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Online Database for Cancer Genomics to Help Clinicians

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Database

This genomics “knowledgebase” is designed to help clinicians determine whether an individual patient’s tumor contains DNA mutations that have been previously characterized.

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February 1, 2017 | by Sarah Hand, M.Sc.

As researchers continue to identify genetic mutations which may be implicated in the development of cancer, the need for a genomics database to organize all of this information is becoming more pressing. Now, researchers at Washington University School of Medicine in St. Louis, have developed an online database aimed at collecting and organizing cancer research from a variety of sources.

This genomics “knowledgebase” is designed to help clinicians determine whether an individual patient’s tumor contains DNA mutations that have been previously characterized. If the database returns a match, clinicians could treat the patient with available drugs designed target the specific mutation.

The online database – Clinical Interpretations of Variants in Cancer (CIViC) – can be added to by anyone, and this information is reviewed by cancer genomics experts. A paper presenting the details on CIViC was published in the journal, Nature Genetics.

“It’s relatively easy now to sequence the DNA of tumors — to gather the raw information — but there’s a big interpretation problem,” said Dr. Obi L. Griffith, assistant director at the McDonnell Genome Institute, Washington University School, and senior author of the study. “What do these hundreds or thousands of mutations mean for this patient? There are a lot of studies being done to answer these questions. But oncologists trying to interpret the raw data are faced with an overwhelming task of plumbing the literature, reading papers, trying to understand what the latest studies tell them about these mutations and how they may or may not be important.”

While other databases exist to organize genomic information collected from patient tumors, the authors say that CIViC is the only open access platform, as far as they know. Anyone can submit genomics information as well as access that which was uploaded by other users.



“We are committed to keeping this resource open and available to anyone who wants to contribute or make use of the information,” said Dr. Malachi Griffith, assistant professor at the McDonnell Genome Institute and lead author of the publication. “We would like it to be a community exercise and public resource. The information is in the public domain. There are no restrictions on its use, academic or commercial.”

So far, over 17,500 users have accessed the database, including professionals from academia, industry and government organizations. Over 700 mutations from 285 genes have been characterized based on their clinical relevance in over 200 distinct cancer types. This information was contributed by 59 users based on a review of nearly 1,100 publications.

“While we believe this is the only such open-access knowledgebase, there are other large research centers with similar resources,” said Griffith. “We did an analysis to compare the big ones. Even though we all have access to the same published literature, if you look at the overlap of the information mined by each of these resources, it’s remarkably small. We’re all approaching the same problem and just by chance — and probably because of the amount of information out there — we haven’t duplicated our efforts very much yet.”


Keywords: Cancer, Genomics, Database


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