RNA Sequencing Resolves Cryptic Pathogenic Variants in Mitochondrial Disease.
RNA sequencing establishes a genetic diagnosis in 25% of previously undiagnosed mitochondrial disease patients.
RNA Sequencing Resolves Cryptic Pathogenic Variants in Mitochondrial Disease.
Mitochondrial diseases are the most common inherited metabolic disorders, characterized by pronounced clinical and genetic heterogeneity that complicates molecular diagnosis.
We aimed to perform RNA sequencing (RNA-seq) of patient-derived skin fibroblasts to enhance the molecular diagnostic efficacy of mitochondrial disease in undiagnosed cases in China.
We performed RNA-seq on skin fibroblasts from 140 pediatric patients with suspected mitochondrial disease who remained genetically undiagnosed after whole exome sequencing (whole exome sequencing).
genetic sequencing found the cause in 1 of every 4 patients
Aberrant splicing explained most candidate-group diagnoses, including variants misclassified by in silico predictors such as SpliceAI.
14% of protein-truncating variants predicted to undergo nonsense-mediated decay (nonsense-mediated decay) escaped degradation, highlighting the functional limits of current predictions.
The most frequent among them was a recurrent synonymous East Asian founder mutation in ECHS1, accounting for seven cases.
Interestingly, across 233 pathogenic variants associated with aberrant RNA phenotypes compiled from this study and prior reports, half were noncoding and half were coding variants.
RNA-seq substantially enhances molecular diagnosis in mitochondrial disease by exposing cryptic splicing, regulatory, and nonsense-mediated decay-escape events invisible to DNA sequencing alone.
These data advocate transcriptome analysis as an essential component of comprehensive genomic diagnostics in neurometabolic disease.