@article{455e946f62ad4a6598e0d91003eef093,
title = "Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards",
abstract = "Harmonization of cancer variant representation, efficient communication, and free distribution of clinical variant-associated knowledge are central problems that arise with increased usage of clinical next-generation sequencing. The Clinical Genome Resource (ClinGen) Somatic Working Group (WG) developed a minimal variant level data (MVLD) representation of cancer variants, and has an ongoing collaboration with Clinical Interpretations of Variants in Cancer (CIViC), an open-source platform supporting crowdsourced and expert-moderated cancer variant curation. Harmonization between MVLD and CIViC variant formats was assessed by formal field-by-field analysis. Adjustments to the CIViC format were made to harmonize with MVLD and support ClinGen Somatic WG curation activities, including four new features in CIViC: (1) introduction of an assertions feature for clinical variant assessment following the Association of Molecular Pathologists (AMP) guidelines, (2) group-level curation tracking for organizations, enabling member transparency, and curation effort summaries, (3) introduction of ClinGen Allele Registry IDs to CIViC, and (4) mapping of CIViC assertions into ClinVar submission with automated submissions. A generalizable workflow utilizing MVLD and new CIViC features is outlined for use by ClinGen Somatic WG task teams for curation and submission to ClinVar, and provides a model for promoting harmonization of cancer variant representation and efficient distribution of this information.",
keywords = "CIViC, ClinGen, ClinVar, cancer, curation",
author = "{Clinical Genome Resource Somatic Working Group and Clinical Interpretation of Variants in Cancer team members} and Danos, {Arpad M.} and Ritter, {Deborah I.} and Wagner, {Alex H.} and Kilannin Krysiak and Dmitriy Sonkin and Christine Micheel and Matthew McCoy and Shruti Rao and Gordana Raca and Boca, {Simina M.} and Angshumoy Roy and Barnell, {Erica K.} and McMichael, {Joshua F.} and Susanna Kiwala and Coffman, {Adam C.} and Lynzey Kujan and Shashikant Kulkarni and Malachi Griffith and Subha Madhavan and Griffith, {Obi L.}",
note = "Funding Information: The ClinGen consortium is funded by the National Human Genome Research Institute (NHGRI) with award numbers: U41HG009649, U41HG009650, U01HG007436 and U01HG007437. A.W. is supported by the National Cancer Institute (NCI) of the National Institutes of Health (NIH) with award number F32CA206247. M.G. is supported by the NHGRI with award number R00HG007940. CIViC is funded by the NCI to O.L.G. under award number U01CA209936. Clinical Interpretations of Variants in Cancer (CIViC) would like to acknowledge the community of curators, editors, and users that make the project possible and remain committed to the free and open sharing of this important knowledge. The Clinical Genome Resource (ClinGen) Somatic Working Group thanks the many cancer experts, biocurators, and working group members who participate in our monthly calls, in-person meetings, and task teams. For those interested in joining our expert-led curation efforts, please contact clingen@clinicalgenome.org. Publisher Copyright: {\textcopyright} 2018 The Authors. Human Mutation published by Wiley Periodicals, Inc.",
year = "2018",
month = nov,
doi = "10.1002/humu.23651",
language = "English",
volume = "39",
pages = "1721--1732",
journal = "Human Mutation",
issn = "1059-7794",
number = "11",
}