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
The Jackson Laboratory
Epigenome in Type 2 Diabetes
Michael Stitzel joked that his research has led him to climb up the evolutionary tree. As an undergraduate he worked with yeast, and over the years, he has worked his way up to studying Drosophila, C. elegans, and, now, people.
Stitzel shifted from the more basic roots of the tree to the biomedical limbs as a matter of motivation. He said that as a graduate student, though he worked on an important and interesting question, when experiments didn't go well, it was hard for him to get motivated. And so, he found himself drawn to questions with more direct relevance to medicine.
He turned to studying type 2 diabetes. Using a genome-wide association study approach, he identified a number of regions in the genome linked to the disease, but many of them were, as he put it, "in the middle of nowhere." This led him to thinking about epigenetics, and then to later uncover what he and his colleagues dubbed 'stretch enhancers,' longer-than-average enhancers that appear to be driving physiological functions.
A team led by Harvard University researchers reports on the sequencing of 99 Ebola virus genomes from infected patients in the current outbreak in West Africa. By comparing the data with Ebola sequence data from past outbreaks, the scientists determined that this year's outbreak likely spread from a previous one in Middle Africa during the last 10 years. Unlike previous outbreaks, this year's virus was also found to originate from a single human-reservoir exchange, then spreading human to human.
A team from New York University, the IBM Thomas J. Watson Research Center, and Columbia University used a combination of deep RNA sequencing and chromatin immunoprecipitation sequencing to look at whether the Notch pathway signaling pathway glitches that have been associated with T cell lymphoblastic leukemia, or T-ALL, impact downstream long non-coding RNA targets. Indeed, the search uncovered lncRNA isoforms stemming from almost 2,000 gene loci, including a lncRNA called LUNAR that not only appeared to be regulated by Notch, but also contributed to T-ALL tumor growth and maintenance.
People on the Move
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.
Vermillion has named David Jansen its VP of marketing, a new position at the firm. Jansen joins Vermillion from Myriad Genetics, where he held senior marketing roles for the past seven years. Vermillion also said that Chief Commercial Officer Marian Sacco will be leaving the company as part of a reorganization and restructuring. Sacco had joined the firm just last December.
Epic Sciences has appointed Greg Lucier as chairman of its board of directors. Lucier was previously chairman and CEO of Life Technologies.
Conferences, Meetings & Deadlines
MSACL 2014 EU
September 2-5 / Salzburg, Austria
The Association for Mass Spectrometry Applications to the Clinical Lab
Researchers from the US, Sierra Leone, and the UK have garnered genetic evidence suggesting that the current Ebola virus disease outbreak in West Africa involves a form of the virus not linked to recent outbreaks in the region. They sequenced the genomes of 99 Ebola virus isolates from 78 patients treated in Sierra Leone between late May and mid-June of this year and found that the strain appears to have diverged from other Ebola virus lineages originating in Middle Africa around a decade ago.
Pacific Biosciences has received a $10 million payment from Roche for hitting a development milestone that is part of the commercialization and license agreement the companies struck in 2013. PacBio didn't disclose what development milestone had been met, but noted that it may receive up to $30 million for reaching additional development milestones. It had received an upfront payment of $35 million at the signing of the deal, under which Roche is developing molecular diagnostics on the SMRT sequencing platform.
Three US funding agencies, along with partners in the UK and Israel, will provide up to $12 million next year to support multidisciplinary research projects that will use genomics among other methods to better understand how infectious disease pathogens are transmitted and evolve. The projects will be funded under the Ecology and Evolution of Infectious Diseases program, and will aim to create quantitative or computational knowledge about and models of infectious disease transmission.
This online seminar will provide an overview of new tools for screening stem cells — in particular, the use of RNA detection probes to detect pluripotency gene expression in live embryonic and induced pluripotent stem cells by fluorescence microscopy without the need for manipulation of the cells.