Genetic testing: The diagnostic power of RNA-seq

Abstract

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Sci. Transl Med. 9, eaal5209 (2017) FURTHER READING Byron, S. A. et al. Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat. Rev. Genet. 17, 257–271 (2016) analysing the transcriptome of diseased muscle tissue ... aids in the diagnosis of genetic primary muscle disorders dvoriain/iStock/G etty Whole-exome sequencing (WES) and whole-genome sequencing (WGS) can only identify rare Mendelian genetic diseases in up to 50% of cases; our ability to interpret the functional and clinical importance of the genetic variants they identify is limited. Here, Cummings et al. show that analysing the transcriptome of diseased muscle tissue, using RNA sequencing (RNAseq), aids in the diagnosis of genetic primary muscle disorders. The authors sourced RNA from the muscle tissue of 63 patients with suspected monogenic muscle disorders; 13 of these patients harboured genetic variants known to affect transcription and 50 patients were undiagnosed following genetic analysis. They then performed RNA-seq using the protocol employed by the Genotype-Tissue Expression (GTEx) Consortium project and looked for transcript-level changes that were unique to patients as compared to 184 skeletal muscle RNA-seq control samples from the GTEx project. Using this approach, RNA-seq could identify the splice aberrations caused by the genetic variants known to cause disease in the 13 diagnosed patients, which validated this approach that subsequently enabled novel diagnoses. Indeed, RNA-seq achieved a diagnosis rate of 35% and provided a diagnosis for 17 of the patients who were undiagnosed by genetic analysis. Coding and non-coding pathogenic variants resulted in a range of splicing defects, such as exon skipping, exon extension and exonic and intronic splice gain, which were not detected at the DNA level. Thus, for several Mendelian muscle disorders, RNA-seq provided a diagnosis and/or mechanistic insight. For example, RNA-seq revealed an additional exon extension event in the NEB gene in a patient with nemaline myopathy that was not picked up by WES, as well as a pathogenic missense variant in the TTN gene and synonymous variants in the RYR1 (causing exonic splice gain) and POMGNT1 (disrupting splice enhancer motifs) genes (the aberrant expression of these genes is associated with fetal akinesia, congenital fibretype disproportion and α-dystroglycanopathy, respectively). Non-coding pathogenic variants, which were identified in eight patients, included an intronic variant in DMD (the gene that is mutated in Duchenne muscular dystrophy) that created a pseudo exon in three patients that was not detected by WGS or WES alone. RNA-seq also revealed three structural variants of DMD, which were confirmed by WGS. Finally, by assessing the transcriptome of these patients, the authors identified a new genetic subtype of severe collagen VI-related dystrophy; RNA-seq identified an intron inclusion event in COL6A1 that resulted in the inclusion of 24 amino acids in a region of collagen VI, the disruption of which causes collagen G E N E T I C T E S T I N G

DOI: 10.1038/nrg.2017.39

Cite this paper

@article{Wrighton2017GeneticTT, title={Genetic testing: The diagnostic power of RNA-seq}, author={Katharine H. Wrighton}, journal={Nature Reviews Genetics}, year={2017}, volume={18}, pages={392-393} }