Georgetown Data Scientist Comments on Biden's Announcement on Open Genomics Database
WASHINGTON (June 6, 2016) – Today, Vice President Joe Biden will reportedly announce (new window) the launch of a cancer database with genomic data and other patient information called “Genomic Data Commons” that will be open to researchers. Biden will discuss the effort when he addresses attendees at the 2016 American Society for Clinical Oncology Annual Meeting in Chicago about the National Cancer Moonshot Initiative.
Georgetown data scientist Subha Madhavan, PhD (new window), welcomes the announcement, and points out that much work needs to be done to shore up appropriate data access, safeguards for patient privacy and data security.
Genomic medicine offers the promise of tailoring cancer treatment based on a patient’s unique genes discovered through genomic sequencing.
“The irony of individualized treatment for one patient is that we have to manage billions of bits of information from thousands of others,” explains Subha Madhavan, PhD, director of the Innovation Center for Biomedical Informatics (ICBI) and chief data/bioinformatics officer at the Georgetown University Medical Center.
“When used appropriately, cancer biomarkers have the potential to improve patient outcomes by guiding the optimal choice of therapies for patients,” Madhavan says. “However, the selection of a precise cancer therapy based on a patient’s molecular profile requires computer-assisted analysis of enormous molecular, clinical, patient history, and pharmacological datasets that often come from very disparate and heterogeneous data sources. For instance, arriving at an optimal decision may involve searching through 177,381 germline variants in ClinVar, over five million somatic variants in Cosmic, over 25 million PubMed articles, over 500 million entries in dbSNP, 137 FDA approved drugs with PGx labeling, and over 300,000 globally registered clinical trials.”
Madhavan points to critical elements that must proceed in lock step with genomic medicine.
“Big data in the biomedical field is driven by the single premise of achieving precision medicine that will significantly improve patient care,” she says. “But the scientific knowledge and the management of massive amounts of information can only move forward with the development of robust informatics platforms such as the Genomic Data Commons and G-DOC (new window)that can link patient medical history to CLIA/CAP molecular tests all the way to patient outcomes . Precision medicine informatics skills are key to realizing this vision. With extensive training, the development of bioinformatics centers of excellence and partnerships with legal and policy experts, we can deliver on the big data promise.”
Another vital element to success is organizing massive amounts of data from electronic health records. Madhavan says, “Structuring unstructured data from clinical notes and literature is critical to genotype-phenotype integration so that we derive meaning from investments in genomics – to gather and organize evidence of clinical utility of cancer molecular profiling to guide treatment.”
Finally, Madhavan says progress can be amplified rapidly with broad collaboration.
“Cloud computing and cognitive computing are on the rise to support precision medicine,” she says. “We need to develop rapid data sharing enclaves and tools to enable novel hypothesis generation for clinical research beyond the walls of well-funded top tier academic institutions. We need to democratize access to these linked datasets to any researcher who has the passion, drive and skills to make a difference in cancer care.”
She concludes, “Advances in the integration of multiple ‘omics’ data is enabling discovery of the causal genetic factors that contribute to precision medicine. With that, we can determine the right target, the right drug and the right patient.”
Madhavan is a recognized leader in data science, clinical informatics and health IT. She leads several biomedical informatics efforts at Georgetown including the software development of Georgetown Database of Cancer (new window)(G-DOC), a resource for both researchers and clinicians to realize the goals of cancer precision medicine.
About Georgetown Lombardi Comprehensive Cancer Center
Georgetown Lombardi Comprehensive Cancer Center, part of Georgetown University Medical Center and MedStar Georgetown University Hospital, seeks to improve the diagnosis, treatment, and prevention of cancer through innovative basic and clinical research, patient care, community education and outreach, and the training of cancer specialists of the future. Georgetown Lombardi is one of only 46 comprehensive cancer centers in the nation, as designated by the National Cancer Institute, and the only one in the Washington, DC, area. For more information, go to http://lombardi.georgetown.edu.
About Georgetown University Medical Center
Georgetown University Medical Center (GUMC) is an internationally recognized academic medical center with a three-part mission of research, teaching and patient care (through MedStar Health). GUMC’s mission is carried out with a strong emphasis on public service and a dedication to the Catholic, Jesuit principle of cura personalis — or “care of the whole person.” The Medical Center includes the School of Medicine and the School of Nursing & Health Studies, both nationally ranked; Georgetown Lombardi Comprehensive Cancer Center, designated as a comprehensive cancer center by the National Cancer Institute; and the Biomedical Graduate Research Organization, which accounts for the majority of externally funded research at GUMC including a Clinical and Translational Science Award from the National Institutes of Health.