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Recovery Act Funds Accelerate Cancer Genomics Research

, by Center for Cancer Genomics Staff

The National Cancer Institute (NCI) has invested a significant portion of its American Recovery and Reinvestment Act (ARRA) funds in existing cancer genomics research programs, including The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Targets (TARGET), and new programs like the Cancer Target Discovery and Development (CTD²) Network. The NCI Office of Cancer Genomics (OCG) provides oversight and input to these and other programs, helping to ensure Recovery Act funds are used to accelerate genomics research.

Funding Enables TCGA Program Expansion, Pursuit of 20 New Tumor Types

NCI's Recovery Act investment in TCGA, under the leadership of Joseph G. Vockley, Ph.D., director of the Office of TCGA Research, has facilitated the move from a pilot project to a full program that will take on the challenge of pursuing approximately 20 new tumor types over the next five years. This funding will support TCGA program areas for a period of two years.

TCGA will concentrate Recovery Act funds in two areas: building a more robust pipeline for accruing tissues and performing large-scale DNA sequencing on samples. Specifically, TCGA is committed to performing genomic analysis on 500 cases of each cancer type over five years. Each case consists of a sample of tumor tissue and normal tissue, often blood, from the same patient. Given its own rigorous standards and past experience, TCGA will need to process a minimum of 40,000 tumor and normal samples to gather the high-quality data needed to extensively profile all the tumor types at the depth of coverage and with the breadth of technologies that make TCGA so unique.

The TCGA expansion builds on the success of the pilot project, including the development of the infrastructure necessary to systematically characterize the genomic changes in hundreds of tumors, the team science approach, and the broad use of the publicly accessible data sets that are enabling innovation. Most recently, TCGA researchers discovered that glioblastoma multiforme (GBM) is not a single disease but four distinct molecular subtypes (Verhaak, Hoadley, Purdom, et al, 2010). Researchers also found that response to aggressive chemotherapy and radiation differed by subtype, a discovery which may ultimately lead to more effective, targeted treatment strategies to combat GBM.

The expansion of TCGA is expected to lead to the most comprehensive understanding of cancer genomes in history. Data generated by the TCGA Network is made available via the TCGA Data Portal, enabling researchers to advance their efforts and improve the prevention, diagnosis, and treatment of cancer.

Recovery Act Investment Enhances TARGET Pediatric Tumor Research Initiatives

The TARGET initiative focuses on the systematic genomic characterization of pediatric tumors. Prior to the Recovery Act investment, TARGET investigators concentrated on two primary areas of research: acute lymphoblastic leukemia (ALL) and neuroblastoma. This new funding has expanded the TARGET initiative to include acute myeloid leukemia (AML), osteosarcoma, and Wilms Tumor. Additionally, the collaborators working on ALL and neuroblastoma have expanded the types of characterization being performed on these tumors and have included cases with recurrent disease. As a result of the changes, TARGET can provide a more comprehensive view of the extent of genomic alteration in these tumors.

Funding Supports Efforts of New CTD² Network

Over the past several years, genomic technologies have improved greatly and different platforms—such as those that detect copy number alterations, gene expression profiles, and methylation status—can now all be performed on DNA or RNA isolated from the same tissue. As these datasets become more abundant, researchers will need to distill these data down to the handful of driver mutations responsible for tumorigenesis, as well as potential targets for pharmacologic treatments. Accordingly, the CTD² Network was created to develop a community of laboratories with experience in performing large-scale screens, optimizing biological assays, and developing informatics approaches that together can apply a systems approach to understanding the underlying genetic make-up of a specific tumor.

The following organizations have been selected as molecular CTD² Centers:

  • University of Texas Southwestern Medical Center Dallas, Texas
    Michael Roth, Ph.D.
  • Cold Spring Harbor Laboratory, Long Island, N.Y.
    Scott Powers, Ph.D.
  • Dana-Farber Cancer Institute, Boston, Mass.
    William Hahn, M.D., Ph.D.; Lynda Chin, M.D.; and Ronald DePinho, M.D.
  • Columbia University, New York, N.Y.
    Andrea Califano, Ph.D.
  • Broad Institute, Cambridge, Mass.
    Stuart Schreiber, Ph.D.
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