Format

Send to

Choose Destination
Hum Mutat. 2018 Nov;39(11):1721-1732. doi: 10.1002/humu.23651.

Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards.

Author information

1
McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, Missouri.
2
Baylor College of Medicine, Houston, Texas.
3
Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, Maryland.
4
Vanderbilt-Ingram Cancer Center, Nashville, Tennessee.
5
Georgetown Lombardi Comprehensive Cancer Center, Washington, District of Columbia.
6
Keck School of Medicine, University of Southern California, Los Angeles, California.
7
Baylor Genetics, Houston, Texas.
8
Dan L. Duncan Cancer Center, Houston, Texas.

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

PMID:
30311370
DOI:
10.1002/humu.23651

Supplemental Content

Full text links

Icon for Wiley
Loading ...
Support Center