Whole genome sequencing enhances molecular diagnosis of primary ciliary dyskinesia

• Published in: Pediatric pulmonology 2024-12, Vol.59 (12), p.3322-3332
• Main Authors: Black, Holly A., Proce, Sophie Marion, Campos, Jose L., Meynert, Alison, Halachev, Mihail, Marsh, Joseph A., Hirst, Robert A., O'Callaghan, Chris, Shoemark, Amelia, Toddie‐Moore, Daniel, Santoyo‐Lopez, Javier, Murray, Jennie, Macleod, Kenneth, Urquhart, Don S., Unger, Stefan, Aitman, Timothy J., Mill, Pleasantine
• Format: Article
• Language: English
• Subjects: Adolescent; Axonemal Dyneins - genetics; Child; Child, Preschool; Ciliary Motility Disorders - diagnosis; Ciliary Motility Disorders - genetics; ciliopathies; Dyskinesia; Female; Genetic Testing - methods; Genomes; Humans; Infant; Kartagener Syndrome - diagnosis; Kartagener Syndrome - genetics; Male; molecular diagnosis; Mutation; Original; primary ciliary dyskinesia; rare respiratory disease; Whole Genome Sequencing
• ISSN: 8755-6863; 1099-0496; 1099-0496
• DOI: 10.1002/ppul.27200

Background Primary ciliary dyskinesia (PCD) is a genetic disorder affecting motile cilia. Most cases are inherited recessively, due to variants in >50 genes that result in abnormal or absent motile cilia. This leads to chronic upper and lower airway disease, subfertility, and laterality defects. Given overlapping clinical features and genetic heterogeneity, diagnosis can be difficult and often occurs late. Of those tested an estimated 30% of genetically screened PCD patients still lack a molecular diagnosis. A molecular diagnosis allows for appropriate clinical management including prediction of phenotypic features correlated to genotype. Here, we aimed to identify how readily a genetic diagnosis could be made using whole genome sequencing (WGS) to facilitate identification of pathogenic variants in known genes as well as novel PCD candidate genes. Methods WGS was used to screen for pathogenic variants in eight patients with PCD. Results 7/8 cases had homozygous or biallelic variants in DNAH5, DNAAF4 or DNAH11 classified as pathogenic or likely pathogenic. Three identified variants were deletions, ranging from 3 to 13 kb, for which WGS identified precise breakpoints, permitting confirmation by Sanger sequencing. WGS yielded identification of a de novo variant in a novel PCD gene TUBB4B. Conclusion Here, WGS uplifted genetic diagnosis of PCD by identifying structural variants and novel modes of inheritance in new candidate genes. WGS could be an important component of the PCD diagnostic toolkit, increasing molecular diagnostic yield from current (70%) levels, and enhancing our understanding of fundamental biology of motile cilia and variants in the noncoding genome.