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Turna Ray is the editor of GenomeWeb's Pharmacogenomics Reporter. She covers pharmacogenomics, personalized medicine, and companion diagnostics. E-mail Turna Ray or follow her GenomeWeb Twitter account at @PGxReporter.
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
New York Genome Center, Columbia University Medical Center
The Workings of the Genome
Tuuli Lappalainen wants to know how the human genome works, and how genetic variation leads to human variation.
"I've always been fascinated by understanding the big picture," Lappalainen said. "Rather than looking deep into one gene or one particular disease or one biological system, I wanted to understand the general patterns of how the genome works."
To do so, she focused on population genetics. Though she really wanted to look at genome-wide patterns, tools weren't quite in place to enable that when she pursued her master's degree. By the time, though, that she was working on her PhD that had changed, and she was able to examine eQTLs and look at gene expression in a genome-wide manner.
"Suddenly, I found myself in a situation where I was able to do the things that I wanted to do," she said.
A team from Denmark and Hong Kong introduces a database designed to discern links between human disease features and small molecules found in plant-based food sources. The resource, dubbed NutriChem, was developed using a systems chemical biology approach that tapped into data from 21 million published abstracts involving plant-based foods, phytochemicals found in plants, and human disease phenotypes. "To the best of our knowledge this database is the only resource linking the chemical space of plant-based foods with human disease phenotypes," the study's authors say, "and provides a foundation for understanding mechanistically the consequences of eating behaviors on health."
The genomic architecture of population divergence between subspecies of the European rabbit
An international team led by investigators in Portugal used a combination of custom capture arrays and targeted high-throughput sequencing to explore regions of divergence in the genomes of rabbits from European sub-species that still hybridize with one another on the Iberian peninsula. The researchers tracked down small regions of differentiation based on SNP patterns identified by sequencing in the genomes of a half a dozen rabbits each from the Oryctolagus cuniculus algirus and O. c. cuniculus sub-species, including regions containing genes involved in transcription or epigenetic processes implicated in speciation by past studies of other model organisms in the lab.
People on the Move
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.
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.
Researchers have produced a high-quality draft genome of the coffee plant, Coffea canephora. Using a combination of Sanger, Roche 454, and Illumina sequencing, they put together a 568.6 million base assembly that stretched over around 80 percent of the plant's 710 million base genome. Their analysis of the genome, combined with comparisons to sequences from related plants, uncovered several gene family expansions in coffee, including a boost in genes involved in plant defense and caffeine production.
Biocartis has raised around $84 million in a private round of financing that will support the firm's commercial roll-out of its Idylla molecular diagnostics platform in Europe later this year, and enable it to expand its commercial reach beyond Europe. The firm also formed a joint venture called MyCartis with protein diagnostics firm Pronota. Biocartis spun off its its DMAT platform, a multiplex system used for rapid and cost-effective detection of protein and nucleic acid biomarkers, to the JV.
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.