Paper

Evolution of the open-access CIViC knowledgebase is driven by the needs of the cancer variant interpretation community

Patel, Ronak Y, Giles, Rachel H, Krysiak, Kilannin, Skidmore, Zachary L, Madhavan, Subha, Delong, Sean, Sheta, Lana, Lever, Jake, Clark, Kaitlin A, Marr, Alex R, Spies, Nicholas C, Terraf, Panieh, Campbell, Katie, Lamping, Mario, Salama, Yasser, Schriml, Lynn M, Wagner, Alex H, Pema, Shahil, Zhou, Xin, Rao, Shruti, Griffith, Malachi, Danos, Arpad M, Kim, Raymond H, Raca, Gordana, Farncombe, Kirsten M, Jones, Steven JM, Kiwala, Susanna, Kanagal-Shamanna, Rashmi, Zhao, Xiaonan, Rieke, Damian T, Coffman, Adam C, Zhang, Jinghui, Mardis, Elaine R, Lin, Wan-Hsin, Walker, Jason R, Jani, Payal, Xu, Xinjie, Griffith, Obi L, Takahashi, Hideaki, Kujan, Lynzey, Horak, Peter, Chiorean, Andreea, Saliba, Jason, Ritter, Deborah I, Li, Brian V, Ainscough, Benjamin J, Ji, Jianling, Cotto, Kelsy C, Barnell, Erica K, McMichael, Joshua F, Milosavljevic, Aleksandar, Grisdale, Cameron J

2021

Overview

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. With nearly 300 contributors, CIViC contains peer-reviewed, published literature curated and expert-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC’s functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new evidence types (predisposing, oncogenic and functional). The growing CIViC knowledgebase distributes clinically-relevant cancer variant data currently representing >2500 variants in >400 genes from >2800 publications.

• Publisher: Cold Spring Harbor Laboratory
• Subject: Genomics