The impact of 22q11.2 copy number variants on human traits in the general population

Abstract

While extensively studied in clinical cohorts, the phenotypic consequences of 22q11.2 copy number variants (CNVs) in the general population remain understudied. To address this gap, we performed a phenome-wide association scan in 405324 unrelated UK Biobank (UKBB) participants using CNV calls from genotyping array. We mapped 236 Human Phenotype Ontology terms linked to any of the 90 genes encompassed by the region to 170 UKBB traits and assessed the association between these traits and the copy-number state of 504 SNP-array probes in the region. We found significant associations for eight continuous and nine binary traits associated under different models (duplication-only, deletion-only, U-shape and mirror model). The causal effect of the expression level of 22q11.2 genes on associated traits was assessed through transcriptome-wide mendelian randomization (TWMR), revealing that increased expression of ARVCF increased BMI. Similarly, increased DGCR6 expression causally reduced mean platelet volume, in line with the corresponding CNV effect. Furthermore, cross-trait multivariable mendelian randomization (MVMR) suggested a predominant role of genuine (horizontal) pleiotropy in the CNV region. Our findings show that within the general population, 22q11.2 CNVs are associated with traits previously linked to genes in the region, with duplications and deletions acting upon traits in different fashion. We also showed that gain or loss of distinct segments within 22q11.2 may impact a trait under different association models. Our results have provided new insights to help further the understanding of the complex 22q11.2 region.