ClassifyCNV: a tool for clinical annotation of copy-number variants

Abstract Copy-number variants (CNVs) are an important part of human genetic variation. They can be benign or can play a role in human disease by creating dosage imbalances and disrupting genes and regulatory elements. Accurate identification and clinical annotation of CNVs is essential, however, man...

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Autores principales:	Tatiana A. Gurbich, Valery Vladimirovich Ilinsky
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/75b37ccd5df5499b8659219af7988a85
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spelling	oai:doaj.org-article:75b37ccd5df5499b8659219af7988a852021-12-02T15:10:19ZClassifyCNV: a tool for clinical annotation of copy-number variants10.1038/s41598-020-76425-32045-2322https://doaj.org/article/75b37ccd5df5499b8659219af7988a852020-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-76425-3https://doaj.org/toc/2045-2322Abstract Copy-number variants (CNVs) are an important part of human genetic variation. They can be benign or can play a role in human disease by creating dosage imbalances and disrupting genes and regulatory elements. Accurate identification and clinical annotation of CNVs is essential, however, manual evaluation of individual CNVs by clinicians is challenging on a large scale. Here, we present ClassifyCNV, an easy-to-use tool that implements the 2019 ACMG classification guidelines to assess CNV pathogenicity. ClassifyCNV uses genomic coordinates and CNV type as input and reports a clinical classification for each variant, a classification score breakdown, and a list of genes of potential importance for variant interpretation. We validate ClassifyCNV’s performance using a set of known clinical CNVs and a set of manually evaluated variants. ClassifyCNV matches the pathogenicity category for 81% of manually evaluated variants with the significance of the remaining pathogenic and benign variants automatically determined as uncertain, requiring a further evaluation by a clinician. ClassifyCNV facilitates the implementation of the latest ACMG guidelines in high-throughput CNV analysis, is suitable for integration into NGS analysis pipelines, and can decrease time to diagnosis. The tool is available at https://github.com/Genotek/ClassifyCNV .Tatiana A. GurbichValery Vladimirovich IlinskyNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-7 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tatiana A. Gurbich Valery Vladimirovich Ilinsky ClassifyCNV: a tool for clinical annotation of copy-number variants
description	Abstract Copy-number variants (CNVs) are an important part of human genetic variation. They can be benign or can play a role in human disease by creating dosage imbalances and disrupting genes and regulatory elements. Accurate identification and clinical annotation of CNVs is essential, however, manual evaluation of individual CNVs by clinicians is challenging on a large scale. Here, we present ClassifyCNV, an easy-to-use tool that implements the 2019 ACMG classification guidelines to assess CNV pathogenicity. ClassifyCNV uses genomic coordinates and CNV type as input and reports a clinical classification for each variant, a classification score breakdown, and a list of genes of potential importance for variant interpretation. We validate ClassifyCNV’s performance using a set of known clinical CNVs and a set of manually evaluated variants. ClassifyCNV matches the pathogenicity category for 81% of manually evaluated variants with the significance of the remaining pathogenic and benign variants automatically determined as uncertain, requiring a further evaluation by a clinician. ClassifyCNV facilitates the implementation of the latest ACMG guidelines in high-throughput CNV analysis, is suitable for integration into NGS analysis pipelines, and can decrease time to diagnosis. The tool is available at https://github.com/Genotek/ClassifyCNV .
format	article
author	Tatiana A. Gurbich Valery Vladimirovich Ilinsky
author_facet	Tatiana A. Gurbich Valery Vladimirovich Ilinsky
author_sort	Tatiana A. Gurbich
title	ClassifyCNV: a tool for clinical annotation of copy-number variants
title_short	ClassifyCNV: a tool for clinical annotation of copy-number variants
title_full	ClassifyCNV: a tool for clinical annotation of copy-number variants
title_fullStr	ClassifyCNV: a tool for clinical annotation of copy-number variants
title_full_unstemmed	ClassifyCNV: a tool for clinical annotation of copy-number variants
title_sort	classifycnv: a tool for clinical annotation of copy-number variants
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/75b37ccd5df5499b8659219af7988a85
work_keys_str_mv	AT tatianaagurbich classifycnvatoolforclinicalannotationofcopynumbervariants AT valeryvladimirovichilinsky classifycnvatoolforclinicalannotationofcopynumbervariants
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ClassifyCNV: a tool for clinical annotation of copy-number variants

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