Rare homozygous cilia gene variants identified in consanguineous congenital heart disease patients

BACKGROUND: Congenital heart defects (CHD) appear in almost one percent of live births. Asian countries have the highest birth prevalence of CHD in the world. Recessive genotypes may represent a significant CHD risk factor in Asian populations, because Asian populations have a high degree of consanguineous marriages, which increases the risk of CHD. Genetic analysis of consanguineous families may represent a relatively unexplored source for investigating CHD etiology. METHODS: To obtain insight into the contribution of recessive genotypes in CHD we analysed a cohort of forty-nine Pakistani CHD probands, originating from consanguineous unions. The majority (82%) of patients malformations were septal defects. We identified protein altering, rare homozygous variants (RHVs) in the patients coding genome by whole exome sequencing. RESULTS: The patients had a median of seven damaging RHVs each, and our analysis revealed a total of 758 RHVs in 693 different genes. By prioritizing these genes based on variant severity, loss-of-function intolerance and specific expression in the developing heart, we identified a set of 23 candidate disease genes. These candidate genes were significantly enriched for genes known to cause heart defects in recessive mouse models (P<2.4e-06). In addition, we found a significant enrichment of cilia genes in both the initial set of 693 genes (P<5.4e-04) and the 23 candidate disease genes (P<5.2e-04). Functional investigation of ADCY6 in cell- and zebrafish-models verified its role in heart development. CONCLUSIONS: Our results confirm a significant role for cilia genes in recessive forms of CHD and suggest important functions of cilia genes in cardiac septation. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The study was supported by grants from the Danish Heart Foundation (17-R116-A7471-22051), Independent Research Fund Denmark (8020-00047B), European Commission Horizon 2020 research and innovation programme Marie Skłodowska-Curie Innovative Training Networks (grant agreement No. 861329), the Novo Nordisk and Novozymes Scholarship Program, Direktør Jacob Madsens og Hustru Olga Madsens Fond, Fonden til Lægevidenskabens Fremme, Helge Peetz og Verner Peetz og hustru Vilma Peetz Legat, Snedkermester Sophus Jacobsen og hustru Astrid Jacobsens Fond. ### 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: The study was approved by the Institutional Review Board GC University Faisalabad, Faisalabad, Pakistan and the Ethical Review Committee (ERC), Punjab Institute of Cardiology, Lahore, Pakistan. 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. Individual exome sequencing data cannot be shared due to concerns over patient privacy. Other data generated or analyzed during this study are included in the main paper or its additional files.