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

Abstract

RATIONALE: 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. OBJECTIVE(S): 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. METHOD(S): 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. MAIN RESULTS: 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. CONCLUSION(S): 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.