Genomewide paired DNA-RNAseq analyses to discover intronic splice mutation hotspots in neurological disorders

Paired DNA-RNA sequencing analyses enhance diagnostic yield in rare disorders by revealing pathogenic splice mutations that cannot be identified using DNAseq based methods alone. However, such analyses are typically restricted to known disease gene panels and focus on causal variants close to intron-exon boundaries. Here, we developed SpliPath (Splicing Pathology), a computational framework to conduct genomewide paired DNA-RNAseq analyses and empower discovery of splice mutation hotspots deeper into intronic sequences. We demonstrate the utility of SpliPath through analyses of CNS tissues in patients afflicted by amyotrophic lateral sclerosis (ALS). Using SpliPath we 1 ) re-discover known ALS mutations, 2 ) discover and experimentally verify a first of kind intronic mutation hotspot within a known ALS gene ( KIF5A ), 3 ) nominate 17 candidate mutation hotspots beyond known ALS genes. Nominated mutation hotspots were supported by enrichment analyses of independent genome sequencing data and provide new evidence implicating ELP3 and tRNA processing dysfunction in ALS. ### Competing Interest Statement The authors have declared no competing interest.