Journal article
Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease
American journal of human genetics, Vol.104(3), pp.466-483
03/07/2019
DOI: 10.1016/j.ajhg.2019.01.012
PMID: 30827497
Abstract
Gene-panel and whole-exome analyses are now standard methodologies for mutation detection in Mendelian disease. However, the diagnostic yield achieved is at best 50%, leaving the genetic basis for disease unsolved in many individuals. New approaches are thus needed to narrow the diagnostic gap. Whole-genome sequencing is one potential strategy, but it currently has variant-interpretation challenges, particularly for non-coding changes. In this study we focus on transcriptome analysis, specifically total RNA sequencing (RNA-seq), by using monogenetic neuromuscular disorders as proof of principle. We examined a cohort of 25 exome and/or panel “negative” cases and provided genetic resolution in 36% (9/25). Causative mutations were identified in coding and non-coding exons, as well as in intronic regions, and the mutational pathomechanisms included transcriptional repression, exon skipping, and intron inclusion. We address a key barrier of transcriptome-based diagnostics: the need for source material with disease-representative expression patterns. We establish that blood-based RNA-seq is not adequate for neuromuscular diagnostics, whereas myotubes generated by transdifferentiation from an individual’s fibroblasts accurately reflect the muscle transcriptome and faithfully reveal disease-causing mutations. Our work confirms that RNA-seq can greatly improve diagnostic yield in genetically unresolved cases of Mendelian disease, defines strengths and challenges of the technology, and demonstrates the suitability of cell models for RNA-based diagnostics. Our data set the stage for development of RNA-seq as a powerful clinical diagnostic tool that can be applied to the large population of individuals with undiagnosed, rare diseases and provide a framework for establishing minimally invasive strategies for doing so.
Details
- Title: Subtitle
- Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease
- Creators
- Hernan D Gonorazky - Division of Neurology, the Hospital for Sick Children, Toronto, ON M5G 1X8, CanadaSergey Naumenko - Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, CanadaArun K Ramani - Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, CanadaViswateja Nelakuditi - Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, CanadaPouria Mashouri - Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, CanadaPeiqui Wang - Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, CanadaDennis Kao - Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, CanadaKrish Ohri - Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, CanadaSenthuri Viththiyapaskaran - Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, CanadaMark A Tarnopolsky - Department of Pediatrics, McMaster University, Hamilton, ON L8S 4L8, CanadaKatherine D Mathews - Departments of Pediatrics and Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USASteven A Moore - Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USAAndres N Osorio - Neuromuscular Unit, Neuropaediatrics Department, Institut de Recerca Hospital Universitari Sant Joan de Deu, Barcelona 08950, SpainDavid Villanova - GenomicTales Parc de la Mola, 10, AD700 Escaldes-Engordany, AndorraDwi U Kemaladewi - Program in Genetics and Genome Biology, Research Institute, the Hospital for Sick Children, Toronto, ON M5G 0A4, CanadaRonald D Cohn - Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1X8, CanadaMichael Brudno - Centre for Computational Medicine, the Hospital for Sick Children, Toronto, ON M5G 1X8, CanadaJames J Dowling - Division of Neurology, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Resource Type
- Journal article
- Publication Details
- American journal of human genetics, Vol.104(3), pp.466-483
- Publisher
- Elsevier Inc
- DOI
- 10.1016/j.ajhg.2019.01.012
- PMID
- 30827497
- ISSN
- 0002-9297
- eISSN
- 1537-6605
- Grant note
- DOI: 10.13039/100008762, name: Genome Canada, award: Disruptive Innovations in Genomics grant, Chase-an-Idea grant mechanism; name: Centre for Brain and Mental Health; name: the Hospital for Sick Children; DOI: 10.13039/100005202, name: Muscular Dystrophy Association, award: MDA 380397; DOI: 10.13039/100008762, name: Genome Canada; DOI: 10.13039/100013062, name: Genome Quebec, award: Restracomp grant; name: the Hospital for Sick Children; DOI: 10.13039/100000002, name: National Institutes of Health, award: U54, NS053672, ; DOI: 10.13039/100000002, name: NIH, award: U01, HG007672
- Language
- English
- Date published
- 03/07/2019
- Academic Unit
- Neurology; Stead Family Department of Pediatrics; Pathology; Iowa Neuroscience Institute; Neurology (Pediatrics)
- Record Identifier
- 9984047657902771
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