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

Area of Science:

• Genetics
• Respiratory Medicine
• Molecular Biology

Background:

• Primary ciliary dyskinesia (PCD) is a rare genetic respiratory disorder affecting motile cilia.
• Current genetic testing often focuses on coding regions, leaving many patients without a complete diagnosis.
• Pathogenic variants in over 50 genes are known to cause PCD.

Purpose of the Study:

• To evaluate the diagnostic yield of genetic testing in 497 patients with suspected PCD.
• To determine the increased diagnostic yield from investigating non-coding DNA regions in 42 patients with incomplete genetic diagnoses.
• To identify novel pathogenic variants in the non-coding regions of PCD genes.

Main Methods:

• Performed end-to-end next-generation sequencing of coding and non-coding regions for 17 PCD genes.
• Utilized in silico tools to predict splice effects of intronic variants.
• Confirmed predicted splice effects using RNA from nasal epithelium.

Main Results:

• Routine genetic testing achieved a complete diagnosis in 46.8% of patients.
• 17.3% of patients had an incomplete genetic diagnosis.
• End-to-end sequencing identified novel pathogenic non-coding variants in 38.1% of patients with incomplete diagnoses, including three recurrent deep-intronic variants.

Conclusions:

• End-to-end gene sequencing enhances the diagnostic yield for PCD.
• Non-coding variants affecting splicing are a significant source of pathogenic variation in PCD.
• This study highlights the clinical value of comprehensive gene or genome sequencing for PCD diagnosis.