Primary Ciliary Dyskinesia (PCD) is a heterogenous disorder of motile cilia. Diagnosis comprises a combination of clinical investigation, analysis of cilia and identification of bi-allelic variants in PCD-related genes. Providing molecular confirmation of a clinical diagnosis enables more effective genetic counselling. Routine genetic testing examines the coding regions of PCD genes and bi-allelic variants are found in up to 70% of patients. The remaining incomplete cases, have either no pathogenic variants or only a single, heterozygous variant. The aim of this work was to determine if non-coding regions of PCD genes harbour pathogenic variants.

Seventeen genes were investigated in 49 patients with a single (likely) pathogenic variant. A custom, next-generation ?whole gene? sequencing panel targeted the coding and non-coding regions of the relevant genes. Variants were analysed using an in-house bioinformatics pipeline. Intronic variants were prioritised using in silico splice prediction tools. RNA analysis was performed to assess an effect on splicing.

Potential disease-causing variants were identified in 17 patients, including 11 in whom an intronic variant likely completes the molecular diagnosis. Four variants were confirmed to cause aberrant splicing. Three deep-intronic variants were found to be recurrent. The whole gene sequencing approach proved more successful at detecting copy number variants than targeted exon-only analysis. Overall, the diagnostic yield within our clinical cohort was increased by 6%.

This work contributes to the growing data pool of non-coding variants and illustrates the future clinical utility of whole genome sequencing, including the analysis of non-coding regions.