iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification
The rapid evolution of Next Generation Sequencing in clinical settings, and the resulting challenge of variant reinterpretation given the constantly updated information, require robust data management systems and organized approaches. In this paper, we present iVar: a freely available and highly cus...
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doaj-762bdb4404e54ef9a376be0ca2a936ac2021-03-09T00:05:44ZengMDPI AGGenes2073-44252021-03-011238438410.3390/genes12030384iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and ClassificationSara Castellano0Federica Cestari1Giovanni Faglioni2Elena Tenedini3Marco Marino4Lucia Artuso5Rossella Manfredini6Mario Luppi7Tommaso Trenti8Enrico Tagliafico9Center for Genome Research, University of Modena and Reggio Emilia, 41125 Modena, ItalyCenter for Genome Research, University of Modena and Reggio Emilia, 41125 Modena, ItalyNabla2 s.r.l. 41124 Modena, ItalyDepartment of Laboratory Medicine and Pathology, Diagnostic hematology and Clinical Genomics Unit, Modena University Hospital, 41124 Modena, ItalyDepartment of Laboratory Medicine and Pathology, Diagnostic hematology and Clinical Genomics Unit, Modena University Hospital, 41124 Modena, ItalyDepartment of Laboratory Medicine and Pathology, Diagnostic hematology and Clinical Genomics Unit, Modena University Hospital, 41124 Modena, ItalyCentre for Regenerative Medicine, Life Sciences Department, University of Modena and Reggio Emilia, 41125 Modena, ItalyDepartment of Medical and Surgical Sciences, University of Modena and Reggio Emilia, 41124 Modena, ItalyDepartment of Laboratory Medicine and Pathology, Diagnostic hematology and Clinical Genomics Unit, Modena University Hospital, 41124 Modena, ItalyCenter for Genome Research, University of Modena and Reggio Emilia, 41125 Modena, ItalyThe rapid evolution of Next Generation Sequencing in clinical settings, and the resulting challenge of variant reinterpretation given the constantly updated information, require robust data management systems and organized approaches. In this paper, we present iVar: a freely available and highly customizable tool with a user-friendly web interface. It represents a platform for the unified management of variants identified by different sequencing technologies. iVar accepts variant call format (VCF) files and text annotation files and elaborates them, optimizing data organization and avoiding redundancies. Updated annotations can be periodically re-uploaded and associated with variants as historically tracked attributes, i.e., modifications can be recorded whenever an updated value is imported, thus keeping track of all changes. Data can be visualized through variant-centered and sample-centered interfaces. A customizable search function can be exploited to periodically check if pathogenicity-related data of a variant has changed over time. Patient recontacting ensuing from variant reinterpretation is made easier by iVar through the effective identification of all patients present in the database carrying a specific variant. We tested iVar by uploading 4171 VCF files and 1463 annotation files, obtaining a database of 4166 samples and 22,569 unique variants. iVar has proven to be a useful tool with good performance in terms of collecting and managing data from a medium-throughput laboratory.https://www.mdpi.com/2073-4425/12/3/384next-generation sequencingdatabasevariant annotationvariant classificationdata managementclinical genomics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Sara Castellano Federica Cestari Giovanni Faglioni Elena Tenedini Marco Marino Lucia Artuso Rossella Manfredini Mario Luppi Tommaso Trenti Enrico Tagliafico |
spellingShingle |
Sara Castellano Federica Cestari Giovanni Faglioni Elena Tenedini Marco Marino Lucia Artuso Rossella Manfredini Mario Luppi Tommaso Trenti Enrico Tagliafico iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification Genes next-generation sequencing database variant annotation variant classification data management clinical genomics |
author_facet |
Sara Castellano Federica Cestari Giovanni Faglioni Elena Tenedini Marco Marino Lucia Artuso Rossella Manfredini Mario Luppi Tommaso Trenti Enrico Tagliafico |
author_sort |
Sara Castellano |
title |
iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification |
title_short |
iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification |
title_full |
iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification |
title_fullStr |
iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification |
title_full_unstemmed |
iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification |
title_sort |
ivar, an interpretation-oriented tool to manage the update and revision of variant annotation and classification |
publisher |
MDPI AG |
series |
Genes |
issn |
2073-4425 |
publishDate |
2021-03-01 |
description |
The rapid evolution of Next Generation Sequencing in clinical settings, and the resulting challenge of variant reinterpretation given the constantly updated information, require robust data management systems and organized approaches. In this paper, we present iVar: a freely available and highly customizable tool with a user-friendly web interface. It represents a platform for the unified management of variants identified by different sequencing technologies. iVar accepts variant call format (VCF) files and text annotation files and elaborates them, optimizing data organization and avoiding redundancies. Updated annotations can be periodically re-uploaded and associated with variants as historically tracked attributes, i.e., modifications can be recorded whenever an updated value is imported, thus keeping track of all changes. Data can be visualized through variant-centered and sample-centered interfaces. A customizable search function can be exploited to periodically check if pathogenicity-related data of a variant has changed over time. Patient recontacting ensuing from variant reinterpretation is made easier by iVar through the effective identification of all patients present in the database carrying a specific variant. We tested iVar by uploading 4171 VCF files and 1463 annotation files, obtaining a database of 4166 samples and 22,569 unique variants. iVar has proven to be a useful tool with good performance in terms of collecting and managing data from a medium-throughput laboratory. |
topic |
next-generation sequencing database variant annotation variant classification data management clinical genomics |
url |
https://www.mdpi.com/2073-4425/12/3/384 |
work_keys_str_mv |
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