Genetic diagnosis of Mendelian disorders via RNA sequencing

Abstract

Across a variety of Mendelian disorders, ∼50–75% of patients do not receive a genetic diagnosis by exome sequencing indicating disease-causing variants in non-coding regions. Although genome sequencing in principle reveals all genetic variants, their sizeable number and poorer annotation make prioritization challenging. Here, we demonstrate the power of transcriptome sequencing to molecularly diagnose 10% (5 of 48) of mitochondriopathy patients and identify candidate genes for the remainder. We find a median of one aberrantly expressed gene, five aberrant splicing events and six mono-allelically expressed rare variants in patient-derived fibroblasts and establish disease-causing roles for each kind. Private exons often arise from cryptic splice sites providing an important clue for variant prioritization. One such event is found in the complex I assembly factor TIMMDC1 establishing a novel disease-associated gene. In conclusion, our study expands the diagnostic tools for detecting non-exonic variants and provides examples of intronic loss-of-function variants with pathological relevance.

Mitochondrial energy generation disorders: genes, mechanisms, and clues to pathology

“…Challenges remain in detecting and interpreting pathogenic DNA variants, particularly in non-coding regions. Analytical approaches continue to evolve and are complemented by improvements in data sharing and comprehensive databases cataloguing population-based genetic variation (91), together with transcriptomic and proteomic analyses (37,92,93). It therefore seems likely that the current rate of gene discovery will continue for some years.…”

Integrative omics for health and disease

“…1), ranging from 10% to 35% 15,16 . In one of these studies, a diagnostic investigation of patients with muscular dystrophy (MD), no causal variants were identified through whole-exome sequencing (WES), but RNA-seq data identified splice anomalies that revealed variants with cryptic splicing effects.…”

“…In Kremer et al 15 and Cummings et al 16 , multi-omics approaches were used to aid in the diagnosis of patients with undiagnosed disease. Although exome and genome sequencing can be effective in identifying causal genetic variation between 20% and 50% of the time, depending on the mode of inheritance and phenotype, the majority of cases cannot be solved by these technologies alone.…”

A Syrian patient with Steel syndrome due to compound heterozygous COL27A1 mutations with colobomata of the eye

“…Blood samples from our patient and both her parents were taken and whole exome sequencing was performed on our patient's DNA (Kremer et al, 2017). Two novel heterozygous variants in COL27A1 (NM_032888.4; hg38 chr9:114155537-114312511), c.93del [p.…”

“…These variants have also not been recorded within the local whole exome dataset of about 12,500 individuals (Munich Exome Server; Kremer et al, 2017). Both variants are single nucleotide deletions predicted to cause a frameshift of the reading frame and the introduction of a premature stop codon.…”