cases than standard serum screening methods in a general population of pregnant women. Based on findings from the study, Illumina's Richard Rava argued that the cell-free DNA screening strategy "really merits consideration as a primary [fetal aneuploidy] screen for the entire obstetrical population."
Laboratory Corporation of America Holdings has acquired Covance's high-complexity genomic laboratory, and the firms entered into a five-year services agreement under which they will continue to offer Covance's laboratory's services to clients. The lab offers gene expression studies, translational biomarker projects, and next-generation sequencing to support drug development work. Covance said it will provide other genomics services to its clients through its central laboratories.
The recently signed Agriculture Act of 2014 authorizes Congress to spend $700 million to fund researchers across the country who are using a range of biotechnology, genomics, and molecular biology approaches to develop better food crops and biofuels, study plant diseases, and improve livestock. The bill provides $200 million to create a new independent entity to be called the Foundation for Food and Agriculture Research, and $400 million will support research through the Specialty Crop Research Initiative.