Disentangling mechanisms behind the pleiotropic effects of proximal 16p11.2 BP4-5 CNVs

Whereas 16p11.2 BP4-5 copy-number variants (CNVs) represent one of the most pleiotropic etiologies of genomic syndromes in both clinical and population cohorts, the mechanisms leading to such pleiotropy remain understudied. Identifying 73 deletion and 89 duplication carriers among unrelated white British UK Biobank participants, we performed a phenome-wide association study between the region’s copy number and 117 complex traits and diseases, mimicking four dosage models. Forty-six phenotypes (39%) were affected by 16p11.2 BP4-5 CNVs, with the deletion-only, mirror, U-shape, and duplication-only models being the best fit for thirty, ten, four, and two phenotypes, respectively, aligning with the stronger deleteriousness of the deletion. Upon individually adjusting CNV effects for either body mass index (BMI), height, cognitive function, or socio-economic status as potential mediators, we found that sixteen testable deletion-driven associations (61%) – primarily with cardiovascular and metabolic traits – were BMI-dependent, with other mediators playing a more subtle role. Bidirectional Mendelian randomization supported that 13 out of these 16 associations (81%) were secondary consequences of the CNV’s impact on BMI. For the 22 traits that remained significantly associated upon individual adjustment for mediators, matched-control analyses found that eleven phenotypes, including musculoskeletal traits, liver enzymes, fluid intelligence, platelet count, pulmonary capacity, pneumonia, and acute kidney injury, remained associated under strict Bonferroni correction, with eight additional nominally significant associations. These results paint a complex picture of 16p11.2 BP4-5’s pleiotropic pattern that involves direct effects on multiple physiological systems and indirect co-morbidities consequential to the CNV’s impact on BMI and cognition, acting through trait-specific dosage mechanisms. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The study was funded by the Swiss National Science Foundation (31003A\_182632, AR; 310030\_189147, ZK), Horizon2020 Twinning projects (ePerMed 692145, AR), and the Department of Computational Biology (ZK) and the Center for Integrative Genomics (AR) from the University of Lausanne. ### 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: UK Biobank data are publically available for registered users (https://www.ukbiobank.ac.uk/enable-your-research/apply-for-access) and were accessed through the application number 16389. 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 UK Biobank data are available for registered users and were accessed through the application number 16389. Summary statistics used for Mendelian randomization studies are publicly available, as described in the Methods. All data produced by this study are available in Supplemental Tables. Code will be made available upon publication at: https://github.com/cauwerx/16p11.2\_BP4-5\_pleiotropy. * ALP : alkaline phosphatase ALT : alanine aminotransferase AKI : acute kidney injury AST : aspartate aminotransferase BMI : body mass index BP : breakpoint CI : confidence interval CKD : chronic kidney disease CNV : copy-number variants COPD : chronic obstructive pulmonary disorder CRP : C-reactive protein EA : educational attainment FVC : forced vital capacity GGT : gamma-glutamyltransferase GWAS : genome-wide association studies HbA1c : glycated hemoglobin HDL : high-density lipoprotein HTN : essential hypertension ICD-10 : International Classification of Diseases, 10th Revision IGF-1 : insulin-like growth factor 1 kb : kilobase pair MR : Mendelian randomization OA : arthritis PheWAS : phenome-wide association study SE : standard error SES : socioeconomic status SHBG : sex hormone binding globulin SNP : single nucleotide polymorphism T1D : type 1 diabetes TDI : Townsend deprivation index UKBB : UK Biobank WHR : waist-to-hip ratio WHRadjBMI : WHR adjusted for BMI.