Enhancing genetic diagnosis of primary ciliary dyskinesia by copy number variants analysis

Primary Ciliary Dyskinesia (PCD) is a rare, genetically heterogeneous disorder. Despite the increasing number of identified causative genes, 20-30% of patients still lack a genetic diagnosis. To date, genetic analyses have primarily focused on single nucleotide variants (SNVs). In this study, we evaluated whether the detection of copy number variants (CNVs) improves the diagnostic yield in our large patient cohort.

We retrospectively evaluated patients with confirmed or suspected PCD who remained genetically unresolved after next-generation sequencing (NGS). CNV analysis was performed using a custom high-density array comparative genomic hybridization (aCGH) platform targeting known PCD-associated genes.

A total of 203 patients with a clinically compatible PCD phenotype were included. NGS-based testing identified pathogenic variants in 175 cases (86.2%). The remaining 28 patients underwent aCGH analysis, which identified CNVs involving PCD-associated genes in 13 cases. Detected variants included homozygous deletions in DNAAF4, CFAP300, and CCDC39, a hemizygous deletion in DNAAF6, and heterozygous CNVs in SPAG1, ODAD4, ODAD1, DNAI2, DNAH11, and DNAH5, in combination with SNVs previously identified by NGS. The pathogenicity of these variants was supported by in silico predictions and was consistent with ciliary ultrastructural and functional abnormalities. Integration of aCGH increased the overall diagnostic yield to 92.6%.

Targeted CNV analysis by custom aCGH increases diagnostic yield in PCD, with potential benefits for earlier diagnosis and treatment, and should be routinely implemented.