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Justin Petrone is the editor of GenomeWeb's BioArray News and covers the microarray and biochip sector of the genomics market. E-mail Justin Petrone or follow his GenomeWeb Twitter account at @BioArrayNews.
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
Building Devices, Building Cells
Ahmad Khalil started out studying how to build things like rocket engines and other mechanical systems as a mechanical engineering major in college. But, he added, he also took a liking to biology and the idea of applying engineering ideas to the study of living systems.
His PhD mentor, Angela Belcher at MIT, impressed upon him the reverse as well, that biological systems could also be used to engineer materials, and from her, he said, is where he got his "inspiration for bio-inspired engineering."
In his new lab at Boston University, Khalil is studying how cells respond to various environmental conditions and stressors.
"We develop engineering approaches and technologies to broadly study how cells behave, how they grow, how they develop, how they communicate," Khalil said, "and, in turn, to also re-direct those behaviors for useful applications for human health and energy and societal problems."
Belgian and Colombian researchers describe their novel sequence capture method and data filtering scheme for simultaneously seeing thousands of tandem repeats in the human genome. The team applied the large-scale analysis approach to profile tandem repeat patterns in the genomes of individuals from a three-generation family. As they report in the Nucleic Acids Research, the investigators detected a de novo variant in the family. They also determined that a significant proportion of the tandem repeats detected in the family — some 7.6 percent — were slightly distinct from those described in the human reference sequence.
The Max Planck Institute for Evolutionary Anthropology's Svante Pääbo and colleagues scrutinized protein-coding sequences from several Neanderthals, using new exome sequences for Neanderthals from Spain and Croatia and existing sequence data for a Siberian Neanderthal. By comparing the Neanderthal exomes to one another and to protein-coding sequences in humans from African, European, and Asian populations, the researchers determined the nature and extent of the protein-coding variation present in Neanderthals. Despite low levels of genetic diversity in Neanderthals, for example, they saw a jump in the proportion of variants expected to alter the amino acid sequences of Neanderthal proteins. The analysis also highlighted variants in that may explain some of the physical differences identified between Neanderthals and modern humans, which appeared to be particularly common in behavior- and pigmentation-related genes.
People on the Move
CollabRx has appointed Paul Billings to its board of directors. Billings is a board certified internist and clinical geneticist and most recently served as chief medical officer for Life Technologies. He is executive chairman of Melanoma Diagnostics, a director of Trovagene, and a co-founder and past medical director of the Cordblood Registry. He was also a senior vice president for corporate development at Laboratory Corporation of America and a co-founder of Omicia. Billings also currently serves on the Scientific Advisory Board of the US Food and Drug Administration, the Genomic Medicine Advisory Committee at the Department of Veterans Affairs, and the National Academy of Sciences Institute of Medicine’s Roundtable on Genomics.
Kathy Hibbs, former senior VP and general counsel at Genomic Health, has joined 23andMe as chief legal and regulatory officer. Hibbs joins 23andMe while the firm is in the midst of regulatory discussions with the US Food and Drug Administration regarding its Personal Genome Service. Hibbs has also worked at Monogram Biosciences and Varian Medical Systems, and is actively engaged in a number of industry groups, such as the American Clinical Laboratory Association, the Coalition for 21st Century Medicine, and the Personalized Medicine Coalition.
Stephen Rusckowski has been named chairman of the American Clinical Laboratory Association's board of directors. Rusckowski has served as Quest Diagnostics' president and CEO since May 2012. Before joining Quest Diagnostics he was CEO of Philips Healthcare.
ProteinSimple has appointed Joe Keegan and Chris van Ingen to its board of directors. Keegan was previously the CEO of ForteBio and Molecular Devices. Van Ingen was previously president of Agilent Technologies' bio-analytical measurement business. He currently serves on the boards of Bruker, Accelrys, and Promega.
An international team of investigators in the UK, Turkey, and elsewhere sequenced the genomes of nearly 100 MRSA isolates — a collection that showed widely variable toxicity profiles in their cell- and mouse-based assays. The team's analysis led to a genetic signature that appeared to coincide with the most pronounced toxicity patterns in the MRSA isolates. Those snippets of sequence subsequently proved useful for predicting which isolates would have high or low toxicity in a mouse model of MRSA infection.
Myriad Genetics has submitted to the US Food and Drug Administration the first module of its premarket approval application for BRACAnalysis as a companion test for AstraZeneca's breast cancer PARP inhibitor olaparib. The test is being used in two Phase III trials to pick out ovarian cancer patients who harbor BRCA mutations and as such are thought to be best responders to olaparib. Myriad filed an investigational device exemption application with the FDA less than a year ago to enable it to use BRACAnalysis in these studies.
A research team at Washington University School of Medicine in St. Louis plans to use an $8 million grant from the National Heart, Lung, and Blood Institute to conduct a large-scale analysis of genetic and lifestyle data from multi-ethnic cohorts. The scientists plan to examine data from more than 30 studies, including genomic information, common cardiovascular measures, and a range of lifestyle factors, to try to identify interactions between genetics and lifestyle that impact cardiovascular disease risk.
GenomeWeb and Myriad RBM invite you to a free online presentation by Matthew Albert of the Institut Pasteur on recent progress in personalized immune response monitoring.
Dr. Albert will share findings from the Milieu Interieur Project, a population-based study that aims to identify the genetic and environmental determinants of immune phenotype variance and establish a path towards personalized medicine.