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

Jiguang Peng, Jiale Xiang, Xiangqian Jin, Junhua Meng, Nana Song, Lisha Chen, Ahmad Abou Tayoun, Zhiyu Peng*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

Abstract

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 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 where 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 athttp://hearing.genetics.bgi.com".
Original languageEnglish
JournalHuman Mutation
Volume42
Issue number12
Pages (from-to)1567-1575
Number of pages9
ISSN1059-7794
DOIs
Publication statusPublished - 2021

Keywords

  • Genetic hearing loss
  • Variant interpretation
  • Bioinformatics
  • Clinical genomics

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