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International Cancer Genome Consortium Moves into Whole-Genome Sequencing Faster than Expected

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By Monica Heger

This story was originally published April 14.

The scope of the International Cancer Genome Consortium, which aims to sequence over 25,000 tumors from 50 different cancer types at the genomic, epigenomic, and transcriptomic levels is growing faster than expected due to falling sequencing prices, according to one of the project's executive members.

"When we were initially planning the project, we originally meant whole-exome sequencing," Tom Hudson, president and scientific director of the Ontario Institute for Cancer Research and ICGC executive member, told In Sequence last week. But, he said, there's been an acceleration in technology development and groups are already adding whole-genome sequencing data to the database.

Hudson predicted that by the end of the year, hundreds of cancer genomes will be sequenced and that by next year, the number will be in the thousands. Once thousands of cancer genomes are sequenced, he thinks groups will start seeing recurrent mutations and mutations that have biological relevance.

"Over time, the large datasets are meant to be hypothesis-generating," said Hudson. "We should be able to uncover a large number of mutations that have clinical relevance." For instance, "there's the potential for making correlations between a person's genome and drug response," he added. "But we will need many more tumors before we can make those correlations."

"We're going up an exponential curve," he added. "Most of the groups are ramping up, and I think there will be a discovery of biological relevance within a year."

In addition, groups in Japan, the UK, Australia and Canada have added new sequence data from liver, breast, and pancreatic cancers to the consortium's database. Also, several new research groups have recently joined the consortium, including two consortia from the European Union that will evaluate breast cancer and kidney cancer, and a group from an Italian university studying rare pancreatic endocrine cancer, said Hudson.

The Wellcome Trust Sanger Institute in the UK is adding data from previously published studies on structural variations from 24 tumor/normal pairs of breast cancer, plus whole genome sequencing of two cancer cell lines (IS 1/5/2010 and 12/22/2009).

Unpublished data available as of last week includes whole-genome sequences, exomes, copy number changes, and transcriptomes of pancreatic cancer tumor/normal samples, xenografts, and cell lines from the Ontario Institute for Cancer Research; whole-genome sequences, copy number changes, and transcriptomes of six pancreatic cancer samples from Queensland University in Australia; and a whole-genome sequence from a liver tumor sample and structural variants from a second liver tumor from Japan's National Cancer Center and the RIKEN center for genomic medicine in Japan.

Additionally, datasets from John Hopkins University regarding specific genes for breast, colon, pancreatic, and brain tumors will be added, as will gene-centric data from the Cancer Genome Atlas for over 350 brain and 350 ovarian cancers.

Hudson added that out of the ICGC's goal of sequencing 25,000 cancer genomes, the project has commitments for 10,000 so far.

The ICGC was launched in April 2008 and is composed of research groups in Australia, Canada, China, France, the UK, Germany, India, Italy, Japan, Spain, and two European Union consortia (IS 4/29/2008). The United States' Cancer Genome Atlas has member-equivalent status, but because of technical and legal issues regarding the distribution of controlled-access data, is not currently a formal member.

The consortium was launched to serve as an umbrella for cancer genome sequencing projects in order to coordinate research efforts and make data available to the entire research community.

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