CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

Kilannin Krysiak; Arpad M. Danos; Jason Saliba; Joshua F. McMichael; Adam C. Coffman; Susanna Kiwala; Erica K. Barnell; Lana Sheta; Cameron J. Grisdale; Lynzey Kujan; Shahil Pema; Jake Lever; Sarah Ridd; Nicholas C. Spies; Veronica Andric; Andreea Chiorean; Damian T. Rieke; Kaitlin A. Clark; Caralyn Reisle; Ajay C. Venigalla; Mark Evans; Payal Jani; Hideaki Takahashi; Avila Suda; Peter Horak; Deborah I. Ritter; Xin Zhou; Benjamin J. Ainscough; Sean Delong; Chimene Kesserwan; Mario Lamping; Haolin Shen; Alex R. Marr; My H. Hoang; Kartik Singhal; Mariam Khanfar; Brian V. Li; Wan Hsin Lin; Panieh Terraf; Laura B. Corson; Yasser Salama; Katie M. Campbell; Kirsten M. Farncombe; Jianling Ji; Xiaonan Zhao; Xinjie Xu; Rashmi Kanagal-Shamanna; Ian King; Kelsy C. Cotto; Zachary L. Skidmore; Jason R. Walker; Jinghui Zhang; Aleksandar Milosavljevic; Ronak Y. Patel; Rachel H. Giles; Raymond H. Kim; Lynn M. Schriml; Elaine R. Mardis; Steven J.M. Jones; Gordana Raca; Shruti Rao; Subha Madhavan; Alex H. Wagner; Malachi Griffith; Obi L. Griffith

doi:10.1093/nar/gkac979

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

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

Hematopathology

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

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. CIViC contains peer-reviewed, published literature curated and expertly-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 has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.

Original language	English (US)
Pages (from-to)	D1230-D1241
Journal	Nucleic acids research
Volume	51
Issue number	1 D
DOIs	https://doi.org/10.1093/nar/gkac979
State	Published - Jan 6 2023

ASJC Scopus subject areas

Genetics

Access to Document

10.1093/nar/gkac979

Cite this

Krysiak, K., Danos, A. M., Saliba, J., McMichael, J. F., Coffman, A. C., Kiwala, S., Barnell, E. K., Sheta, L., Grisdale, C. J., Kujan, L., Pema, S., Lever, J., Ridd, S., Spies, N. C., Andric, V., Chiorean, A., Rieke, D. T., Clark, K. A., Reisle, C., ... Griffith, O. L. (2023). CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. Nucleic acids research, 51(1 D), D1230-D1241. https://doi.org/10.1093/nar/gkac979

Krysiak, K, Danos, AM, Saliba, J, McMichael, JF, Coffman, AC, Kiwala, S, Barnell, EK, Sheta, L, Grisdale, CJ, Kujan, L, Pema, S, Lever, J, Ridd, S, Spies, NC, Andric, V, Chiorean, A, Rieke, DT, Clark, KA, Reisle, C, Venigalla, AC, Evans, M, Jani, P, Takahashi, H, Suda, A, Horak, P, Ritter, DI, Zhou, X, Ainscough, BJ, Delong, S, Kesserwan, C, Lamping, M, Shen, H, Marr, AR, Hoang, MH, Singhal, K, Khanfar, M, Li, BV, Lin, WH, Terraf, P, Corson, LB, Salama, Y, Campbell, KM, Farncombe, KM, Ji, J, Zhao, X, Xu, X, Kanagal-Shamanna, R, King, I, Cotto, KC, Skidmore, ZL, Walker, JR, Zhang, J, Milosavljevic, A, Patel, RY, Giles, RH, Kim, RH, Schriml, LM, Mardis, ER, Jones, SJM, Raca, G, Rao, S, Madhavan, S, Wagner, AH, Griffith, M & Griffith, OL 2023, 'CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase', Nucleic acids research, vol. 51, no. 1 D, pp. D1230-D1241. https://doi.org/10.1093/nar/gkac979

