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The New York Genome Center and IBM Watson Group In Genomic Medicine Collaboration

March 19, 2014
by John DeGaspari
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Clinical study will bring together technology partner in genomic treatment of brain cancer patients

The New York Genome Center (NYGC) and IBM announced on March 19 an initiative to accelerate genomic medicine with the use of IBM’s Watson cognitive system. At a press briefing in New York attended by Healthcare Informatics, the partners said they will test a Watson prototype designed specifically for genomic research as a tool to help oncologists deliver more personalized care to cancer patients. 

NYGC and nine of its medical partner institutions plan to initially evaluate Watson’s ability to help oncologists develop more personalized care to patients with glioblastoma, an aggressive and malignant brain cancer that kills more than 13,000 people in the U.S. each year. Few patients benefit from personalized treatment of this type of cancer in a way that is tailored to their individual cancer mutations. The disease progresses rapidly: mean time between diagnosis and time of death is 12 to 14 months.

Clinicians currently lack adequately automated tools and time required to bring DNA-based treatment options to their patients and to do so, they must manually correlate data from genome sequencing to reams of medical journals, new studies and clinical records, at a time when medical information is doubling every five years, according to NYGC.

The NYGC-Watson initiative aims to speed up this complex process by identifying patterns in genome sequencing and medical data to unlock insights that will help clinicians bring the promise of genomic medicine to their patients. The combination of NYGC’s genomic and clinical expertise, coupled with the power of IBM’s Watson system, will enable further development and refinement of the Watson tool with the shared goal of helping medical professionals develop personalized cancer care. 

The new cloud-based Watson system will be designed to analyze genetic data along with comprehensive biomedical literature and drug databases. Watson can continually “learn” as it encounters new patient scenarios, and as more information becomes available through new medical research, journal articles and clinical studies. Given the depth and speed of Watson’s ability to review massive databases, the goal of the collaboration is to increase the number of patients who have access to care options tailored to their disease’s DNA. 

“Since the human genome was first mapped more than a decade ago, we’ve made tremendous progress in understanding the genetic drivers of disease. The real challenge before us is how to make sense of massive quantities of genetic data and translate that information into better treatments for patients,” said Robert Darnell, M.D., Ph.D., CEO, president and scientific director of the New York Genome Center. “Applying the cognitive computing power of Watson is going to revolutionize genomics and accelerate the opportunity to improve outcomes for patients with deadly diseases by providing personalized treatment.” 

The first task of the initiative will be a clinical study that will sequence the tumors of 20 patients in great detail, Darnell said. “The amount of information we will be generating is enormous,” he said. All glioblastoma tumors differ from each other, he said. Interpreting the vast amount of data is a limiting factor now for doctors delivering the power of sequencing back to the patient. Initially, the NYGC will learn how to capture the data and analyze it, working with its academic and clinical partners. Once the information is captured, it will be analyzed to identify the mutations in each tumor. 

This is where Watson comes in, Darnell said. “There are thousands of mutations that are present in any patient’s tumor, as well as a robust set of medical literature describing the meaning of those mutations, their pathways, how they drive the tumor and the relevance to the patients. Watson will process the huge amount s of data for each patient “to find the needles in the enormous sequence haystacks.” Using that information, it will identify the best available drugs to attack the patient’s tumor in a timely manner, given the urgency of the disease, he said. Watson has the ability to ingest millions of journal articles a day.

Watson will complement rapid genome sequencing and is expected to dramatically reduce the time it takes to correlate an individual’s genetic mutations with reams of medical literature, study findings, and therapeutic indications that may be relevant. It will provide comprehensive information to enable clinicians to consider a variety of treatment options that the clinician can tailor to their patient’s genetic mutations. It will also help NYGC scientists understand the data detailing gene sequence variations between normal and cancerous biopsies of brain tumors. 

“As genomic research progresses and information becomes more available, we aim to make the process of analysis much more practical and accessible through cloud-based, cognitive innovations like Watson,” said Dr. John E. Kelly III, senior vice president and director of IBM Research. “With this knowledge, doctors will be able to attack cancer and other devastating diseases with treatments that are tailored to the patient’s and disease’s own DNA profiles. If successful, this will be a major transformation that will help improve the lives of millions of patients around the world.”