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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.
A Max Planck Institute for Evolutionary Anthropology-led team publishes the genome sequence of a 45,000-year-old modern human man from Siberia, who lived right around the time that western and eastern Eurasia populations split. The researchers report that the man carried a similar level of Neanderthal ancestry as present-day Eurasians, though he had longer genomic segments of Neanderthal ancestry. Their analysis suggests that the Neanderthal gene flow into the ancestors of this individual occurred some 7,000 years to 13,000 years before he lived. Previous estimates of interbreeding between modern humans and Neanderthal range from 37,000 years to 86,000 years ago, but the new data point to that gene flow occurring roughly between 50,000 years and 60,000 years ago.
A University of California at San Francisco-led team present CRISPR-based strategies to systematically repress and activate the transcription of endogenous human genes. As they report in Cell, the researchers started by screening the activity of short guide RNAs (sgRNAs) tiling to sequences in and around transcription start sites for dozens of genes mediating ricin susceptibility in cells. From there, they detected patterns associated with activation or repression, ultimately developing genome-scale libraries of CRISPR repressors, called CRISPRi, and CRISPR activators (CRISPRa) that they used for subsequent screens for genes related to cell growth features.
People on the Move
Former Life Technologies CEO and Chairman Greg Lucier has joined the board of directors at Invuity, a medical device company based in San Francisco. Prior to Life Tech, Lucier was chairman and CEO of Invitorgen, which merged with Applied Biosystems in 2008 to form Life Technologies. He previously held senior management positions at General Electric including CEO and president of Medical Systems Information Technologies for GE Healthcare.
Nabsys said that Anthony Shuber has joined the company as VP and chief scientific officer. He joins the firm from Ignyta, an oncology precision medicine firm, where he served as chief technology officer. Prior to joining Ignyta, Shuber was co-founder and CTO of Predictive Biosciences, and scientific co-founder of Exact Sciences. He also previously worked for Genzyme Genetics/Integrated Genetics and Genetics Institute.
Ruby Gadelrab has been named vice president of commercial marketing for 23andMe. Gadelrab most recently served as head of marketing and commercial development at Invitae, and prior to that had worked at Affymetrix, where she most recently served as head of international marketing and clinical development. She also has worked at Life Technologies, Dharmacon, and AbGene.
Luminex President and CEO Patrick Balthrop has retired, the firm announced this week. His retirement is effective immediately, as is his retirement from the firm's board of directors. He has been succeeded as president and CEO by Nachum Shamir, who is expected to be invited to join Luminex's board of directors.
Shamir most recently served as president and CEO of Given Imaging, which was acquired by Covidien earlier this year. He previously was president of Eastman Kodak's transaction and industrial solutions business. He also was president and CEO of Scitex.
Researchers from the Broad Institute, Massachusetts General Hospital, Yale School of Medicine, and elsewhere used a combination of genetic, gene expression, and epigenetic marker information to map the causal variants contributing to 21 inflammatory autoimmune conditions and begin unraveling their regulatory effects. Their results suggest that roughly 90 percent of the causal variants identified in these conditions so far fall in non-coding parts of the genome, affecting enhancers and other regulatory sites.
Qiagen has signed a master collaboration agreement to develop and commercialize companion diagnostics to pair with drugs being developed by Astellas Pharma for cancer and other diseases. The deal provides Tokyo-based Astellas access to Qiagen's development capabilities for assays based on PCR, next-generation sequencing, and multi-modal testing technologies using liquid and tissue biopsies. Qiagen noted that the agreement with Astellas is its eighth framework agreement for developing CDx tests in collaboration with biopharma companies.
The University of Oxford received a £35 million grant from the Higher Education Funding Council for England through its UK Research Partnership Investment Fund to launch the Precision Cancer Medicine Institute, a center that will use genomics and molecular diagnostics, among other technologies, to carry out research into cancer therapies. The center expects to receive more than £75 million from financial contributions and support in kind from partners in the project, such as Cancer Research UK, Roche Diagnostics, and GE Healthcare.