How does a $2 million-a-year cancer research effort with a team of nine scientists keep pace with a $100 million-a-year project with a team of 200? Pretty well, it turns out.
With the Cancer Genome Atlas project in the news lately—the New York Times recently reported on progress in its colon cancer work—we decided to compare some of its data with that of the Life Raft Group’s Research Team and its D-Day Project. Our research focuses on GIST.
LRG Research Team Findings:
—Both groups have performed next generation sequencing including whole genome sequencing and exome sequencing. With much greater funding, the colon cancer project has sequenced about six times as many samples (although more are being planned in GIST).
—Both groups have performed extensive supporting screens, including DNA copy number changes and expres-sion arrays. The colon cancer project has also performed promoter methylation screens, and the LRG Research Team is in the process of doing so. The LRG sponsored a grant to gather/extract human Interstitial Cells of Cajal (ICCs) to act as normal controls for a future meth-ylation screen and expanded its team to include Dr. Tamas Ordog of the Mayo Clinic to help get this done. ICCs are the pacemaker cells of the GI tract.
—The D-Day project also sponsored two major initiatives that were not included in the colon cancer project. These included functional screens to evaluate the importance of individual genes in GIST tumors (11,000 gene knockdown, Kinase panel knockdown, phosphatases knockdown and proteases knockdown) and a drug-screening program that tested more than 200 different drugs.
—Both projects worked with the Broad Institute to perform their screens.
More Reports to Come
The colon cancer report by the Can-cer Genome Atlas project will be followed by findings on its efforts in lung and breast can-cers and acute myeloid leukemia later this year. The sweeping project is being financed by two government agen-cies, the National Cancer Institute and the National Human Genome Research Institute.
In contrast, the LRG’s research works toward finding a cure for GIST, which many consider to be a model cancer for researchers because many of its mechanisms are being uncovered.
The Times article, by Gina Kolata, explained the importance of the research: “Scientists increasingly see can-cer as a genetic disease defined not so much by where it starts — colon, liver, brain, breast — but by genetic aberrations that are its Achilles’ heel. And with a detailed understanding of which genetic changes make a cancer grow and thrive, they say they can figure out how best to mount an attack.”
For example, mutations in the BRAF gene were identified in some cases of colon cancer and have also been found to play a role in some cases of GIST.
The LRG Research Team is led by Dr. Jonathan Fletcher of Brigham & Women’s Hospital and Harvard University. Team members update their strategic plan annually and share information with each other at quarterly meetings. Their Pathway to a Cure research plan was launched in 2006, and four years later the D-Day Project was initiated.
The D-Day Project takes a four-pronged approach to finding a cure for GIST, emphasizing sequencing, gene knockdowns, drug screening and validation studies. This is what makes it distinct from the Cancer Genome Atlas project.
The focus is on finding a cure. Team member Dr. Brian Rubin of the Cleveland Clinic puts it this way, “The Life Raft Group has revolutionized the way we do research by relieving traditional barriers to collaboration and encouraging a group dynamic…This type of fo-cused collaboration would not happen without the funding of the Life Raft Group …(it) is a game changer for patients with GIST.”