Advocates of the effort at the NIH say rapid progress in genetic sequence and analysis technologies make this the right time to embark on such an ambitious project. At the start of the human genome project, sequencing cost $10 per base of DNA; it’s now down to one-tenth of a penny, and the price continues to drop.
The pilot project will provide grants to cancer and sequencing centers across the nation to analyze hundreds of tumor samples for gene variations and larger-scale structural changes, such as gene duplications and deletions. And the findings will be compiled in a massive central database that will be publicly accessible.
“This is like the beginnings of the human genome project,” says Richard K Wilson, a geneticist at the Washington University School of Medicine in St. Louis, MO. “We are putting our heads together and pooling our resources to figure out how to bring technology to bear on the cancer field.”
Wilson is looking for genes involved in tumor metastasis, the crucial step when cancer cells migrate away from the original tumor and produce cancers in other tissues. To do this, they look for genetic differences in two tumors, one that metastasized and one that did not. “To answer that question, you need to look at a lot of sequence,” says Wilson.
His group and others will also test some new technologies that will be crucial for a larger-scale project, including novel sequencing machines that can drastically reduce the time and money needed to read a cancer cell’s genome. The National Cancer Institute and NHGRI are also asking for proposals outlining high throughput methods to analyze epigenetics – indirect factors, such as DNA methylation, that affect gene expression.
Other researchers, such as Matthew Meyerson of the Dana-Farber Cancer Institute and Harvard Medical School in Boston, plan to look directly for mutations in potential drug targets, such as the enzymes implicated in cancer. Last year, Meyerson’s lab and another research group independently identified the mutation that makes some lung cancer tumors respond well to the drugs Iressa and Tarceva.
However, some scientists still question whether the pilot project will be worth the investment. “You have to ask, is this the best use of money for solving the problem of cancer?” says Stephen J. Elledge, a geneticist at Harvard Medical School, who is concerned that the project will take money away from other cancer research efforts.
“We understand everyone’s anxiety about the constrained [NIH] budget, but that’s not a reason not to do it,” NHGRI’s Collins told Technology Review.
Prior to advancing to the next phase, the institutes will evaluate the three-year pilot project to determine how efficient it has been in collecting data, and how well that data has translated into clinic, Collins says.