The National Cancer Institute's (NCI's) Board of Scientific Advisors (BSA) last week unanimously endorsed a 3-year pilot project to assess the feasibility of sequencing genomic changes in human tumors on a large scale. The Human Cancer Genome Pilot Project (HCGPP) will be conducted as a partnership between NCI and the National Human Genome Research Institute (NHGRI).

"This is truly an integrated effort," said Dr. Anna Barker, NCI deputy director for strategic scientific initiatives, "not just an NCI project." Dr. Barker told BSA that by leveraging both institutes' funding, resources, and expertise, the collaboration will allow a greater return on those investments.

Enabled by the reference human sequence from the Human Genome Project, NCI and NHGRI hope the pilot project will establish a firm foundation for molecular oncology by focusing on a combination of genome characterization and resequencing to identify genetic aberrations in major cancer types. By identifying the molecular pathways that underlie cancer, the HCGPP could provide valuable new targets for cancer prevention, detection, diagnosis, and drug development.

"The mission of this pilot project is to develop a systematic approach to identifying genetic alterations in cancer that have meaningful clinical impact in a few rationally selected cancer types," said Dr. Gregory Downing, director of NCI's Office of Technology and Industrial Relations. "Paramount to this whole initiative is the systematic approach, which will establish public data sets and other resources to facilitate research by individual investigators."

Investigators throughout the cancer community are already identifying and sequencing genes thought to be involved in carcinogenesis - although not in a systematic, integrated manner. The HCGPP could provide an approach to eventually consolidate this effort and make the resulting data widely and publicly available. NCI-supported genome characterization centers will utilize robust genomic technologies to measure gene copy number, expression arrays, and epigenomic and other changes, and will collaborate with NHGRI's sequencing centers to select genes for resequencing and data integration.

"This is not just about sequencing," said Dr. Francis Collins, NHGRI director. "This is an integrated effort that puts together sequence data with multiple other types of data, and the sum is clearly going to be much more than the parts."

To reduce the problem of the heterogeneity of most cancers and ultimately optimize opportunity for clinical impact, the pilot project is currently planned to focus on two cancers. Although final selections will consider information provided by the cancer community through a request for information, it is likely that a hematologic tumor and a solid tumor with poor prognosis would best support the pilot project.

Because the mission of the pilot project is to assess the feasibility of a full-scale effort, BSA advised that a defined criterion be used to monitor the initiative over the next 3 years. Several benchmarks were offered by the project team and recommended by BSA, including robust genomic analysis of two tumors to produce a "pipeline" of candidate genes/regions for resequencing; the ability to find and correlate genomic changes (e.g., copy number changes, deletions, amplifications, etc.) through in-depth sequencing; new cancer genes discovered beyond known pathways; the ability to differentiate tumor subtypes based on genomic characterization and sequence data; a precompetitive public database of genomic characterization, sequence, and clinical data to enable discovery and translational research; and technology advances that provide the capability to differentiate significant genomic changes from "noise."

BSA also recommended that funds requested to support genomic analysis technologies be increased.

In endorsing the pilot project, several BSA members noted that this is an extremely important effort for NCI to undertake at this time.