Utilization of Targeted RNA-Seq for the Resolution of Variant Pathogenicity and Enhancement of Diagnostic Yield in Dysferlinopathy

• Type of Material: Article
• Authors: Laura Rufibach, Jain Foundation, Inc.; Kiera Berger, Georgia Institute of Technology; Samya Chakravorty, Emory University; Sarah Emmons, Jain Foundation, Inc.; Laurie Long, Jain Foundation, Inc.; Gregory Gibson, Emory University; Madhuri Hegde, Emory University
• Language: English
• Date: 2023-03-01
• Publisher: MDPI
• Publication Version: Final Published Version
• Copyright Statement: © 2023 by the authors.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.3390/jpm13030520
• Title of Journal or Parent Work: JOURNAL OF PERSONALIZED MEDICINE
• Volume: 13
• Issue: 3
• Grant/Funding Information: This research was funded by a Jain Foundation focused research grant and Muscular Dystrophy Association Development Grant (MDA578400) to S.C. S.C. was also supported by Sanofi-Genzyme Investigator Sponsored Studies Grant (SGZ-2017-11829).
• Keywords: genetic diagnosis; diagnostic yield; Life Sciences & Biomedicine; General & Internal Medicine; RNA-Seq; GENE; ACMG guidelines; Health Care Sciences & Services; LGMD2B; MEMBRANE REPAIR; dysferlinopathy; Miyoshi myopathy; SKELETAL-MUSCLE; Science & Technology; ASSAY; MIYOSHI MYOPATHY; IDENTIFICATION; Medicine, General & Internal; LGMD; variants of unknown significance; MUSCULAR-DYSTROPHY; LGMDR2
• Research Categories: Health Sciences, Medicine and Surgery

Abstract

For inherited diseases, obtaining a definitive diagnosis is critical for proper disease management, family planning, and participation in clinical trials. This can be challenging for dysferlinopathy due to the significant clinical overlap between the 30+ subtypes of limb–girdle muscular dystrophy (LGMD) and the large number of variants of unknown significance (VUSs) that are identified in the dysferlin gene, DYSF. We performed targeted RNA-Seq using a custom gene-panel in 77 individuals with a clinical/genetic suspicion of dysferlinopathy and evaluated all 111 identified DYSF variants according to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines. This evaluation identified 11 novel DYSF variants and allowed for the classification of 87 DYSF variants as pathogenic/likely pathogenic, 8 likely benign, while 16 variants remained VUSs. By the end of the study, 60 of the 77 cases had a definitive diagnosis of dysferlinopathy, which was a 47% increase in diagnostic yield over the rate at study onset. This data shows the ability of RNA-Seq to assist in variant pathogenicity classification and diagnosis of dysferlinopathy and is, therefore, a type of analysis that should be considered when DNA-based genetic analysis is not sufficient to provide a definitive diagnosis.