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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 Chicago
Different Approach for Cancer Therapeutics
Tanguy Seiwert knew that he wanted to be able to contribute something to society, and when he was searching for a specialty during his medical training, he thought that the two areas with the highest need were neuroscience and oncology. Cancer, though, seemed to Seiwert to be a more interesting problem, and it also touched home as his grandfather died from cancer.
Cancer therapeutics in particular seemed to suddenly be accelerating, Seiwert said, as new and targeted therapies became available.
Currently, Seiwert is working on unraveling the similarities that seemingly certain disparate cancers share. While he is focused on head and neck squamous cell tumors, Seiwert noted that those tumors are similar not only to lung squamous cell tumors but also to esophageal squamous cell tumors and to bladder squamous cell tumors.
"One of my interests is to look at these cross-tumor biological principles," Seiwert said.
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
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.
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.
An international team led by investigators at the Max Planck Institute for Evolutionary Anthropology has sequenced the genome of a modern human Ust'-Ishim man who lived in Siberia some 45,000 years ago, at a time when Neanderthals still resided in Europe and Western Asia. The team calculated that there was intermingling between his human ancestors and Neanderthals that stretched back an estimated 7,000 to 13,000 years before the Ust'-Ishim individual was born.
Enigma Diagnostics and Beijing Leadman Biochemistry have formed a joint venture agreement aimed at bringing Enigma's point-of-care molecular diagnostic system to China. The deal covers the Enigma Mini Laboratory system, a fully automated MDx platform being targeted to both the clinical laboratory and point-of-care spaces, and as part of the agreement Enigma will license its technology and IP to the JV for the development of molecular assays and other products.
The University of Manchester was awarded £24 million ($38.5 million), including funding for omics-directed projects, from the UK government. It will use £13 million to create a Clinical Proteomics Centre, and it received £5 million to create the Manchester Single Cell Research Centre, where scientists will be able to characterize circulating tumor cells and specific stem cells that can help regenerate damaged tissues, such as muscle, joints, skin, and blood vessels.