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Genomic Data Commons ushers in new era for information sharing

2016; Wiley; Volume: 122; Issue: 18 Linguagem: Inglês

10.1002/cncr.30278

1097-0142

Carrie Printz,

Ethics in Clinical Research

When the National Cancer Institute (NCI) introduced the Genomic Data Commons (GDC) system in June 2016, the agency launched what it hopes will be a new era for genomic and clinical data sharing among researchers around the world. “Genomics is the key to developing personalized, precision medicine approaches to target pathways in cancer activated by various genetic abnormalities,” says Louis Staudt, MD, PhD, director of the NCI Center for Cancer Genomics and a team leader of the new GDC. “The NCI has been a big contributor to the amount of genetic sequencing and associated clinical data developed from patient biopsies from around the world.” Although the data currently are publicly available to researchers, the process of obtaining and analyzing them is highly cumbersome. The new GDC seeks to make the data much more accessible and interpretable. NCI officials say it will be a core component of the National Cancer Moonshot and the President's Precision Medicine Initiative. It will receive funding from $70 million allocated to lead efforts in cancer genomics as part of the Precision Medicine Initiative for Oncology. The GDC will centralize, standardize, and make accessible data from large-scale NCI programs such as The Cancer Genome Atlas (TCGA) and its pediatric equivalent, Therapeutically Applicable Research to Generate Effective Treatments (TARGET). In addition to these data sets, which are some of the largest and most comprehensive in the world, the GDC will accept submissions of both cancer genomic and clinical data from researchers worldwide. By submitting their data, these and other researchers will have access to the GDC's state-of-theart analytic methods, which will allow them to compare their findings with other GDC data. “Now, there is no uniform way of presenting this data,” says Taofeek Owonikoko, MD, PhD, associate professor in the department of hematology and medical oncology at Emory University School of Medicine in Atlanta, Georgia. “The GDC will help researchers overcome that hurdle of having to go through multiple sites to put the data together, and they will have the benefit of large data sets to perform their analyses.” He adds that the data are “well-curated and harmonized in a format that is easy for the average investigator to understand and digest.” Patrick A. Zweidler-McKay, MD, PhD, section chief for pediatric leukemia and lymphoma at The University of Texas MD Anderson Cancer Center in Houston, agrees. He has obtained such data through the NCI's old system and describes the process as challenging. The GDC, he says, is “a wonderful thing.” “They will have the data available through a Web site that will allow us to ask questions about it, such as the number of available patients and expressions,” he says. “Whereas about 5% of researchers went through the process to get the data previously, now if 70% to 80% of researchers access the information, the vision is that it will spread across the entire community and generate more research.” Under the old system, downloading all the data from the TCGA would take approximately 4 to 6 weeks and require $1 million worth of computer equipment to store and use. Furthermore, the data were not presented in any uniform manner, says Dr. Staudt. Now, the GDC will enable researchers to download only those data they need while also helping them to analyze them, he says. The storage of raw genomic data in the GDC also will allow the data to be reanalyzed as computational methods and genome annotations improve. In addition, the platform will house data from a number of newer NCI programs that will sequence the data of patients enrolled in NCI clinical trials. All the information will lead to a deeper understanding of which therapies are most effective for individual patients with cancer. At the same time, it will integrate both genetic and clinical data, such as imaging, histological information on the molecular profiles of tumors, and treatment response. The GDC will help researchers overcome that hurdle of having to go through multiple sites to put the data together, and they will have the benefit of large data sets to perform their analyses. —Taofeek Owonikoko, MD, PhD The GDC will provide that statistical power. Together, TCGA and TARGET have generated information from approximately 14,500 patients, and the database soon will have many more. In late June, leaders announced a data sharing agreement with Foundation Medicine, a molecular information company that has generated genomic profiles of people with cancer. The company's additional sequencing from 18,000 adult patients with a wide variety of cancers will provide a significant increase in available data, and that number will continue to grow as researchers around the world upload their information, Dr. Staudt says. He points to the ROS1 translocation subtype, which is present in approximately 1% to 3% of patients with lung cancer, as a perfect example of a rare subtype in which targeted therapy has achieved excellent results. “We have evidence that there are a lot of other examples of rare genetic mutations that might yield exciting results for patients,” he says. “The GDC will help us know if rare subtypes exist so we can then conduct clinical trials and feed the results back into the database.” Initially, research scientists will be the primary users of the GDC, but this scenario will morph over time to include more clinicians who are seeking to have individual cancers genetically analyzed and interpreted. Because only a small percentage of genetic mutations actually drive cancer, the GDC will help scientists home in on the important mutations, thereby developing a more extensive knowledge system for cancer, says Dr. Staudt. Dr. Zweidler-McKay calls the effort to provide all the analytics and informatics online a huge job. “If they're successful, they will have created a remarkable resource,” he says. As a pediatric oncologist, he is challenged by the fact that there are limited sequencing data available concerning children. “For pediatric patients, it's really imperative that people combine their data, and this provides us with the first public database to do that,” he adds. “To make this resource as powerful as possible, we need to encourage people to submit their data to this common site.” Although Dr. Zweidler-McKay praises the NCI's efforts in creating the GDC, he adds that patients should understand exactly how they are likely to benefit from it. “The number of patients who will actually directly benefit from this sequencing is small; that is the reality of personalized medicine,” he says. “But it will improve our understanding of the biology of cancer and, ultimately, that will improve care.” In addition to increasing the numbers of cases available for analysis, the GDC will provide a genomic life history of patients' cancers, Dr. Owonikoko says. As a result, researchers will be able to examine each unique genomic profile over time: from the results at diagnosis to those at treatment response to those at response failure. “It will improve the complexity of the data,” he says. “We know cancer has very dynamic conditions, so it would be good to have the historical data set.” Although much progress will occur over the next 2 years for the GDC, seeing its impact will take considerably more time, Dr. Staudt says, adding, “It will be driven by how fast or slow the clinical trials take to conduct and how many patients have their genetic sequencing done.”