BGI Tech Solutions, a subsidiary of BGI, a genomics research organization, and South Texas Accelerated Research Therapeutics (START), are collaborating on the San Antonio 1000 Cancer Genome Project (SA1kCGP), a cancer genome study designed to link genetic alterations that underlie different cancers to detailed clinical outcomes. Such findings could enable scientists to pursue the development of targeted, personalized cancer treatments. All data generated from SA1kCGP will be made available publicly and freely to researchers and others worldwide.
SA1kCGP is conducting whole genome sequencing of cancerous and normal tissue and blood samples from patients with one of 10 cancers. BGI Tech will provide next-generation, high-throughput genomic sequencing to identify mutations associated with specific cancers, as well as gathering, analyzing and archiving at BGI all genetic and clinical data generated through the tumor sequencing and clinical analyses. START, which initiated SA1kCGP, will conduct patient recruitment, tumor sample acquisition and collect clinical patient information.
SA1kCGP is unique relative to other major cancer genome research projects, given the project's direct linkage of genomic and clinical information, including both treatment and survival data, using START's electronic medical records and proprietary Clinical Synchrony software technology, so that the relationship of genomic alterations and clinical outcome can be realized. This cannot be done with data from other major cancer genome research projects that only collect minimal clinical information, such as The Cancer Genome Atlas, a research program conducted by the NIH, which costs approximately $375 million.
SA1kCGP, launched in 2012, has already exceeded its initial goal of collecting samples from 1,000 patients. With a 90% consent rate and growing pace of enrollment, 1,200 patients have agreed to have their tumor tissues sampled. SA1kCGP plans to sequence the cancer genomes of 10,000 patients at a fraction of the cost of other major cancer genome projects. The budget for SA1kCGP currently stands at $5 million, with approximately $1 million raised exclusively through community contributions.
SA1kCGP has assembled a team of more than 200 San Antonio area cancer surgeons, pathologists, researchers and oncologists from numerous hospitals, most of which are local providers at community-based facilities where 90% of cancer care and where clinical studies occur. These hospitals are enrolling cancer patients into the research project, and collecting the tissue samples to be sequenced and analyzed. By working through this community network, referral bias (influence of disparate data source) will be avoided since the patient population will be typical of the representative cancer patient in the community, as opposed to patients in tertiary cancer centers. This increases the ability to generate large enough data sets for analysis through predicative algorithms that could ultimately explain underlying biological causes of cancer.
In contrast to past research, where sample preservation was formaldehyde based for 30 years, hematology and oncology researchers involved in SA1kCGP have agreed to change the paradigm for genomic oncology by using fresh tissue for this analysis. The logistics of obtaining fresh tissue is a major hurdle to large scale genomic research in oncology, a barrier that START has addressed by targeting community treatment centers. These samples will also be available for further research in areas of RNA and protein analysis to complement the DNA sequencing.