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It's personal: New database aims to change how cancer is treated

Doctors will be able to tailor treatment to patients by seeing what has worked for others with similar tumors

June 3, 2014
Paul Fearn and Sarah Ramsay

HIDRA's Biomedical Informatics Lead Paul Fearn, right, and Sarah Ramsay, director, CIT Informatics, are key stakeholders in the construction of the Fred Hutch-led database, which will be operational this fall.

Robert Hood / Fred Hutch

In the world of cancer research and treatment, information is king. At Fred Hutchinson Cancer Research Center, bright minds are putting serious brain power into gathering, classifying, deciphering and, ultimately, translating massive amounts of tumor data into improved outcomes for cancer patients.

The idea, said Fred Hutch’s Dr. Eric Holland, is to link a patient’s clinical data with his or her tumor’s genetic data, and to integrate this information from thousands of patients. Ultimately, when someone is diagnosed, a physician will be able to enter the patient’s information and see which treatments were most effective for others with similar cancers.

By examining data from so many patients, “you can get a pretty good idea of a pattern,” explained Holland, who acts as the scientific overseer of HIDRA — Hutch Integrated Data Repository and Archive — a massive database currently under construction that will combine clinical records with tumor genetics and molecular data with the aim of eventually helping doctors choose the best targeted treatment.

“When a patient walks in the door, you can put them or their tumor in a neighborhood of similar patients or similar tumors,” said Holland.  

Researchers can then analyze these tumor neighborhoods to determine which mutations correlate with a fantastic response to a specific chemo drug — or no response at all.

“We can ask questions, like what did we do differently for some patients in this neighborhood that affected their outcome? Eventually, HIDRA will help oncologists make actual decisions about patient care,” said Holland, director of Fred Hutch’s Human Biology Division, the Solid Tumor Translational Research group and the Alvord Brain Tumor Center at the University of Washington.

Holland is helping direct this effort to combine records from Fred Hutch and its Cancer Consortium partners (UW Medicine, Seattle Children’s and Seattle Cancer Care Alliance) to build a single database to help researchers find these patterns. HIDRA will also collect molecular data from tumors, such as those stored in NWBioTrust’s tissue bank. The first web-based application designed to query and visualize this wealth of data is Argos, which will debut this summer as a pilot focused on brain tumor research before rapidly extending to other tumor types.

Seattle researchers predict the tool will change how we treat cancer while increasing efficiency and speed of translational research.

”HIDRA will set us apart from all other cancer centers in the country,” said Dr. Barbara Goff, a Fred Hutch researcher who specializes in women’s cancers, treats patients at SCCA and directs the Division of Gynecologic Oncology at UW.

This potential — to tangibly impact individual patients — is HIDRA’s great strength, said Goff, pointing to other patterns waiting to be divined: “We can look for missed opportunities. Why are some cancers diagnosed at late stages? What’s being missed?”

HIDRA will also aid Cancer Consortium oncologists in providing the highest quality of care by allowing them to compare their patients’ outcomes to national benchmarks and adjust care accordingly, she said.

Stitching the stories together

Currently, cancer researchers looking for patterns to help them tailor patients’ cancer treatments are stymied by the fact that the information they need is usually scattered among many different databases. A cancer patient in Seattle, for instance, may receive chemotherapy at SCCA, undergo surgery at UW Medicine, enter a Fred Hutch-run clinical trial, and agree to let a piece of their tumor be housed in NWBioTrust’s repository for further study.

Seattle Children’s Hospital, meanwhile, curates its own database on pediatric patients. Information about a patient’s treatment response might be divorced from critical data regarding their tumor’s particular genetic makeup. Often, data may be stored in different formats that computers need help reconciling.

For the Cancer Consortium, HIDRA is a single “patient-centric” database that surmounts this problem by collecting all these bits of information in one place. Additionally, HIDRA will perform the Herculean task of converting the information into the right format — its true superpower, explained Paul Fearn, biomedical informatics lead at Fred Hutch and the Cancer Consortium, who’s shepherding HIDRA’s development.  After being converted, information from free-form clinician-written medical notes will be as easily understood by computer programs as discrete numerical values from lab tests.

Once collected, patient data can be arranged into individual medical stories, said Holland. Databases across the Cancer Consortium will feed information on consenting cancer patients into HIDRA and combine it with data from NWBioTrust’s tissue bank, creating a mosaic that researchers can use to search for patterns.

Once the data is amassed and parsed, scientists will be able to “slice and dice” the information, said Tony Bozzuti, Fred Hutch’s chief information officer. The first user interface that allows scientists to “slice and dice” the data themselves will be Argos, developed by Fred Hutch partner LabKey Software.

When the Argos web interface goes live this summer, researchers will get a taste of how powerful a deep database of patient information can be. Soon after the pilot for brain cancer, Argos will expand to serve other disease groups.

HIDRA’s underlying technology — “plumbing” and automation to funnel reams of data into one giant pool — has been under development for two years. This fall these “pipes” will also be turned on, said Fearn. “Then Argos and other tools based on HIDRA will become so much more powerful.”

Location, location, location

Certain areas of cancer care that have historically lagged, like long-term follow-up, could receive an enormous boost from HIDRA, Goff added. Currently, it’s time-consuming and expensive to administer programs that follow long-term cancer survivors, but by automatically generating electronic questionnaires, programs connected to HIDRA could save researchers time and money while aiding in patient care and adding to scientists’ knowledge about life after cancer.

HIDRA’s wealth of historical data on the types of patients who pass through the Cancer Consortium will also benefit researchers planning future clinical trials. For example, scientists looking to design a clinical trial around patients with a particular type of brain tumor could look at how many of these patients pass through the Cancer Consortium in a given year and predict future trial enrolment.

“We’re creating a resource that doesn’t exist elsewhere,” said Sarah Ramsay, Fred Hutch’s director of informatics for Center IT and HIDRA’s operations and services supervisor. It will enable “more coordinated scientific projects and will be a resource to attract top scientists.”

Fred Hutch and the Cancer Consortium provide the right environment to create a project like HIDRA, said Fearn. Enough patients pass through the consortium that researchers will be able to glean real insights to improve patient care, and HIDRA collaborators bring all necessary know-how to the table.

Holland concurred. “We have the strengths in computation and dealing with big data to make this work,” he said. “Researchers need a lot more than just generating data — we need to know what to do with it, and how to structure it.”

Additionally, Seattle’s culture of collaboration is key to making HIDRA happen. “It’s not treated as a ‘me’ thing,” Holland said. It would be difficult to build HIDRA other places, but here “so many people from so many different disciplines and entities are joining together and contributing their skill sets to do the right thing for humanity. That’s what’s fun.”

Solid tumors, such as those of the brain, are the focus of Solid Tumor Translational Research, a network comprised of Fred Hutchinson Cancer Research Center, UW Medicine and Seattle Cancer Care Alliance. STTR is bridging laboratory sciences and patient care to provide the most precise treatment options for patients with solid tumor cancers.

Sabrina Richards is a staff writer at Fred Hutchinson Cancer Research Center. She has written about scientific research and the environment for The Scientist and OnEarth Magazine. She has a Ph.D. in immunology from the University of Washington, an M.A. in journalism and an advanced certificate from the Science, Health and Environmental Reporting Program at New York University. Reach her at srichar2@fredhutch.org.

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Fred Hutchinson Cancer Research Center is a world leader in research to prevent, detect and treat cancer and other life-threatening diseases.