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American Reinvestment and Recovery Act

Recovery Act Investment Update: Working toward the Creation of a Cancer Genome Atlas

Scientists involved with the National Cancer Institute's (NCI) The Cancer Genome Atlas (TCGA) program have been making significant headway since the initiative was featured on the NCI Recovery Act website in November 2009. TCGA is a collaborative effort involving research scientists and clinicians working at universities and institutions around the world. This effort is making high-quality, comprehensive genomic characterization sequencing data freely-available to the cancer research community. These data will enable researchers to explore the spectrum of genomic changes that occur in various types of cancers and gain a better understanding of how these genetic changes lead to the development of cancer. TCGA findings will provide insights into the development of improved methods to diagnose cancer and more effective ways to treat this disease.

Masaya Baba, M.D., Ph.D., W. Marston Linehan, M.D. and Sunil Sudarshan, M.D. lend their expertise to the management and research of kidney cancer. (Pictured from left to right.) Masaya Baba, M.D., Ph.D., W. Marston Linehan, M.D. and Sunil Sudarshan, M.D. lend their expertise to the management and research of kidney cancer. (Pictured from left to right.)

"The TCGA initiative would have been inconceivable without the substantial support provided by the Recovery Act funds," said Kenna Shaw, Ph.D., director of The Cancer Genome Atlas Program. "This is the first public cancer genomics resource at this scale, and the TCGA team has done a remarkable job of organizing and guiding the project, which has been a massive logistical and scientific challenge."

Cancer is a disease of the genome and data being produced by TCGA have led to the discovery that for many tumor types, subtypes exist that have their own set of characteristic genetic changes. TCGA data have contributed to the work of many researchers who are identifying the genomic characteristics of ovarian cancer and a type of brain cancer called glioblastoma, in addition to many other types of cancer (see a list of publications using TCGA data). In addition, TCGA data are providing the necessary infrastructure for studying the underlying molecular biology of various types of cancers. This infrastructure will support the research of a new generation of cancer researchers and clinicians working to develop more effective therapies that are targeted to specific genetic mutations within cancer cells.

"The fact is we need better therapies for patients with cancer. And the good news is that significant progress has been made. However, we need to do better. We've got to accelerate finding effective drugs with less toxicity for these patients and their families," said W. Marston Linehan, M.D., Chief of the Urologic Oncology Branch at NCI and co-chair of the TCGA Kidney Cancer Working Group.

So far, the TCGA program is about half way to collecting 500 qualified cases from 20 types of cancer (see the list of cancers selected for study). These tumor and germline samples are evaluated to ensure that they meet the standards set by TCGA to produce the highest-quality genomic data.

One type of tumor being studied by TCGA scientists is kidney cancer.  The von Hippel-Lindau (VHL) gene was the first gene identified in which mutations cause kidney cancer. According to Dr. Linehan, it took NCI scientists 10 years to discover this one gene. The TCGA project will help scientists target their research to gain a better understanding of genes that go awry in kidney cancer and ultimately aid in the pursuit of much-needed treatments for this disease.

By releasing genomic data as they are generated, TCGA is providing the entire cancer research community with data they can leverage to develop better ways to prevent and treat cancer. Prior to TCGA, researchers were unable to observe an integrated picture of the cancer genome because they were examining its individual parts without context. With the provision of Recovery Act funds, a greater understanding into the pathways involved in these cancers has been sped up dramatically.

"The complexity and depth and breadth of the data being generated from each individual tumor type will be an invaluable resource that will catalyze the work of a generation of cancer scientists and clinicians," said Dr. Linehan. "I am confident that this will take us to novel therapies that we can only dream of now."