Abstract
South Texas Accelerated Research Therapeutics and BGI Tech Solutions will collaborate on the San Antonio 1000 Cancer Genome Project, which will integrate whole-genome sequencing of tumors from 10 cancer types with data from patient records.
A new integrated database may offer a powerful resource for cancer genomics analysis by merging whole-genome sequencing data with clinical information.
Current efforts such as The Cancer Genome Atlas (TCGA) typically offer few details about the patients' responses to treatments, notes Anthony Tolcher, MD, director of clinical research for South Texas Accelerated Research Therapeutics (START) in San Antonio. For maximal use, genomic data need to be closely linked to detailed clinical treatment and outcome data, he says.
In September, START and BGI Tech Solutions of Shenzhen, China, announced that BGI will handle sequencing and analysis of genomic data that will be integrated with clinical data in the San Antonio 1000 Cancer Genome Project. Launched last year, the project is generating and studying sequences from 10 cancer types, using frozen tissue samples.
In addition to its focus on integrating clinical data, the initiative differs from most cancer genome efforts in the type of patients it is enrolling, Tolcher says. Patients come mainly from community-based hospitals in the San Antonio area, not from academic medical centers, and thus may be more representative of cancer patients in the general population. Software created by START gathers a variety of information from the participants' files, including tumor staging, treatments, survival, and lab results.
So far, about 1,200 patients have signed on. “Ideally, we want to get up to 10,000 patients,” says Tolcher.
All of the genomic and patient information will be housed in a database that will be publicly accessible to researchers worldwide, and should be online next year, Tolcher says.
More than 200 San Antonio–area cancer surgeons, pathologists, researchers, and oncologists have joined the effort. Drawing heavily on time donated by these medical professionals, the project is projected to cost $5 million, all raised from donations.
“It is important to link the genomic data with clinical information,” says Lynda Chin, MD, chair of the department of genomic medicine and scientific director of The University of Texas MD Anderson Cancer Center in Houston, who isn't involved in the project. “It's great that they are going to target community physicians, and it's great that they will use frozen tissues.”
However, Chin is concerned that the project's small budget—just over 1% of the price tag for TCGA—might not support the careful specimen collection and meticulous quality control necessary to ensure the data's accuracy and usefulness. “I think they have underestimated the challenge of getting the samples,” she suggests.
For more news on cancer research, visit Cancer Discovery online at http://CDnews.aacrjournals.org.
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