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Researchers Outline Phase II of TCGA at AACR

By Andrea Anderson

WASHINGTON, DC (GenomeWeb News) – The Cancer Genome Atlas (TCGA) plans to completely characterize 200 samples from each of 10 tumor types over the next two years and 20 tumor types within five years, attendees at the American Association for Cancer Research annual meeting heard here yesterday.

As in the pilot stage of the project, Phase II of TCGA will involve sequence, SNP, and copy number analyses for each cancer type, as well as studies of expression, methylation, and small RNA profiles.

To achieve these goals, members of the consortium intend to exploit and expand on the standard operating procedures, infrastructure, and integrated analysis methods designed for the pilot phase of TCGA, National Cancer Institute Deputy Director Anna Barker explained during the session, which featured more than half a dozen TCGA representatives.

While the data analysis pipeline employed in the next stage of the project will be similar to that used during the pilot, they noted, Phase II will also include Genome Data Analysis Centers charged with processing and integrating TCGA data and making it more accessible to the cancer research community at large.

As GenomeWeb Daily News sister publication In Sequence reported in November, six Genome Data Analysis Centers — the Broad Institute, Institute for Systems Biology, Lawrence Berkeley National Laboratory, University of Texas/MD Anderson Cancer Center, Memorial-Sloan Kettering Cancer Center, and the University of California at Santa Cruz — secured $7 million from NCI in fiscal year 2009.

In addition, TCGA will use some of the funding it received through the 2009 American Recovery and Reinvestment Act to support the collection of high quality, clinically validated tumor and matched normal tissue samples. TCGA secured roughly $175 million in ARRA funds, In Sequence reported last year.

In the past, TCGA relied on retrospective tissue samples that were linked to clinical data, explained Joe Vockley, who directs the NCI arm of TCGA. Down the road, though, they plan to start collecting samples through a so-called prospective tissue accrual network. Genomic information for these samples will be integrated with clinical data as it becomes available in the future.

Upcoming stages of the TCGA project will increasingly rely on high-throughput sequencing platforms, researchers explained. For instance, high-throughput sequencing is expected to be used for messenger RNA and microRNA profiling in the immediate future, LBL researcher Joe Gray noted during the session, and may also be employed for methylation studies down the road.

Consequently, TCGA data capture, storage, and analysis methods and IT infrastructure are all expected to be improve and become optimized as the project gets scaled up.

Still, Barker said a great deal of progress has been made on the TCGA project since last year's AACR meeting, when researchers mainly discussed the final stages of the TCGA pilot project.

Also speaking during yesterday's session, Lynda Chin, a cancer researcher affiliated with the Dana-Farber Cancer Institute and Harvard Medical School, discussed some of the findings from that pilot — which focused on glioblastoma multiforme, ovarian cancer, and lung cancer — as well as lessons learned from that initial effort.

Meanwhile, Richard Gibbs, director of Baylor College of Medicine's Human Genome Sequencing Center, outlined the challenges associated with sequencing cancer genomes — touching on everything from biological and technical noise to the widespread variation within normal, matched genomes.

David Haussler, who leads the Genome Bioinformatics Group at the University of California at Santa Cruz, spoke about how TCGA data gets analyzed and disseminated to the broader research community, while Douglas Levine, a gynecological oncology researcher at Memorial Sloan-Kettering Cancer Center, discussed strategies for expanding the translation and application of TCGA data to other types of cancer research and the clinic, using ovarian cancer as an example.

"We really need some very nice, simple tools that basically everyone who comes in contact with a cancer patient can use," Levine said.

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