Exome Sequencing Gains Ground as Key Approach for Identifying Genetic Causes of Disease

February 09, 2010

Proponents of exome sequencing say the approach is useful for studying both Mendelian and complex diseases, and is more cost-effective than whole-genome sequencing.

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In this issue of In Sequence

Young Investigator Profile

Ipsita Banerjee

Assistant Professor
Department of Chemical and Petroleum Engineering
University of Pittsburgh

Regeneration Research

Ipsita Banerjee is working at understand the differentiation and lineage commitment of pluripotent cells in order to shift paradigms in regenerative medicine and stem cell bioengineering. Using a system of embryonic stem cells differentiating to pancreatic islets, her lab is currently aiming to answer questions regarding the role that transcription factors play in controlling and deciding on a cell lineage and the influence of environmental perturbations on these networks toward desired lineage.
Blog

For LabCorp, It's Sue and Be Sued

Over the past few weeks, the reference lab has been embroiled in two suits: In one it accused Cardinal Health Systems of breaching a non-compete agreement, and in the other it has been accused by Aetna for issuing misleading reimbursement information.

September 08, 2010

Get On Your Hip-Boots: The Plavix-CYP2C19 Quagmire Has Just Gotten Thicker

Now comes news that could cause cardiologists to shelve Plavix altogether -- and with it any CYP2C19 testing that might have tagged along. But don't count it out just yet.

September 08, 2010

Lineagen to Launch Autism Test Nationwide in Q1 2011

The so-called FirstStep Dx test, which uses whole-genome chromosomal microarrays and Fragile X testing, is being performed by an undisclosed national CLIA lab.

September 08, 2010

Cloud Computing Tool for RNA Sequence Analysis

John Hopkins University researchers develop RNA sequence analysis tool for cloud computing.

September 08, 2010
Papers of Note

Genetic Basis for Cyanobacteria Sunscreen Biosynthesis
Balskus and Walsh, Science
Emily Balskus and Christopher Walsh at Harvard Medical School describe the "genetic and molecular basis for sunscreen biosynthesis in cyanobacteria." They show that a mycosporine-like amino acid biosynthetic gene cluster generates four enzymes in vitro. "In addition to clarifying the origin of the MAAs, these efforts have revealed two unprecedented enzymatic strategies for imine formation," Balskus and Walsh write.

Database of Predicted Protein Phosphorylation Sites
Schwartz and Church, Science Signaling
The University of Connecticut's Daniel Schwartz and George Church of Harvard describe "the viral post-translational modification database, which contains a comprehensive list of 329 accurately localized phosphorylation sites in proteins from 52 human viruses published between 1986 and the present." The team also used the scan-x tool to make thousands of phosphorylation predictions in more than 200 human viruses. Using scan-x, Schwartz and Church found "at least 4,000 as yet unidentified phosphorylation sites on hundreds of viral proteins," they write.
People on the Move

The National Human Genome Research Institute said this week that it has chosen Daniel Kastner to be its new scientific director. Kastner, who will join NHGRI in October, currently is clinical director and director of translational research at the National Institute of Arthritis and Musculoskeletal and Skin Diseases.

Former Genome Canada President and CEO Martin Godbout has been appointed chairman of MethylGene's board of directors. Godbout, who held the top post at Genome Canada between 2000 and 2009, has served as a member of MethylGene's board since 2002. He also has been senior VP of BioCapital and president and GM of Société Innovatech Québec.

Emergent Biosolutions has appointed former National Cancer Institute Director John Niederhuber to serve on its board of directors.

Niederhuber was director at NCI from 2005 to 2010, and he recently joined Inova Health System as executive VP and CEO of the Inova Institute for Translational Research and Personalized Medicine. He also still works as an adjunct investigator at NCI’s Center for Cancer Research.
Upcoming Events

Conferences, Meetings & Deadlines

4th CPTC Annual Meeting: Establishing the Standards in Clinical Proteomics
Sep. 8-9 / Bethesda, MD
NCI

Quantitative and Systems Pharmacology Workshop II
Sep. 9-10 / Bethesda, MD
NIGMS

Global Biomarker Conference
Sep. 10 / Vancouver, Canada
GBC

Personal Genomes
Sep. 10-12 / Cold Spring Harbor, NY
CSHL

50th Interscience Conference on Antimicrobial Agents and Chemotherapy Meeting
Sep. 12-15 / Boston, MA
American Society for Microbiology

Abstract & Registration Deadlines

more

Science
Members of the International HapMap 3 Consortium reported that they have genetically characterized individuals from 11 different populations, genotyping nearly 1,200 individuals and re-sequencing specific genomic regions in almost 700 individuals from 10 of the populations, comparing SNP and copy number variation patterns across the populations tested.
Business
Roche announced a cost-cutting initiative, dubbed a "Group-wide Operational Excellence initiative," that will be implemented in 2011-2012. It said that the initiative, which "aims to adapt cost structures and accelerate productivity improvements Group-wide," is in response to "mounting pressures to curb healthcare costs," particularly in the US and Europe.
Funding
The NIH will provide $161.3 million in funding to expand a nationwide effort to advance personalized medicine through the use of pharmacogenomics. The Pharmacogenomics Research Network program will support research into genetic variants linked to responses to a range of medicines for cancer, heart disease, asthma, and addiction.
Genome Technology Magazine
Many researchers are switching over to RNA-seq from microarrays for their transcriptomic studies. But RNA-seq is still a young technique and researchers are struggling to handle all the data it generates.

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Exome Sequencing Gains Ground as Key Approach for Identifying Genetic Causes of Disease

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In this issue of In Sequence

Young Investigator Profile

Blog

Papers of Note

People on the Move

Upcoming Events

Science

Business

Funding

Genome Technology Magazine

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