@article{c543c0c8afd9442ab830ce42e2a1b680,

title = "CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase",

abstract = "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. CIViC contains peer-reviewed, published literature curated and expertly-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{\textquoteright}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 has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.",

author = "Kilannin Krysiak and Danos, {Arpad M.} and Jason Saliba and McMichael, {Joshua F.} and Coffman, {Adam C.} and Susanna Kiwala and Barnell, {Erica K.} and Lana Sheta and Grisdale, {Cameron J.} and Lynzey Kujan and Shahil Pema and Jake Lever and Sarah Ridd and Spies, {Nicholas C.} and Veronica Andric and Andreea Chiorean and Rieke, {Damian T.} and Clark, {Kaitlin A.} and Caralyn Reisle and Venigalla, {Ajay C.} and Mark Evans and Payal Jani and Hideaki Takahashi and Avila Suda and Peter Horak and Ritter, {Deborah I.} and Xin Zhou and Ainscough, {Benjamin J.} and Sean Delong and Chimene Kesserwan and Mario Lamping and Haolin Shen and Marr, {Alex R.} and Hoang, {My H.} and Kartik Singhal and Mariam Khanfar and Li, {Brian V.} and Lin, {Wan Hsin} and Panieh Terraf and Corson, {Laura B.} and Yasser Salama and Campbell, {Katie M.} and Farncombe, {Kirsten M.} and Jianling Ji and Xiaonan Zhao and Xinjie Xu and Rashmi Kanagal-Shamanna and Ian King and Cotto, {Kelsy C.} and Skidmore, {Zachary L.} and Walker, {Jason R.} and Jinghui Zhang and Aleksandar Milosavljevic and Patel, {Ronak Y.} and Giles, {Rachel H.} and Kim, {Raymond H.} and Schriml, {Lynn M.} and Mardis, {Elaine R.} and Jones, {Steven J.M.} and Gordana Raca and Shruti Rao and Subha Madhavan and Wagner, {Alex H.} and Malachi Griffith and Griffith, {Obi L.}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2023",

month = jan,

day = "6",

doi = "10.1093/nar/gkac979",

language = "English (US)",

volume = "51",

pages = "D1230--D1241",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "1 D",

}

TY - JOUR

T1 - CIViCdb 2022

T2 - evolution of an open-access cancer variant interpretation knowledgebase

AU - Krysiak, Kilannin

AU - Danos, Arpad M.

AU - Saliba, Jason

AU - McMichael, Joshua F.

AU - Coffman, Adam C.

AU - Kiwala, Susanna

AU - Barnell, Erica K.

AU - Sheta, Lana

AU - Grisdale, Cameron J.

AU - Kujan, Lynzey

AU - Pema, Shahil

AU - Lever, Jake

AU - Ridd, Sarah

AU - Spies, Nicholas C.

AU - Andric, Veronica

AU - Chiorean, Andreea

AU - Rieke, Damian T.

AU - Clark, Kaitlin A.

AU - Reisle, Caralyn

AU - Venigalla, Ajay C.

AU - Evans, Mark

AU - Jani, Payal

AU - Takahashi, Hideaki

AU - Suda, Avila

AU - Horak, Peter

AU - Ritter, Deborah I.

AU - Zhou, Xin

AU - Ainscough, Benjamin J.

AU - Delong, Sean

AU - Kesserwan, Chimene

AU - Lamping, Mario

AU - Shen, Haolin

AU - Marr, Alex R.

AU - Hoang, My H.

AU - Singhal, Kartik

AU - Khanfar, Mariam

AU - Li, Brian V.

AU - Lin, Wan Hsin

AU - Terraf, Panieh

AU - Corson, Laura B.

AU - Salama, Yasser

AU - Campbell, Katie M.

AU - Farncombe, Kirsten M.

AU - Ji, Jianling

AU - Zhao, Xiaonan

AU - Xu, Xinjie

AU - Kanagal-Shamanna, Rashmi

AU - King, Ian

AU - Cotto, Kelsy C.

AU - Skidmore, Zachary L.

AU - Walker, Jason R.

AU - Zhang, Jinghui

AU - Milosavljevic, Aleksandar

AU - Patel, Ronak Y.

AU - Giles, Rachel H.

AU - Kim, Raymond H.

AU - Schriml, Lynn M.

AU - Mardis, Elaine R.

AU - Jones, Steven J.M.

AU - Raca, Gordana

AU - Rao, Shruti

AU - Madhavan, Subha

AU - Wagner, Alex H.

AU - Griffith, Malachi

AU - Griffith, Obi L.

PY - 2023/1/6

Y1 - 2023/1/6

N2 - 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. CIViC contains peer-reviewed, published literature curated and expertly-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 has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.

AB - 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. CIViC contains peer-reviewed, published literature curated and expertly-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 has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.

UR - http://www.scopus.com/inward/record.url?scp=85145973231&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85145973231&partnerID=8YFLogxK

U2 - 10.1093/nar/gkac979

DO - 10.1093/nar/gkac979

M3 - Article

C2 - 36373660

AN - SCOPUS:85145973231

SN - 0305-1048

VL - 51

SP - D1230-D1241

JO - Nucleic acids research

JF - Nucleic acids research

IS - 1 D

ER -

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this