Copy number variants differ in frequency across genetic ancestry groups

Copy number variants (CNVs), which are duplicated or deleted genomic segments larger than 1000 base pairs1, have been implicated in a variety of neuropsychiatric and cognitive phenotypes2-4. In the first large-scale of examination of genome-wide CNV frequencies across ancestry groups, we found that deleterious CNVs are less prevalent in non-European ancestry groups than they are in European ancestry groups of both the UK Biobank (UKBB) and a US replication cohort (SPARK). We also identified specific recurrent CNVs that consistently differ in frequency across ancestry groups in both the UKBB and SPARK. These ancestry-related differences in CNV prevalence present in both an unselected community population and a family cohort enriched with individuals diagnosed with autism spectrum disorder (ASD) strongly suggest that genetic ancestry should be considered when probing associations between CNVs and health outcomes.