ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines.

Humans Genetic Testing Genetic Variation Genome, Human Genomics
Clinical Genome Resource Consortium Clinical genetics Precision medicine Variant curation

Journal

Genome medicine
ISSN: 1756-994X
Titre abrégé: Genome Med
Pays: England
ID NLM: 101475844

Informations de publication

Date de publication:
18 01 2022
Historique:
received: 13 02 2021
accepted: 12 11 2021
entrez: 18 1 2022
pubmed: 19 1 2022
medline: 17 3 2022
Statut: epublish

Résumé

Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking. Here we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. The VCI is among a suite of tools developed by the NIH-funded Clinical Genome Resource (ClinGen) Consortium and supports an FDA-recognized human variant curation process. Essential to this is the ability to enable collaboration and peer review across ClinGen Expert Panels supporting users in comprehensively identifying, annotating, and sharing relevant evidence while making variant pathogenicity assertions. To facilitate evidence-based improvements in human variant classification, the VCI is publicly available to the genomics community. Navigation workflows support users providing guidance to comprehensively apply the ACMG/AMP evidence criteria and document provenance for asserting variant classifications. The VCI offers a central platform for clinical variant classification that fills a gap in the learning healthcare system, facilitates widespread adoption of standards for clinical curation, and is available at https://curation.clinicalgenome.org.

Sections du résumé

BACKGROUND
Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking.
RESULTS
Here we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. The VCI is among a suite of tools developed by the NIH-funded Clinical Genome Resource (ClinGen) Consortium and supports an FDA-recognized human variant curation process. Essential to this is the ability to enable collaboration and peer review across ClinGen Expert Panels supporting users in comprehensively identifying, annotating, and sharing relevant evidence while making variant pathogenicity assertions. To facilitate evidence-based improvements in human variant classification, the VCI is publicly available to the genomics community. Navigation workflows support users providing guidance to comprehensively apply the ACMG/AMP evidence criteria and document provenance for asserting variant classifications.
CONCLUSIONS
The VCI offers a central platform for clinical variant classification that fills a gap in the learning healthcare system, facilitates widespread adoption of standards for clinical curation, and is available at https://curation.clinicalgenome.org.

Identifiants

DOI: 10.1186/s13073-021-01004-8 PMID: 35039090 PMC: PMC8764818
pubmed: 35039090
doi: 10.1186/s13073-021-01004-8
pii: 10.1186/s13073-021-01004-8
pmc: PMC8764818
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

6

Subventions

Organisme : NIH HHS
ID : U41HG009649
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG006834
Pays : United States
Organisme : NIH HHS
ID : U01HG007436
Pays : United States
Organisme : NIH HHS
ID : U01HG007434
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG009649
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG009650
Pays : United States
Organisme : NIH HHS
ID : U41HG006834
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG009649
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG006834
Pays : United States
Organisme : NIH HHS
ID : U41HG009650
Pays : United States

Informations de copyright

© 2021. The Author(s).

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Auteurs

Christine G Preston (CG)

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA, 94305, USA.

Matt W Wright (MW)

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA, 94305, USA.

Rao Madhavrao (R)

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA, 94305, USA.

Steven M Harrison (SM)

Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

Jennifer L Goldstein (JL)

Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.

Xi Luo (X)

Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, 77030, USA.

Hannah Wand (H)

Center for Inherited Cardiovascular Disease, Stanford Health Care, Stanford, CA, 94305, USA.

Bryan Wulf (B)

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA, 94305, USA.

Gloria Cheung (G)

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA, 94305, USA.

Mark E Mandell (ME)

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA, 94305, USA.

Howard Tong (H)

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA, 94305, USA.

Shaung Cheng (S)

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA, 94305, USA.

Michael A Iacocca (MA)

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA, 94305, USA.

Arturo Lopez Pineda (AL)

Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA.

Alice B Popejoy (AB)

Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA.

Karen Dalton (K)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.

Jimmy Zhen (J)

Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.

Selina S Dwight (SS)

Grace Science LLC, Menlo Park, CA, 94025, USA.

Lawrence Babb (L)

Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

Marina DiStefano (M)

Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

Julianne M O'Daniel (JM)

Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.

Kristy Lee (K)

Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.

Erin R Riggs (ER)

Autism & Developmental Medicine Institute, Geisinger Health System, Lewisburg, PA, 17837, USA.

Diane B Zastrow (DB)

Sutter Health, Mountain View, CA, 94040, USA.

Jessica L Mester (JL)

GeneDx Inc., Gaithersburg, MD, 20877, USA.

Deborah I Ritter (DI)

Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, 77030, USA.

Ronak Y Patel (RY)

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.

Sai Lakshmi Subramanian (SL)

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.

Aleksander Milosavljevic (A)

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.

Jonathan S Berg (JS)

Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.

Heidi L Rehm (HL)

Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.

Sharon E Plon (SE)

Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, 77030, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.

J Michael Cherry (JM)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.

Carlos D Bustamante (CD)

Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.

Helio A Costa (HA)

Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA, 94305, USA. hcosta@stanford.edu.
Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA. hcosta@stanford.edu.

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