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

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) devel...

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Autores principales: Danos, Arpad M., Ritter, Deborah I., Wagner, Alex H., Krysiak, Kilannin, Sonkin, Dmitriy, Micheel, Christine, McCoy, Matthew, Rao, Shruti, Raca, Gordana, Boca, Simina M., Roy, Angshumoy, Barnell, Erica K., McMichael, Joshua F., Kiwala, Susanna, Coffman, Adam C., Kujan, Lynzey, Kulkarni, Shashikant, Griffith, Malachi, Madhavan, Subha, Griffith, Obi L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282863/
https://www.ncbi.nlm.nih.gov/pubmed/30311370
http://dx.doi.org/10.1002/humu.23651
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author Danos, Arpad M.
Ritter, Deborah I.
Wagner, Alex H.
Krysiak, Kilannin
Sonkin, Dmitriy
Micheel, Christine
McCoy, Matthew
Rao, Shruti
Raca, Gordana
Boca, Simina M.
Roy, Angshumoy
Barnell, Erica K.
McMichael, Joshua F.
Kiwala, Susanna
Coffman, Adam C.
Kujan, Lynzey
Kulkarni, Shashikant
Griffith, Malachi
Madhavan, Subha
Griffith, Obi L.
author_facet Danos, Arpad M.
Ritter, Deborah I.
Wagner, Alex H.
Krysiak, Kilannin
Sonkin, Dmitriy
Micheel, Christine
McCoy, Matthew
Rao, Shruti
Raca, Gordana
Boca, Simina M.
Roy, Angshumoy
Barnell, Erica K.
McMichael, Joshua F.
Kiwala, Susanna
Coffman, Adam C.
Kujan, Lynzey
Kulkarni, Shashikant
Griffith, Malachi
Madhavan, Subha
Griffith, Obi L.
author_sort Danos, Arpad M.
collection PubMed
description 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.
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spelling pubmed-62828632018-12-14 Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards Danos, Arpad M. Ritter, Deborah I. Wagner, Alex H. Krysiak, Kilannin Sonkin, Dmitriy Micheel, Christine McCoy, Matthew Rao, Shruti Raca, Gordana Boca, Simina M. Roy, Angshumoy Barnell, Erica K. McMichael, Joshua F. Kiwala, Susanna Coffman, Adam C. Kujan, Lynzey Kulkarni, Shashikant Griffith, Malachi Madhavan, Subha Griffith, Obi L. Hum Mutat Special Issue Articles 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. John Wiley and Sons Inc. 2018-10-11 2018-11 /pmc/articles/PMC6282863/ /pubmed/30311370 http://dx.doi.org/10.1002/humu.23651 Text en © 2018 The Authors. Human Mutation published by Wiley Periodicals, Inc. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Special Issue Articles
Danos, Arpad M.
Ritter, Deborah I.
Wagner, Alex H.
Krysiak, Kilannin
Sonkin, Dmitriy
Micheel, Christine
McCoy, Matthew
Rao, Shruti
Raca, Gordana
Boca, Simina M.
Roy, Angshumoy
Barnell, Erica K.
McMichael, Joshua F.
Kiwala, Susanna
Coffman, Adam C.
Kujan, Lynzey
Kulkarni, Shashikant
Griffith, Malachi
Madhavan, Subha
Griffith, Obi L.
Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards
title Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards
title_full Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards
title_fullStr Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards
title_full_unstemmed Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards
title_short Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards
title_sort adapting crowdsourced clinical cancer curation in civic to the clingen minimum variant level data community‐driven standards
topic Special Issue Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282863/
https://www.ncbi.nlm.nih.gov/pubmed/30311370
http://dx.doi.org/10.1002/humu.23651
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