High diagnostic rate of whole genome sequencing in primary ciliary dyskinesia

Aim Primary ciliary dyskinesia (PCD) is a genetic disorder affecting motile cilia. Most cases are inherited recessively, due to variants in more than 50 genes that result in abnormal or absent motile cilia. This leads to chronic upper and lower airway disease, sub-fertility and laterality defects in some cases. 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. Here, we aimed to identify how readily a genetic diagnosis could be made in a clinically diagnosed population using whole genome sequencing (WGS) to facilitate identification of pathogenic variants in known genes as well as identify novel PCD candidate genes. Maethods WGS was used to screen for variants causing PCD in 8 clinically diagnosed PCD patients, sequenced as trios where parental samples were available. Results Seven of the eight cases (87.5%) had homozygous or biallelic variants in DNAH5 , DNAAF4 or DNAH11 that were classified as pathogenic or likely pathogenic. Three of the variants were deletions, ranging from 3kb to 13kb, for which WGS identified precise breakpoints, permitting confirmation by Sanger sequencing. WGS yielded a high genetic diagnostic rate from this clinically diagnosed population, in part through detection of structural variants as well as identification of a de novo variant in a novel PCD gene TUBB4B . Conclusion A molecular diagnosis allows for appropriate clinical management for cases and their families, including prediction of phenotypic features correlated to genotype. Here, WGS uplifted genetic diagnosis in cases of clinically diagnosed PCD by identifying structural variants and novel modes of inheritance in new candidate genes. Our study suggests that WGS could be a powerful part of the PCD diagnostic toolkit to increase the current molecular diagnostic yield from 70%. It provides important new insight into our understanding of fundamental biology of motile cilia as well as of variation in the non-coding genome in PCD. Summary Whole genome sequencing (WGS) yielded a high genetic diagnostic rate (100%) in eight Scottish patients with clinically diagnosed primary ciliary dyskinesia (PCD) by detection of large structural variants, homology modelling and identification of a novel disease gene with a dominant mode of inheritance. Prioritised WGS may facilitate early genetic diagnosis in PCD. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The Scottish Genomes Partnership is funded by the Chief Scientist Office of the Scottish Government Health Directorates [SGP\_1] and the MRC Whole Genome Sequencing for Health and Wealth Initiative (MC\_PC\_15080). We acknowledge support from the MRC (PM: MC\_UU\_00007\_14, MR\_Y015002\_1); an MRC Career Development Award (MR\_M02122X\_1) and Lister Prize Fellowship to JAM; an NHS Research Scotland fellowship to SU; and an NRS/R+D fellowship from the NHS Lothian R&D office to DU. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Signed and informed consent was obtained from the affected individual as well as relatives through approved protocols. Sample IDs were assigned and the key known only those within the research group. The study was approved by the London-West London and Gene Therapy Advisory Committee Research Ethics Committee (REC number 11/LO/0883). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.