Noncoding DNA Variants Increase the Genetic Diagnostic Yield in Primary Ciliary Dyskinesia

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 biallelic pathogenic variants are reported in as many as 70% of patients. Many patients remain with an incomplete or no genetic diagnosis. Objectives: To retrospectively analyze the diagnostic yield in 496 patients referred for genetic testing and the increase in yield by investigating pathogenic DNA variants in the noncoding regions of PCD genes in 42 patients with an incomplete genetic diagnosis. Methods: End-to-end next-generation gene sequencing including coding and noncoding regions of 17 PCD genes was performed, following routine genetic diagnosis of a panel of more than 46 genes. Intronic variants were prioritized for pathogenicity using in silico tools to predict splice effects that were subsequently confirmed in RNA extracted from nasal epithelium. Measurements and 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, noncoding variants were identified in 16 of 42 patients (38.1%). Three recurrent deep-intronic variants were found. Conclusions: Diagnostic yield for PCD is increased by end-to-end gene sequencing. Noncoding 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 gene or genome sequencing for PCD.