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Adam Bonislawski is the editor of GenomeWeb's ProteoMonitor. He covers proteomics and life science mass spectrometry. E-mail Adam Bonislawski and follow his GenomeWeb Twitter account at @ProteoMonitor.
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 team from South Korea, the US, and Australia present a draft genome sequence and annotation for a cold-tolerant teleost fish called the Antarctic bullhead notothen, Notothenia coriiceps, that's found in frigid waters in the Southern Ocean. Using Roche 454, Illumina, and Pacific Biosciences instruments, the researchers put together a 637 million base hybrid assembly for the fish, which contained an estimated 32,260 protein-coding genes. By analyzing the genome and comparing it with sequences from other fish, they began untangling clues to the Antarctic bullhead notothen's cold adaptation, including changes to genes coding for mitochondrial contributors, hemoglobin, and heat shock proteins.
Researchers from São Paulo University have linked a microdeletion in chromosome 15 to obsessive-compulsive disorder. Using array-based comparative genomic hybridization in their pilot study of 16 patients with early onset OCD and 12 controls, the researchers uncovered a 64 kilobase deletion in chromosome 15q13.3 from one male patient with very early onset OCD. The patient's father has the same deletion, but does not have OCD, the researchers note. Additionally, the deletion affects part of the FMN1 gene, which is involved with the glutamatergic system. This, the researchers argue, underscores the idea that a complex network of genes contributes to OCD risk, and that the glutamatergic system plays a role in the condition.
People on the Move
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.
Rubicon Genomics has hired Karl Hecker as vice president of product development. Previously, he was a principal scientist at HTG Molecular Diagnostics. He has also held positions at Quidel, PerkinElmer, Invitrogen, and Transgenomic.
RainDance Technologies has named John Luckey as its new vice president of product development.
Luckey has held senior product and platform development positions at companies such as Roche NimbleGen, where he directed research and development activities for improving and expanding the company's core DNA microarray synthesis technology and related instrumentation; and MJ Research, where he contributed to the design and development of the Opticon product family and Opticon Monitor software. While at Roche, he also liaised with 454 Life Sciences development teams and participated on the global team tasked with defining a strategy to apply next-generation sequencing technology to clinical diagnostics.
John Flannery has been named president and CEO of GE Healthcare. He starts the post immediately, taking over for John Dineen, who is leaving the firm. He most recently was senior vice president of business development for GE, leading business development activity related to the purchase of Alstom's energy and transmission businesses, the spinoff of Retail Finance, and the sale of GE Appliances. Prior to that, he was the president and CEO of GE India and a senior leader at GE Capital. Flannery has been with GE for 27 years.
A Cornell University-led team has sequenced and started analyzing the genome of the domestic house fly, Musca domestica, in the hopes of detecting genetic clues for dealing with the pest and pathogens it carries. The team put together — and annotated — a 691 million base assembly that spans more than three-quarters of the fly's complete genome sequence and contains an estimated 14,810 protein-coding genes. Relative to the fruit fly, the house fly genome contained far more repetitive sequence elements and copy number variants, they noted.
Becton Dickinson has acquired Irish sample prep automation firm GenCell Biosystems, marking BD's entry into the next-generation sequencing market. GenCell has developed a proprietary microdroplet reaction technology called Composite Liquid Cell (CLC). One of its first applications is an automated library preparation platform for next-generation sequencing, called CLiC LP, that promises lower running costs than other methods. GenCell was planning to start shipping the instrument this summer.
The National Institutes of Health awarded $29 million in fiscal 2014 to expand the Rare Diseases Clinical Research Network. RDCRN is led by the National Center for Advancing Translational Sciences, and as part of the 2014 funding, six new consortia were established, including the Rare Lung Diseases Consortium: Molecular Pathway-Driven Diagnostics and Therapeutics for Rare Lung Diseases, and a consortium called Developmental Synaptopathies Associated with TSC, PTEN, and SHANK3 Mutations.