A Blacklight for Bioinformatics

February 2012

By Matthew Dublin

A new supercomputing system with an innovative memory network proves itself a vital tool for genomics research.

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Video Spotlight

Shashikant Kulkarni at ACMG

BioArray editor Justin Petrone sat down with Shashikant Kulkarni, an associate professor at Washington University School of Medicine at St. Louis, to discuss chromosomal microarrary analysis in the clinic, SNP arrays versus CGH platforms for post-natal testing, and more.

May 16, 2012

Miragen Therapeutics' Eva van Rooij

Miragen Therapeutics' Eva van Rooij discusses microRNA-based therapeutics, the challenges associated with chronic microRNA knockdown, therapeutic microRNA antagonists, and more.

May 08, 2012

A Conversation with CeGaT's Saskia Biskup

In this video, Julia Karow, Editor of Clinical Sequencing News, interviews Saskia Biskup, CEO of the Center for Genomics and Transcriptomics, or CeGaT, at the company's headquarters in Tübingen, Germany.

May 02, 2012

A Tour of Illumina's CLIA Lab

In this video, Illumina's CLIA laboratory manager Suneer Jain gives InSequence and Clinical Sequencing News Editor Monica Heger a tour of Illumina's CLIA lab at the company's San Diego headquarters.

April 25, 2012
Young Investigator Profile

James Noonan

Assistant Professor
Yale University

Development Deciphered

The Noonan lab is studying changes in developmental gene regulation during human evolution on multiple levels. They are refining statistical methods to quantify the rate of human-specific sequence change in noncoding DNA, in order to identify regulatory elements that changed rapidly in human evolution. In addition, the lab is also characterizing individual cis-regulatory elements with human-specific developmental functions by reverse genetic analysis in mouse models.
Blog

A New and Improved Database

A group of researchers from Yale University may have reinvented the database with a solution that's not even a database.

May 16, 2012

Disease Uncovered

Next-generation sequencing may enhance clinical diagnosis and disease management, researchers report.

May 16, 2012

This Week in the Journal of Clinical Pathology

In the Journal of Clinical Pathology this week: NF1 isoforms in sporadic breast cancer, more.

May 16, 2012

They Go Together

Genes and genetics are not separate entities, one blogger says.

May 16, 2012
Papers of Note

Melanoma Genome Sequence Shows PREX2 as a Significantly Mutated Gene
Berger, Hodis et al., Nature
A team led by investigators at the Broad Institute reports having sequenced the genomes of 25 metastatic melanomas and matched germline DNA, through which it identified a "wide range of point mutation rates," and PREX2 as a significantly mutated gene in melanomas.

Developmental Milestones in the Caenorhabditis Embryo
Levin, Hashimshony et al., Developmental Cell
Technion Israel Institute of Technology's Itai Yanai and his colleagues report that "embryonic development in five Caenorhabditis species proceeds through two distinct milestones, in which the transcriptome is resistant to differences in species-specific developmental timings." Comparing the complete protein-coding transcriptomes of individually timed embryos across ten morphological markers, Yanai et al. found that these milestones "can be characterized by their expression dynamics and activation of key developmental regulators."
People on the Move

Genomic Health has appointed Richard Tompane as president of its new subsidiary InVitae, which will focus on developing next-generation-based sequencing diagnostics for genetic diseases. Tompane was previously president and CEO of Gemfire and has also served as an independent consultant.

LaserGen has appointed Mimi Healy its new CEO and member of the board of directors. She previously served as CEO of Houston-based Bacterial Barcodes, a spin-off company of BCM Technologies.

Trovagene has named Carlo Croce to serve on its scientific advisory board. Croce is director of the Human Cancer Genetics Program and the Genetics Institute at The Ohio State University, and he is John W. Wolfe Chair in Human Cancer Genetics.
Upcoming Events

Conferences, Meetings & Deadlines

The iMedicine & Mobile Life Sciences World Summit
May 16-17 / Boston
Arrowhead Publishers

New Perspectives on Immunity to Infection
May 19-22 / Heidelberg, Germany
EMBL

TIDES: Oligonucleotides and Peptide Technology & Product Development
Applications of Nucleic Acids Technologies in Molecular Diagnostics, Oligonucleotide Therapeutics Discovery, and Peptide Discovery and Development
May 20-23 / Las Vegas
IBC Life Sciences

Microtubules: Structure, Regulation and Functions
May 23-26 / Heidelberg, Germany
EMBL

Evidence for Clinical Utility of Molecular Diagnostics in Oncology: A Workshop
May 24 / Washington, DC
Institute of Medicine

Abstract & Registration Deadlines

more

Science
Researchers from Duke University and the University of Michigan successfully diagnosed around half of the individuals that they tested during a pilot study on the use of clinical exome sequencing. The investigators did whole-exome sequencing on individuals from a dozen parent-child trios for the study and pinned down likely causal mutations in six of the individuals, including new mutations in genes linked to Mendelian diseases.
Business
Fluidigm and the Broad Institute launched a new center, housed at the Broad's Cambridge, Mass.-based headquarters, aimed at developing new methods and discoveries in mammalian single-cell genomics. The center intends to develop novel single-cell, microfluidic methods for gene expression profiling, RNA/DNA sequencing, and epigenetic analysis with an aim at making single-cell research accessible to the greater research community.
Funding
Launching what will be the maiden initiative for the months-old National Center for Advancing Translational Sciences, NIH Director Francis Collins unveiled a program that will support researchers using biomarker-based studies and other approaches to repurpose compounds owned by three of the world's largest drug developers. NCATS will provide up to $20 million in 2013 through two types of cooperative agreements to fuel the new projects.
Genome Technology Magazine
While whole-genome sequencing is useful for studying disease, it is less likely to be useful in predicting whether a healthy individual will develop a disease, a study recently published in Science Translational Medicine says. At the American Association for Cancer Research meeting in Chicago, study author Bert Vogelstein from the Johns Hopkins Kimmel Cancer Center spoke about the work, saying that, for cancer, predictive whole-genome sequencing is not better for ensuring health than conventional risk-management strategies like regular check-ups and an overall healthy lifestyle.

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A Blacklight for Bioinformatics

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