Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease Academic Article uri icon

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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.

authors

  • Gonorazky, Hernan D
  • Naumenko, Sergey
  • Ramani, Arun K
  • Nelakuditi, Viswateja
  • Mashouri, Pouria
  • Wang, Peiqui
  • Kao, Dennis
  • Ohri, Krish
  • Viththiyapaskaran, Senthuri
  • Tarnopolsky, Mark
  • Mathews, Katherine D
  • Moore, Steven A
  • Osorio, Andres N
  • Villanova, David
  • Kemaladewi, Dwi U
  • Cohn, Ronald D
  • Brudno, Michael
  • Dowling, James J

publication date

  • March 2019