Non-Coding DNA Variants Increase the Genetic Diagnostic Yield in Primary Ciliary Dyskinesia

Primary ciliary dyskinesia (PCD) is a rare respiratory disorder of motile cilia caused by pathogenic variants in >50 known genes. Genetic testing routinely examines the coding regions of these genes and bi-allelic pathogenic variants are reported in up to 70% of patients. Many patients remain with an incomplete or no genetic diagnosis. To retrospectively analyse the diagnostic yield in 497 patients referred for genetic testing and the increase in yield by investigating pathogenic DNA variants in the non-coding regions of PCD genes, in 42 patients with an incomplete genetic diagnosis. End-to-end next-generation gene sequencing including coding and non-coding regions of 17 PCD genes was performed, following routine genetic diagnosis of a panel of 46+ genes. Intronic variants were prioritised for pathogenicity using in silico tools to predict splice effects, that were subsequently confirmed in RNA extracted from nasal epithelium. 232 of 496 patients (46.8%) had a complete genetic diagnosis of PCD after stringent variant assessment during routine genetic testing. Eighty-six patients (17.3%) had an incomplete genetic diagnosis, 42 of whom had end-to-end gene sequencing. Novel, potentially pathogenic, non-coding variants were identified in 16 of 42 patients (38.1%). Three recurrent deep-intronic variants were found. Diagnostic yield for PCD is increased by end-to-end gene sequencing. Non-coding variants that affect splicing are recurrent and are an important source of pathogenic genomic variation in patients with PCD. This work illustrates the potential clinical utility of end-to-end geneor genome sequencing for PCD.