Cancer Variant Interpretation Hackathon and Curation Jamboree

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 CIViC Project

A one-day hackathon and curation jamboree lead by the CIViC project team in collaboration with the CCGA and the ClinGen Somatic Cancer CDWG.

Eric P. Newman Education Center

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. Open access, open source, community-driven web resources such as CIViC (Clinical Interpretation of Variants in Cancer) and CCGA (Compendium of Cancer Genome Aberrations) provide publicly accessible tools to support cancer variant curation and interpretation in a disease-specific context. Targeted curation projects and efforts to standarize somatic cancer varaint interpretation through the creation and modification of variant classiciation guidelines are led by the the ClinGen Somatic Cancer Clincal Domain Working Group (CDWG). <ul><li>CIViC (<a href="https://civicdb.org/welcome" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">www.civicdb.org</a>) aims to enable precision medicine by providing an educational forum for dissemination of knowledge and active discussion of the clinical significance of cancer genome alterations. </li><li>The CCGA (<a href="http://www.ccga.io" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">www.ccga.io</a>) is a program of the Cancer Genomics Consortium (CGC) and provides a centralized online resource of genetic correlates for pathologic entities in cancer, structured using the current disease-level WHO classification system. The Wiki style interface allows for real-time updating and sharing of clinically relevant content that is peer-reviewed and easily searchable.</li><li>The ClinGen Somatic Cancer CDWG (<a href="https://clinicalgenome.org/working-groups/clinical-domain/somatic-cancer-cdwg/" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">clinicalgenome.org/working-groups/clinical-domain/somatic-cancer-cdwg</a>) facilitates the development of data curation guidelines and standards to determine the clinical actionability of somatic alterations in cancer, thereby enhancing their usability, dissemination, and implementation.</li></ul>A hackathon and curation jamboree will be held as a pre-meeting of the <a href="https://www.cancergenomics.org/meetings/cgc_annual_meeting_2022.php" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">CGC annual conference</a>, lead by the CIViC project team in collaboration with the CCGA and the ClinGen Somatic Cancer CDWG, and hosted at Washington University in St. Louis. The focus of this meeting will be to continue developing community consensus on data standards for interpretation of variants in cancer, engage software developers for improved variant interpretation software and data visualizations, and engage clinical experts for curation of content and enhance integration and interoperability of resources. Additional related topics will be proposed by meeting participants.

Meeting Goals (included but not limited to)<ul><li>Establish community standards and best practices for curation and representation of clinically actionable variants in cancer.</li><li>Promote formation of a collaborative network for community-based development of precision medicine resources.</li><li>Enhance integration and interoperability of resources through standardization of entities, improvement of APIs, and use of ontologies.</li><li>Develop a strategy for integration of CIViC and CCGA resources.</li><li>Introduce users to CCGA and CIViC curation. </li><li>Optimize automation and processes of wiki-based templating and structured data integration to streamline content creation and alteration in CCGA.</li><li>Develop best practices for data visualizations.</li><li>Improve drug normalization in variant interpretation knowledgebases.</li><li>Further develop text-mining strategies for identifying evidence of clinically actionable variants (e.g., CIViCmine).</li><li>Examine ways to incentivize the curation community, e.g. Zenodo, bioCADDIE for citable records.</li><li>Develop methodology for implementation of assertions for variant oncogenicity.</li><li>Teach participants how to use CIViC 2.0 UI and APIs.</li><li>Specific meeting topics will be proposed by meeting participants (see below).</li></ul>

Proposed topics for curation and hackathonParticipants can create an issue describing a proposed topic and apply the 'hackathon' or 'curation' label for CIViC or CCGA at: <a href="https://github.com/griffithlab/civic-meeting" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">https://github.com/griffithlab/civic-meeting</a>

Meeting formatThe Cancer Variant Interpretation hackathon and jamboree will take the form of an unconference with minimal presentations and an emphasis on hands-on activities, breakout sessions to discuss emerging standards, learning to curate variants, or work on tools for variant interpretation or site optimization. Participants will self-form into groups to tackle domain-specific variant or disease curation (jamboree), programmatic data querying (hackathon), the problem of motivating public resource curation, or other topics proposed by meeting participants.Lunch and afternoon snacks will be provided. Please note any dietary restrictions in the appropriate field during signup.

Pre-requisitesParticipants should bring their own laptop in order to participate.

Target audienceHackathon: Software developers, engineers, computational biologists, and bioinformaticians interested in learning how to interact with CIViC 2.0, CCGA or work on related tools to facilitate variant interpretation and resource automation and optimization. Prerequisites: Familiarity with Ruby, Wiki syntax, and/or Python would be beneficial.Curation Jamboree: Pathologists and oncologists (certified or in training), genome scientists, and those interested in the problem of sequence and structural variant interpretation for cancer precision medicine or promotion of public biocuration resources. Prerequisites: Basic understanding of the genetic basis of cancer.

Bug reports and feature requestsFor CIViC, please create an issue in the CIViC 2.0 github repo: <a href="https://github.com/griffithlab/civic-v2/issues" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">https://github.com/griffithlab/civic-v2/issues</a>For CCGA please email ccga@cancergenomics.orgFor ClinGen please email: coordinator.sc.cdwg@gmail.com

Curation HelpFor questions or assistance with the CIViC curation interface please email: help@civicdb.org. For CCGA please email: ccga@cancergenomics.org.For ClinGen please email: coordinator.sc.cdwg@gmail.com

AcknowledgementsThe CIViC resource and this meeting is supported by the National Cancer Institute (NCI) of the National Institutes of Health (NIH) under Award Number U24CA237719 to Obi Griffith (with Malachi Griffith as co-PI). The CCGA is supported by the Cancer Genomics Consortium (<a href="http://cancergenomics.org" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">cancergenomics.org</a>). The ClinGen Somatic Cancer CDWG is supported by the National Human Genome Research Institute ( NHGRI) U24 HG009650.

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Cancer Variant Interpretation Hackathon and Curation Jamboree

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