Laboratoire de Génétique Médicale, U1112, INSERM, IGMA, FMTS, Université de Strasbourg, Strasbourg, France.
Unité de Génétique Chromosomique, CHU Montpellier, France.
Nucleic Acids Res. 2021 Jul 2;49(W1):W21-W28. doi: 10.1093/nar/gkab402.
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.
随着泛基因组分析的急剧增加，人类遗传学家已经生成了大量的基因组数据，包括数百万个小变体（SNV/indel），还有数千个结构变体（SV），主要来自下一代测序和基于阵列的技术。虽然有可能识别出患者完整的 SV 谱，但每个 SV 的解释仍然具有挑战性。为了帮助识别人类致病性 SV，我们开发了一个专门用于其注释和排序（AnnotSV）以及可视化和解释（knotAnnotSV）的网络服务器，可在以下地址免费获得：https://www.lbgi.fr/AnnotSV/。我们的网络服务器集成了来自 20 多个来源的大量注释，包括基因、单倍不足、三倍敏感、调控元件、已知的致病性或良性基因组区域、表型数据等。一个符合 ACMG/ClinGen 的优先级模块允许对 SV 进行评分和排序，将 SV 分为从致病性到良性的 5 个 SV 类别。最后，可视化界面以交互方式显示注释的 SV，包括弹出窗口、搜索字段、过滤选项、高级着色以突出显示致病性 SV 和超链接到 UCSC 基因组浏览器或其他公共数据库。这个网络服务器是为诊断和研究分析而设计的，为用户提供了重要的资源。
