Optimized RNA-seq workflow for routine diagnosis of mitochondrial diseases using aberrant expression analysis and phenotype-driven prioritization.

Fibroblast RNA-seq: aberrant expression detection (OUTRIDER) with multiple testing correction restricted to disease-relevant genes and HPO-driven phenotype prioritization

Mitochondrial diseases remain without a molecular diagnosis in nearly half of patients despite exome and genome sequencing, partly because variants affecting splicing or gene expression are hard to interpret. The authors evaluated the implementation of fibroblast RNA-seq in a routine diagnostic workflow in 38 patients: 8 analyzed with a candidate-gene approach and 30 with an untargeted strategy. In untargeted analyses, aberrant expression detection with OUTRIDER was complemented by multiple testing correction restricted to disease-relevant gene sets and Z-score-based outlier detection combined with phenotype-driven prioritization using Human Phenotype Ontology terms. Pathogenicity was confirmed in 75% of targeted cases (6/8), and new molecular diagnoses were established in 13% of untargeted patients (4/30), despite fewer samples than typically recommended and minimized costs. The authors propose a practical framework for implementation alongside genome sequencing.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

This is one of the few studies to address RNA-seq under routine constraints (sample numbers, cost) rather than in a research setting, and the proposed framework is directly transferable. Numbers remain small (4 diagnoses out of 30), and the abstract specifies neither the genes involved nor the share of diagnoses attributable to the disease-relevant gene restriction. Reliance on fibroblasts, which requires a skin biopsy, remains a practical hurdle.

Analysis by Dr Thibaut Benquey