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Background: Copy number variants (CNVs) can have stronger effects on disorders than SNPs as CNVs often span multiple genes. Association studies of rare CNVs have successfully identified pathogenic CNVs for a variety of diseases. However, relatively little is known about the contribution of CNVs to broader range of complex traits than currently studied (such as neuroticism, intelligence or height). We therefore aimed to investigate associations of CNVs with complex traits. In addition, we investigated the extent of pleiotropy in CNVs across a variety of traits as measured in the UK Biobank cohort.

Methods: CNVs were called for approximately 387,000 unrelated European subjects from UK Biobank using PennCNV and iPsychCNV. After standard QC, consensus calls were defined by taking the intersection of CNVs called by both methods. Subjects with an excess of CNVs (> 30 CNVs or> 10% of any chromosome is …