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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
University of Kentucky
What Underlies Diversity
When she was little, Catherine Linnen liked picking up whatever bugs or lizards she could find outside. And so it was only natural that she grew up to study the diversity of the natural world.
"I always liked living things and thought they were fascinating," she said.
In particular, Linnen is now curious about the genetic mechanisms underlying that diversity and how species adapt. Her work currently focuses on two natural populations: deer mice and pine sawflies.
After the glaciers retreated in North America some 8,000 to 10,000 years ago, mice moved into the Sand Hills region of Nebraska and adapted to that environment. Mice living there have lighter coats and a different tail stripe pattern than other mice. In this system, Linnen and her colleagues are exploring the genes and mutations responsible for the mice adapting to that environment.
Similarly, the pine sawflies have adapted to different host pine trees — including one that was introduced to North America within the last couple of hundred years — and she and her colleagues are studying the mechanisms driving that adaptation.
An international team led by investigators in the UK and Argentina describe population structure, ancestry profiles, and admixture patterns detected through SNP testing on more than 7,300 individuals from Brazil, Chile, Colombia, Mexico, and Peru. Using information at a few dozen informative SNPs, the researchers estimated relative proportions of African, European, and Native American ancestry in the genomes of those tested, looking at not only at population structure, but also at ancestry patterns associated with individuals' physical traits and self-reported ancestry. While individuals' perception of their own ancestry often correlated with genetic information, for instance, the study's authors found that "certain physical attributes have a strong impact on self-perception and bias self-perception of ancestry relative to genetically estimated ancestry."
The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development Chen, Bracht, et al. Cell
Researchers from the US and Switzerland sequenced the germline genome of the single-celled ciliate Oxytricha trifallax in an effort to understand the characteristic genome disassembly and rearrangement that the organism undergoes during development. When the team compared the Oxytricha germline genome — found in its micronucleus — to sequences from the organism's transcriptionally active somatic macronucleus, it uncovered more than 3,500 genes that are scrambled in the somatic genome, along with genes that get post-translationally modified as the genome is rearranged. Another 800 or more genes appear to be germline restricted, the investigators report, noting that the new genome "provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement."
People on the Move
The Personalized Medicine Coalition announced that Daryl Pritchard will be its new VP of science policy, in charge of promoting the organization's science-related policies and of raising awareness of precision healthcare issues among policymakers, providers, and patients. Before joining PMC, Pritchard was director of policy research at the National Pharmaceutical Council; director of research programs advocacy and personalized medicine at the Biotechnology Industry Organization; and the director of government affairs for the American Association for Dental Research.
Nabsys has appointed Steve Lombardi to president, CEO, and to its board of directors. Previously, he was CEO of Real Time Genomics, and before that he was CEO of Helicos BioSciences. He has also served as senior vice president of Affymetrix and vice president of genetic analysis at Applied Biosystems.
Roche said this week that Arthur Levinson has resigned from its board of directors, effective immediately. The drugmaker said Levinson, who was chairman and CEO at Genentech from 1999 to 2014, made the decision to avoid any conflict with his post as CEO at Calico, a Google-backed startup. Levinson has served on Roche's board since 2010.
Sanford Burnham Medical Research Institute said this week it has named Perry Nisen as its CEO and as holder of the Donald Bren Chief Executive Chair. Nisen joins Sanford Burnham from GlaxoSmithKline, where he was senior VP of science and innovation.
The New York Genome Center has named Carol Ashe its new chief business officer. She previously served as VP of corporate development for pharmaceutical firm Endo International, and prior to that was a partner at GlaxoSmithKline's venture capital fund, SR One. Ashe also led GSK's US corporate legal group, which supported M&A transactions and the business development legal transactions team.
Researchers from the NIH and Pacific Biosciences used long-read, PacBio single-molecule real-time sequencing to profile antibiotic resistance enzyme-containing plasmids present in gram-negative Enterobacteriaceae isolates collected at an NIH hospital during and after a 2011 outbreak of antibiotic resistant Enterobacteriaceae. This approach allowed them to look at both bacterial genome sequences and sequences from plasmids carried by the cell, and enabled the team to identify potential transmission events involving specific plasmids and microbial species.
Australian molecular diagnostics firm Genetic Technologies is undertaking a restructuring aimed at ramping up its US molecular diagnostic operations and commercializing the new version of its BrevaGen breast cancer risk test. Its board has approved the sale and/or divestment of the company's non-core assets, and the firm has finalized commitments for a A$2.15 million (US$1.94 million) financing to support its US MDx plans. The firm plans to soon launch BrevaGenplus test, which would have use for African-American and Hispanic women, as well as Caucasian women.
The National Institute on Aging plans to award up to $800,000 next year to investigators' efforts to develop and plan research projects that will examine epigenetic factors involved in age-related diseases, addressing important questions in the emerging field of geroscience. The researchers will plan and design research projects that will investigate epigenetic risk factors for age-related diseases and conditions, or will undertake small-scale pilot projects focused on the same goals. NIA expects that these projects will receive more funding when they are fully developed.