Transcriptome Sequencing Finds Diagnostic Mutation for Rare Ovarian Tumor Type

June 16, 2009

By Julia Karow

The study, published online last week in the New England Journal of Medicine, underscores how next-generation sequencing can directly benefit the clinic and indicates that whole-genome sequencing may not always be needed to discover important cancer mutations.

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In this issue of In Sequence

Young Investigator Profile

Christopher Maher

University of Michigan Medical School
Research Investigator

Gene Fusions and Transcriptome Sequencing

Christopher Maher is focused on elucidating gene fusions, which he first became acquainted with during his potdoctoral work at the Michigan Center for Translational Pathology. Maher hopes to continue discovering novel gene fusions as well as draw new findings out of already-known gene fusions. Last year, he published a paper in Nature in January of 2009 entitled "Transcriptome sequencing to detect gene fusions in cancer," which he says provides a validation for the approach of using next-gen sequencing to find gene fusions in cancer. This was followed up by a PNAS paper in July which demonstrated the gene fusion concept using paired-end transcriptome sequencing.
Blog

Why HMMER users shouldn't bother Sean Eddy

Sean Eddy offers some simple guidelines to help troubleshoot problems with HMMER.

March 15, 2010

LabCorp Says No More Freebies — Just Steep Discounts — to Low-Income Florida Residents

Since LabCorp acquired a local clinical lab in Naples, Fla., nearly three years ago, it has offered certain lab services for free to low-income people through local clinics. The program ended today.

March 15, 2010

An Interest in Seeds

The New York Times takes a look at the seed industry.

March 15, 2010

Leena Peltonen-Palotie Dies

Leena Peltonen-Palotie Dies

March 15, 2010
Papers of Note

Family-Based Whole-Genome Sequencing Reveals Candidates for Mendelian Disease
Roach, Glusman et al., Science
Researchers at the Institute for Systems Biology and Complete Genomics have identified candidate disease-causing genes for Miller syndrome and ciliary dyskinesia, both Mendelian disorders. They sequenced the genomes of a family of four, allowing them to determine recombination sites with precision (at 99.999 percent accuracy) and identify rare single-nucleotide polymorphisms. "Our results demonstrate the unique value of complete genome sequencing in families," the authors write.

Resequencing the Domestic Chicken Genome
Rubin, Zody et al., Nature
An international research team reports their resequencing efforts of the Gallus gallus domesticus — domestic chicken — genome. Using a massively parallel approach, they sequenced the chicken genome to 44.5-fold coverage and identified candidate mutations that may have played a role in the animal's domestication. The authors also suggest their results imply "the importance of the domestic chicken as a model organism for biomedical research."
People on the Move

Wellcome Trust Sanger Institute Professor Leena Peltonen-Palotie died this week of cancer at her home in Finland, according to the Sanger Institute. Peltonen-Palotie was head of human genetics at Wellcome Trust, and she held appointments at the Broad Institute at MIT and Harvard and the Institute for Molecular Medicine Finland.

Three leaders from the Human Genome Project — David Botstein, Francis Collins, and Eric Lander — have been named co-winners of the 2010 Albany Medical Center Prize in Medicine and Biomedical Research, which carries with it a purse of $500,000.

Adrian Dillon will resign from his job as executive VP of finance and administration and CFO of Agilent Technologies to become chief financial and administrative officer at Skype. He will be replaced at the beginning of April by Didier Hirsch, who currently is VP of corporate controllership and taxes and who will serve as acting CFO.
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Science
Researchers from the Institute for Systems Biology and elsewhere used Complete Genomics' sequencing service to identify mutations behind a Mendelian condition called Miller syndrome and an inherited lung disorder called ciliary dyskinesia in a family of four.
Business
Bruker will acquire certain mass spectrometry and chromatography product lines from Varian, clearing the way for Agilent to complete its $1.5 billion acquisition of Varian. The divestitures were part of conditions set by EU authorities for approval of the merger.
Funding
HHS expects that in 2010 NIH will spend another roughly $5.2 billion overall in stimulus funds that were left over from ARRA's first year. NIH still has more than $1.6 billion to spend in stimulus funds for lab construction and renovation, buildings and facilities, and shared instruments.
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Transcriptome Sequencing Finds Diagnostic Mutation for Rare Ovarian Tumor Type

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