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New Cancer Consortium to Study 25K Samples

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An international research consortium plans to catalog genetic alterations in 50 different types of cancer in what amounts to be the largest human genome resequencing project launched to date.

The International Cancer Genome Consortium, which launched in late April, was created to serve as an umbrella for existing and future cancer genome projects worldwide.

Over the next decade or so, the group will use new sequencing technologies and other molecular tools to comprehensively analyze approximately 25,000 cancer genome samples for a total estimated cost of $1 billion, and to make the data publicly available.

"It's very much the next-generation sequencing technologies which are driving this consortium, … which we could not even imagine three years ago" because of the prohibitive cost, says Tom Hudson, president and scientific director of the Ontario Institute for Cancer Research in Toronto, which serves as the ICGC's headquarters.

Current members hail from North America, China, Singapore, Japan, the European Union, Australia, and India. Members fund the projects they contribute to the consortium.

"It's a very ambitious project," says ICGC member Mike Stratton, deputy director of the Wellcome Trust Sanger Institute and head of the institute's Cancer Genome Project. "There will never have been a sample collection in cancer as big as this one will be in its aggregate."

Projects like Sanger's Cancer Genome Project or the US National Institutes of Health's Cancer Genome Atlas will continue their work but will contribute their data to the ICGC and adhere to its mandates, according to the consortium.

The central aim of the consortium is to catalog genomic abnormalities, or somatic mutations, in 50 cancer types or subtypes, including SNPs, insertions, deletions, copy number changes, translocations, and other chromosomal rearrangements.

Researchers will also generate gene expression and DNA methylation data for these samples.

Julia Karow

Sequencing Notes

Applied Biosystems and Illumina upgraded their high-throughput sequencing platforms. Illumina recently began shipping the Genome Analyzer II, an upgrade to the GA that triples output from 1 to 3 gigabases per run. The company also is selling a paired-end module for it. ABI plans to ship an upgraded version of its SOLiD platform, doubling the output from 3 to 6 gigabases per run and reducing the run time.

Invitrogen CEO Greg Lucier said his company plans to be a "key player" in next-generation sequencing in the next few years thanks to an R&D team working on better reagents.

ZS Genetics, which is developing a sequencing method based on modified transmission electron microscopy and atomic labeling, joined the Archon X Prize for Genomics competition.

Datapoint

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Baylor's genome center will get six ABI SOLiD systems for use in the pilot phase
of the 1,000 Genomes Project.

Funded Grants

$290,126/FY2007
Sequencing by Recognition
Grantee: Stuart Lindsay, Arizona State University
Began: Aug. 1, 2007; Ends: July 31, 2010

NHGRI awarded Lindsay this grant to explore a nanopore-based sequencing approach based on recognition of the DNA bases via enhanced electron-tunneling. Preliminary data suggests the viability of the approach, which the researchers say could be developed into an array of nanopores that would yield 99.99 percent accuracy.

$422,398/FY2007
Continuous Sequencing-By-Synthesis Based on a Digital Microfluidic Platform
Grantee: Richard Fair, Duke University
Began: Aug. 1, 2007; Ends: July 31, 2010

Fair and his team got this NHGRI grant to continue development on their microfluidic sequencing platform. Needed improvements, they say, include extending the read length of the droplet-based pyrosequencing reaction chemistry. They'll also work to make sure homopolymers do not present a problem with this technology.

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