The Cancer Genome Atlas: Recovery Act Investment Report
Public Health Burden of Cancer
Cancer is the second leading cause of death in the United States after heart disease. In 2009, it is estimated that nearly 1.5 million new cases of invasive cancer will be diagnosed in this country and more than 560,000 people will die of the disease.
TCGA is a large-scale collaborative effort, co-funded by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHRGI), to comprehensively characterize the genomic alterations and molecular pathways involved in the development of human adult cancers. It was initiated in 2006 as a 3-year pilot project focused on the characterization of three tumor types: brain (glioblastoma multiforme), ovary (serous cystadenocarcinoma), and lung (squamous cell carcinoma).
TCGA involves a broad cross-section of the cancer research community, including basic and clinical researchers, bioinformatics specialists, bioethicists, doctors, nurses, cancer patients, and advocates. In TCGA, all data sets and analytical tools are made publicly accessible to the research community in an effort to accelerate translation of the latest scientific findings into new cancer therapies and diagnostic approaches.
The pilot project established a research network consisting of five principal components, each one critical to success:
- Biospecimen Core Resource: Carefully catalogs, processes, performs quality assurance, and stores tissue samples, complete with important medical information about the patients who donated them. All personally identifiable information about the patients (that is, information that can be used alone or together with other information to identify them) is removed before making the data publicly accessible.
- Contributing Tissue Sources: Institutions that contribute tumor samples in a manner consistent with TCGA's requirements.
- Cancer Genome Characterization Centers: Facilities that use advanced and complementary analytical technologies to strategically characterize the genomic and epigenomic alterations in tumors. They provide a catalog of DNA deletions, DNA rearrangements, amplifications of large segments of chromosomes, transcriptional alterations, and changes in methylation patterns and identify areas of the genome (e.g., specific genes) for mutation analysis by the Genome Sequencing Centers.
- Genome Sequencing Centers: High-throughput centers that identify DNA sequence alterations that are associated with specific types of cancer.
- Data Coordinating Center: Centrally manages the data generated through TCGA and enters this information into publicly accessible databases as it becomes available. Data centralization facilitates information transfer across the network and the research community and makes data analysis more efficient.
TCGA and ARRA
ARRA funding is allowing the expansion of TCGA to include more than 20 additional cancer types. Breast cancer and kidney cancer are the latest tumor types added. ARRA funds will also be used to create new bioinformatics tools and computational models for the analysis of integrated genomic data. In another important development, TCGA will use ARRA funding to build a more-robust pipeline for acquiring the large number of tumor specimens and matched normal-tissue samples required for the project's scale-up. The increase in sample throughput, combined with the emergence of powerful new technologies to sequence and analyze cancer genomes, will fundamentally change cancer research and, ultimately, cancer treatment. For example, TCGA data will enable the private sector to pursue targeted therapies aimed at the specific molecular pathways involved in the development of individual cancer types or subtypes. This new level of insight promises to substantially shorten the time and reduce the costs involved in drug development.
In addition to the scientific stimulus that ARRA is providing, it will also create a large number of technically focused employment opportunities and preserve existing jobs. For example:(1, 2, 3, 4, 5, 6, 7, 8)
- Multiple full-time positions will be preserved and created in the academic and private sectors. Job creation will derive from the scope of TCGA, which requires an unprecedented number of individuals in both academia and private industry who must collaborate to generate and analyze vast amounts of data. Ultimately, TCGA will support thousands of scientists, physicians, computer scientists, laboratory technicians, bioinformatics specialists, and other professionals.
- Continued support of ongoing work at the TCGA Cancer Genome Characterization Centers will allow those centers to maintain existing staff dedicated to the project. ARRA funding will also allow more rapid completion of a number of remaining pilot-phase projects and will require selected sites to hire individuals at all points in the research and development pipeline.
- TCGA project sites are located at universities and centers across the United States. Therefore, ARRA funding will result in a wide geographic distribution of employment opportunities, bolstering regional economies.
- Stimulus funding will have an immediate impact on jobs in Los Angeles, San Francisco, New York, Boston, Baltimore, Huntsville, Phoenix, and other cities. Moreover, new start-up biotechnology companies are already beginning to emerge based on TCGA data, and it is anticipated that others will follow in the near term.
- 3U24CA126561-03S1 — Cancer Genome Characterization Center at Johns Hopkins — Baylin, Stephen B. (MD)
- 3U24CA126551-03S1 — The Berkeley Cancer Genome Center — Gray, Joe W. (CA)
- 3U24CA126554-03S1 — Cancer Genomics Center — Kucherlapati, Raju S. (MA)
- 3U24CA126543-03S1 — The TCGA Cancer Genome Characterization Center at MSKCC — Ladanyi, Marc (NY)
- 3U24CA126546-04S1 — Center for Cancer Genome Characterization — Meyerson, Matthew L. (MA)
- 3U24CA126544-03S1 — Cancer genome characterization using gene expression and DNA copy number analysis — Perou, Charles M. (NC)
- 3U24CA126563-03S1 — Hudson-Alpha Cancer Genome Characterization Center — Myers, Richard M. (AL)
- Contract HHSN261200800001E N01CO-2008-00001 (4 Supplements) — The Cancer Genome Atlas (TCGA) — SAIC-Frederick (MD)