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$3.7 million supports crowdsourced database of cancer genomics

Open-source database aims to connect genetics of a tumor to possible treatments

by Julia Evangelou StraitOctober 15, 2019

Matt Miller

Scientists at Washington University School of Medicine in St. Louis have received a $3.7 million grant from the National Institutes of Health (NIH) to support an open-source database aimed at boosting personalized approaches to cancer treatment. The database is designed to help doctors match cancer mutations — found in patients’ tumors — with drugs that target such genetic errors.

The online resource was started by computational biology specialists Obi L. Griffith, PhD, an associate professor of medicine and of genetics, and Malachi Griffith, PhD, an assistant professor of medicine and of genetics. Both are research members of the McDonnell Genome Institute and Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine.

The database’s name is CIViC, which stands for Clinical Interpretations of Variants in Cancer. According to its founders, it is the only entirely open-source online resource for querying tumor mutations — like a Wikipedia for cancer genomics. Comparing CIViC to Wikipedia — an online encyclopedia maintained by volunteers — the Griffiths, who are twin brothers, designed a system that allows anyone to create an account and contribute information to the database. Experts in the field serve as editors, curating data that is incorporated into the system. It is also free for anyone to use.

“Maintaining up-to-date and comprehensive information about the significance of genetic mutations in cancer — and what such mutations may mean for patients — is a major bottleneck to improving cancer care,” said Obi Griffith. “CIViC is the kind of tool that can help relieve that bottleneck. With that in mind, it’s important to make this data open and accessible to anyone who needs it. This research is funded by public taxpayer dollars, and it should be accessible to and benefit the general public.

“Often, doctors have some genetic information about a patient’s tumor, but it’s not clear what that might mean for treatment,” he added. “Searching the scientific literature is time-consuming, and important data still could be missed. The purpose of CIViC is to streamline and automate that process. It’s a resource that can help clinicians determine the specific type of cancer a patient has, the prognosis and, in some cases, identify a drug that has the potential to help the patient. This new grant will help us continue to develop CIViC into an even better resource to make this type of personalized medicine more widely available.”

Genetic variants that might be significant for a cancer patient include those that: help predict how a patient might respond to a drug; differentiate between different types of cancer that might appear to be the same tumor type; indicate how aggressive the cancer is likely to be; and signal how likely a person is to develop a certain type of cancer in the future.

CIViC is one of several similar resources attempting to make information about significant cancer genomic variants more accessible to doctors who treat such patients. That it is fully open access, including the source code that underlies how it works, makes CIViC unique. According to the researchers, CIViC has more than 3,000 monthly visitors and 80,000 unique users to date, primarily from cancer research institutes and hospitals. These users are from 163 countries, including the U.S., China, Japan, Germany, India, the United Kingdom and South Korea. Some top institutions that make use of CIViC include the NIH, Stanford University, the University of California at San Francisco, the Mayo Clinic, Memorial Sloan Kettering Cancer Center, Genentech, M.D. Anderson and Baylor College of Medicine. Many of these users have set up their clinical work stations to automatically receive information from CIViC so the tool is constantly updated and can be incorporated into doctors’ workflows when treating patients.

“We receive millions of hits to the CIViC application from outside clients, including academic institutions and companies that use CIViC data in their own tools,” Malachi Griffith said. “We are trying to work with other similar genomic data resources to develop standards for interpreting all this information and to make sure we are including as much available information as possible — including new discoveries — without duplicating too many of our efforts.”

The Griffiths also are active in international efforts to collaborate with researchers doing similar work and combine their systems so such resources are available to all cancer patients, wherever they may receive treatment. The researchers helped form the Variant Interpretation for Cancer Consortium, an initiative that helps guide efforts by the Global Alliance for Genomics & Health to develop data-sharing standards, so that doctors one day may make queries in one place but have access to multiple cancer Wikipedia-like databases, including CIViC, that are all governed by the same standard guidelines. The goal is to ensure doctors have access to the most information at the highest levels of evidence for clinical decision-making.

Washington University School of Medicine’s 1,500 faculty physicians also are the medical staff of Barnes-Jewish and St. Louis Children’s hospitals. The School of Medicine is a leader in medical research, teaching and patient care, ranking among the top 10 medical schools in the nation by U.S. News & World Report. Through its affiliations with Barnes-Jewish and St. Louis Children’s hospitals, the School of Medicine is linked to BJC HealthCare.