It is relatively easy now to sequence the DNA of tumors - to gather
the raw information - but there's a big interpretation problem.
Researchers at Washington University School of Medicine in St. Louis
have developed an online "knowledgebase" intended for the gathering and
organization of cancer genomics so that clinicians have improved
chances of identifying important mutations in a patient's tumor and
potentially connecting genetic errors with drugs known to target them.
‘An online "knowledgebase" intends to gather and organize cancer genomics so that clinicians have improved chances of identifying important mutations in a patient's tumor and potentially connecting genetic errors with drugs known to target them.’
The online resource, called CIViC, is described in Nature Genetics
The body of knowledge on cancer genomics is massive and
ever-expanding. But this wealth of potentially critical information is
far less likely to be of help to patients if it is inaccessible to the
doctors who treat them.
CIViC stands for Clinical Interpretations of Variants in Cancer, and
the researchers liken it to a Wikipedia of cancer genetics. Anyone can
create an account and contribute information. That information is then
curated by editors and moderators who are experts in the field.
Senior author Obi L. Griffith, an assistant professor of medicine, said,
"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."
The CIViC knowledgebase is an attempt to solve this problem. While
the investigators said this is one of many efforts to collect and
interpret such information, CIViC is the only one that is entirely open
access, to their knowledge. Anyone is free to contribute and use the
content as well as the source code.
"We are committed to keeping this resource open and available to
anyone who wants to contribute or make use of the information," said
Malachi Griffith, an assistant professor of medicine. "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
Obi and Malachi Griffith, who are twin brothers, are assistant directors of the university's McDonnell Genome Institute.
Though anyone can submit a new piece of information or suggest edits
to existing data, at least two independent contributors must agree that
the new information should be incorporated, and one of those users must
be an expert editor. Expert editors are not permitted to approve their
own submissions. Information on the CIViC website provides details about
how new users may be promoted to expert editors and administrators.
To date, the site has seen over 17,500 users from academic
institutions, governmental organizations and commercial entities around
the world. Since CIViC's launch, 59 users have volunteered their time to
contribute their knowledge to CIViC, including descriptions of the
clinical relevance of 732 mutations from 285 genes for 203 types of
cancer, all gleaned from reviewing 1,090 scientific and medical
Despite the fact there are many groups attempting to collect and
interpret genomic variants in cancer, the investigators said the sheer
volume of information has resulted in relatively little overlap in data
gathered so far.
"While we believe this is the only such open-access knowledgebase,
there are other large research centers with similar resources," Malachi
Griffith said. "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."
Obi and Malachi Griffith said finding a way to combine these
resources is the primary goal of an international group they are helping
lead called the Variant Interpretation for Cancer Consortium, which is a
part of the Global Alliance for Genomics and Health (GA4GH).
"We're just scratching the surface of the potential this holds for
precision medicine," Obi Griffith said. "There's a lot of work to do."