VIP‐HL: Semi‐automated ACMG/AMP variant interpretation platform for genetic hearing loss | Zendy

Peng Jiguang | Zendy; Xiang Jiale | Zendy; Jin Xiangqian | Zendy; Meng Junhua | Zendy; Song Nana | Zendy; Chen Lisha | Zendy; Abou Tayoun Ahmad | Zendy; Peng Zhiyu | Zendy

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VIP‐HL: Semi‐automated ACMG/AMP variant interpretation platform for genetic hearing loss

Author(s) -

Peng Jiguang,

Xiang Jiale,

Jin Xiangqian,

Meng Junhua,

Song Nana,

Chen Lisha,

Abou Tayoun Ahmad,

Peng Zhiyu

Publication year - 2021

Publication title -

human mutation

Language(s) - Uncategorized

Resource type - Journals

SCImago Journal Rank - 1.981

H-Index - 162

eISSN - 1098-1004

pISSN - 1059-7794

DOI - 10.1002/humu.24277

Subject(s) - medical genetics , interpretation (philosophy) , hearing loss , genomics , computational biology , computer science , biology , genetics , audiology , gene , medicine , programming language , genome

The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss. This study developed a tool named Variant Interpretation Platform for genetic Hearing Loss (VIP-HL), aiming to semi-automate the HL ACMG/AMP rules. VIP-HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7. We benchmarked VIP-HL using 50 variants in which 82 rules were activated by the ClinGen HL-EP. VIP-HL concordantly activated 93% (76/82) rules, significantly higher than that of by InterVar (48%; 39/82). VIP-HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other. VIP-HL is available with a user-friendly web interface at http://hearing.genetics.bgi.com/.

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