Robust detection of pathogenic HYDIN variants that cause primary ciliary dyskinesia using RNA-seq of nasal mucosa

Primary ciliary dyskinesia (PCD, OMIM 244400) is a rare genetic disorder that affects motile cilia and is characterised by impaired mucociliary clearance of the airway epithelium, which results in chronic upper and lower airway infections. While short-read next-generation sequencing technology has been used for the genetic testing of PCD, its effectiveness is limited in identifying variants in the HYDIN gene because of the nearly identical pseudogene HYDIN2 . As we confirmed that the HYDIN2 gene was not expressed in airway cells, we obtained nasal mucosa biopsy specimens for total RNA sequencing (RNA-seq) with library enrichment using exome oligos. Among the 34 nasal samples from patients suspected of having PCD, three aberrant splicing patterns in HYDIN were identified in two samples. Variant calls from RNA-seq combined with long-read amplicon sequencing of genomic DNA detected four pathogenic variants exclusively in the HYDIN gene. Therefore, RNA-seq in combination with long-read sequencing significantly facilitates the accurate genetic diagnosis of PCD caused by HYDIN variants.