Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease
| Autor: | Pouria Mashouri, Krish Ohri, Andrés Nascimento Osorio, Ronald D. Cohn, Peiqui Wang, Steven A. Moore, Arun K. Ramani, Katherine D. Mathews, Hernan Gonorazky, James J. Dowling, Michael Brudno, Dwi U. Kemaladewi, Mark A. Tarnopolsky, Senthuri Viththiyapaskaran, David Villanova, Sergey Naumenko, Dennis Kao, Viswateja Nelakuditi |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
Adult
Genetic Markers Male muscular dystrophy 0301 basic medicine Adolescent transdifferentiation Muscle Fibers Skeletal RNA-Seq Disease Computational biology Biology Article Cohort Studies Transcriptome Young Adult Exon transcriptomics 03 medical and health sciences Rare Diseases 0302 clinical medicine Muscular Diseases diagnostics Genetics Humans Child Exome Cells Cultured Genetics (clinical) 030304 developmental biology 0303 health sciences Intron Genetic Variation High-Throughput Nucleotide Sequencing Correction RNA Exon skipping 3. Good health 030104 developmental biology myotubes Mutation Female RNA-seq Mendelian disease 030217 neurology & neurosurgery |
| Zdroj: | American Journal of Human Genetics |
| ISSN: | 0002-9297 |
| DOI: | 10.1016/j.ajhg.2019.01.012 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|