Project

CIViC: Clinical Interpretations of Variants in Cancer

Discover supported clinical interpretations of mutations related to cancer and collaborate with colleagues to add variants and support for cancer-related mutations.

CIViC: Clinical Interpretations of Variants in Cancer Details

Precision medicine refers to the use of prevention and treatment strategies that are tailored to the unique features of each individual and their disease. In the context of cancer this might involve the identification of specific mutations shown to predict response to a targeted therapy. The biomedical literature describing these associations is large and growing rapidly. Currently these interpretations exist largely in private or encumbered databases resulting in extensive repetition of effort. Realizing precision medicine will require this information to be centralized, debated and interpreted for application in the clinic. CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer. Our goal is to enable precision medicine by providing an educational forum for dissemination of knowledge and active discussion of the clinical significance of cancer genome alterations.

The Interpretation Bottleneck of Personalized Medicine

A typical cancer genomics workflow involves (1) the production of millions of short sequence reads from a tumor sample; (2) alignment to the reference genome and application of event detection algorithms; (3) filtering, manual review and validation to identify high-quality events; and (4) annotation of events and application of functional prediction algorithms. These steps culminate in (5) the production of dozens to thousands of potential tumor-driving events that must be interpreted by a skilled analyst and synthesized in a report. Each event must be researched in the context of current literature, drug-gene interaction databases, relevant clinical trials and known clinical actionability from knowledgebases. In our opinion, this attempt to infer clinical actionability represents the most severe bottleneck of the process. The analyst must find their way through the dark by extensive manual curation before handing off (6) a report for clinical evaluation and application by medical professionals. The CIViC resource attempts to address this interpretation bottleneck by organizing and crowdsourcing the curation process and providing interfaces for efficient access to this information.

How You Can Contribute to CIViC

  1. Add: Propose a new genomic variant (e.g. single nucleotide substitution, structural variant, gene fusion, etc.), add evidence statements that support clinical actions associated with such variants, or help create a synthesized interpretation or summary of the corpus of evidence for a variant.
  2. Approve: Community Editors and Moderators may approve submitted evidence items, after which the community may view and edit the item.
  3. View: Make use of the community-created content in your own research by browsing, searching, and examining detailed evidence items. All CIViC data and source code are provided freely for almost any use.
  4. Edit: Submit a correction or addition to any details about a genomic event, evidence statement, or interpretation.
  5. Discuss: Participate in an ongoing discussion in an effort to reach community consensus on the appropriate clinical action(s) for a genomic event.
  6. Apply/Reject: Editors and Moderators may apply or reject the edits made by other community members, after taking into account community discussions and opinion.

CIViC Principles

  • We believe that the interpretations of clinical actionability required to enable precision medicine should be freely available and openly discussed across a diverse community.
  • An interdisciplinary approach is needed to combine the expertise of genome scientists and health care providers, whose efforts are often isolated.
  • Content should be created with transparency, kept current, be comprehensive, track provenance, and acknowledge the efforts of creators.
  • The interface should be both structured enough to allow computational data mining and agile enough to handle the product of openly-debated, human interpretation.
  • CIViC is committed to providing unencumbered and efficient access to community-driven curation and interpretation of cancer mutations. Curated knowledge will remain free and can be accessed anonymously without login unless the user wishes to contribute to content.
  • To encourage both academic and commercial engagement, CIViC is released with minimal restrictions under a Creative Commons license (CC0). No fees or exclusive access will be introduced. While sharing improvements is strongly encouraged, the data can be adopted and used for nearly any purpose including the creation of commercial applications derived from the knowledge. We require only that attribution be given to the community that created the content.

The CIViC Web Interface

Visit CIViCdb.org today to explore and contribute to the interpretation of clinically actionable mutations for precision medicine in cancer.