AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis

Author:

Geoffroy Véronique1,Guignard Thomas2,Kress Arnaud3,Gaillard Jean-Baptiste2,Solli-Nowlan Tor4,Schalk Audrey5,Gatinois Vincent2,Dollfus Hélène16,Scheidecker Sophie15,Muller Jean157ORCID

Affiliation:

1. Laboratoire de Génétique Médicale, U1112, INSERM, IGMA, FMTS, Université de Strasbourg, Strasbourg, France

2. Unité de Génétique Chromosomique, CHU Montpellier, France

3. Complex Systems and Translational Bioinformatics, ICube, UMR 7357, University of Strasbourg, CNRS, FMTS, Strasbourg, France

4. Department of Medical Genetics, Oslo University Hospital, Oslo, Norway

5. Laboratoires de Diagnostic Génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France

6. Centre de référence pour les Affections Rares en Génétique Ophtalmologique, Filière SENSGENE, Hôpitaux Universitaires de Strasbourg, Strasbourg, France

7. Unité Fonctionnelle de Bioinformatique Médicale appliquée au diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France

Abstract

Abstract With the dramatic increase of pangenomic analysis, Human geneticists have generated large amount of genomic data including millions of small variants (SNV/indel) but also thousands of structural variations (SV) mainly from next-generation sequencing and array-based techniques. While the identification of the complete SV repertoire of a patient is getting possible, the interpretation of each SV remains challenging. To help identifying human pathogenic SV, we have developed a web server dedicated to their annotation and ranking (AnnotSV) as well as their visualization and interpretation (knotAnnotSV) freely available at the following address: https://www.lbgi.fr/AnnotSV/. A large amount of annotations from >20 sources is integrated in our web server including among others genes, haploinsufficiency, triplosensitivity, regulatory elements, known pathogenic or benign genomic regions, phenotypic data. An ACMG/ClinGen compliant prioritization module allows the scoring and the ranking of SV into 5 SV classes from pathogenic to benign. Finally, the visualization interface displays the annotated SV in an interactive way including popups, search fields, filtering options, advanced colouring to highlight pathogenic SV and hyperlinks to the UCSC genome browser or other public databases. This web server is designed for diagnostic and research analysis by providing important resources to the user.

Funder

Inserm

University of Strasbourg

Strasbourg University Hospital

Publisher

Oxford University Press (OUP)

Subject

Genetics

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