NCI to Expand TCGA to Up to 25 Tumor Types; Use Next-Gen Sequencing on Childhood Cancers

April 28, 2009

By Julia Karow

NCI Director John Niederhuber said last week that the institute plans to expand the Cancer Genome Atlas project to 20 to 25 major tumor types, and to apply next-generation sequencing to at least 100 tumor samples for each of several types of childhood cancers under the TARGET initiative.

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In this issue of In Sequence

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Sponsored Video: Ambry Genetics - "Fully-Automated"

RainDance's ThunderStorm System is a fully-automated and walkaway high-throughput targeted sequencing solution that enables researchers to process 96 samples per day run on a proven platform that generates higher-quality data faster than ever before.

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ScienceOnline2012

Genome Technology's Tracy Vence interviewed Sandra Porter, president of Digital World Biology, and Kristi Holmes, a bioinformaticist at the Becker Medical Library, Washington University School of Medicine at ScienceOnline2012.

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Highlights from SC11 Part IV

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Young Investigator Profile

Helge Grosshans

Friedrich Miescher Institute for Biomedical Research
Senior Group Leader

MicroRNA Mediation

The Grosshans lab is aiming to find out how miRNAs achieve repression of their target mRNAs and how miRNAs are made and regulated using C. elegans. In addition to exploiting its traditional strengths in genetics and cell biology, they are also developing and applying biochemical assays. So far, they have been able to identify an miRNA degradation pathway that prevents detrimental increases in mature miRNA levels and to recapitulate this process biochemically.
Blog

DOE Study Says Clouds Can't Replace Supercomputers

A two-year study conducted by the US Department of Energy finds that cloud can't replace supercomputers.

February 09, 2012

This Week in Experimental and Molecular Pathology

In Experimental and Molecular Pathology this week: minichromosome maintenance protein 2 in myelodysplastic syndromes, methylation in hepatitis, and more.

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Parkinson's Disease in a Dish

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The Wave-Makers

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Papers of Note

The Drosophila melanogaster Genetic Reference Panel
Mackay, Richards et al., Nature
North Carolina State University's Trudy Mackay and her colleagues present the Drosophila melanogaster Genetic Reference Panel, "a community resource for analysis of population genomics and quantitative traits."

Temporal Shifts in the Skin Microbiome Associated with Atopic Dermatitis, Treatment
Kong, Oh et al., Genome Research
Investigators at the US National Institutes of Health this week show that temporal shifts in the skin microbiome are associated with atopic dermatitis disease flares and treatment. Among others, the NIH team shows that in atopic dermatitis disease state, "the proportion of Staphylococcus sequences, particularly S. aureus, was greater during disease flares than at baseline or post-treatment and correlated with worsened disease severity." In addition, "representation of the skin commensal S. epidermidis also significantly increased during flares," the team found.
People on the Move

Life Technologies this week named Alan Sachs as head of global research and development and Ronnie Andrews as president of medical sciences.

Sachs was previously the vice president of exploratory and translational sciences for Merck Research Laboratories, where he spent 10 years in various leadership roles, Life Tech said. Prior to that Sachs served an associate professor of biochemistry and molecular biology at the University of California, Berkeley, and as a Whitehead fellow at the Whitehead Institute for Biomedical Research.

Andrews joins Life Tech from GE Molecular Diagnostics, where he served as a segment leader following GE's 2010 acquisition of Clarient, where Andrews was CEO. Andrews has also held executive positions with Abbott Diagnostics, Roche Diagnostics, and Immucor.

Stephen O'Brien has left the National Cancer Institute's Laboratory of Genomic Diversity after 25 years to help launch a genome bioinformatics program at St. Petersburg University in Russia. O'Brien received a $5 million grant from the Russian Ministry of Education and Science last year under a program that aims to lure big-name researchers to Russia. Over the coming three years, O'Brien will spend at least four months per year in Russia working at the center, which is scheduled to open in May.

Saladax Biomedical said today that President and CEO Edward Erickson has resigned due to personal and family reasons, and that he will be replaced by Kevin Harter on an interim basis. Erickson will remain a member of the company's board of directors. Harter is a co-founder and senior VP of the Life Sciences Greenhouse, and he has served as executive chairman at Saladax.
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Science
Members of the International Stroke Genetics Consortium and the Wellcome Trust Case Control Consortium 2 did a GWAS involving thousands of individuals of European descent with or without a history of stroke and found a new genetic variant that contributes to a form of stroke called large vessel ischemic stroke. The variant was found in in the histone deacetylase 9 coding gene HDAC9 on chromosome 7.
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PerkinElmer reported fourth-quarter revenue growth of 15 percent, or 6 percent organically, compared to Q4 2010 and beat analysts' estimates on the top and bottom line. The firm is in the process of integrating Caliper Life Sciences and a few bioinformatics companies, and company officials said there would be a pause in M&A activity for the next several months - though diagnostics remains a "significant priority."
Funding
Canada launched a new program that will pump C$67.5 million (US$67.3 million) into projects that will use genomics-based research to advance personalized healthcare. The 2012 Large-Scale Applied Research Project Competition in Genomics and Personalized Health is funded with C$40 million from Genome Canada, C$22.5 million from the Canadian Institute of Health Research, and C$5 million from the Cancer Stem Cell Consortium.
Genome Technology Magazine
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NCI to Expand TCGA to Up to 25 Tumor Types; Use Next-Gen Sequencing on Childhood Cancers

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