Association of Rare Copy Number Variants With Risk of Depression | Depressive Disorders | JAMA Psychiatry | JAMA Network
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Original Investigation
April 17, 2019

Association of Rare Copy Number Variants With Risk of Depression

Author Affiliations
  • 1MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, Wales, United Kingdom
  • 2Centre for Academic Mental Health, Department of Population Health Sciences, University of Bristol, Bristol, United Kingdom
JAMA Psychiatry. 2019;76(8):818-825. doi:10.1001/jamapsychiatry.2019.0566
Key Points

Question  Are rare copy number variants associated with depression in a large population sample?

Findings  In this case-control study of 407 074 individuals in the UK Biobank study, neurodevelopmental disorder copy number variants appear to be associated with the risk of depression in those without neurodevelopmental disorders. Physical health, educational attainment, social deprivation, smoking status, and alcohol consumption are variables that partially explain this association, and no evidence was found of an association between measures of copy number variant burden and depression.

Meaning  Neurodevelopmental copy number variants appear to be associated with increases in the risk of depression in those without neurodevelopmental disorders.


Importance  The role of large, rare copy number variants (CNVs) in neuropsychiatric disorders is well established, but their association with common psychiatric disorders, such as depression, remains unclear.

Objective  To examine the association of a group of 53 CNVs associated with neurodevelopmental disorders and burden of rare CNVs with risk of depression.

Design, Setting, and Participants  This case-control study used data from the UK Biobank study sample, which comprised 502 534 individuals living in the United Kingdom. Individuals with autism spectrum disorder, intellectual disability, attention-deficit/hyperactivity disorder, schizophrenia, or bipolar affective disorder diagnoses were excluded. Analyses were further restricted to individuals of European genetic ancestry (n = 407 074). The study was conducted from January 2017 to September 2018.

Exposures  CNV carrier status.

Main Outcomes and Measures  For the primary outcome, individuals who reported that a physician had told them they had a depression diagnosis were defined as cases. Analyses were repeated using 2 alternative depression definitions: self-reported lifetime depression with current antidepressant prescription at the time of visit 1, and hospital discharge diagnosis of depression.

Results  Copy number variants were identified in 488 366 individuals aged 37 to 73 years. In total, 407 074 individuals with European genetic ancestry (220 201 female [54.1%]; mean [SD] age of 56.9 [8.0] years) were included in the study. Of these individuals, 23 979 (5.9%) had self-reported lifetime depression and 383 095 (94.1%) reported no lifetime depression. The group of 53 neurodevelopmental CNVs was associated with self-reported depression (odds ratio [OR], 1.34; 95% CI, 1.19-1.49, uncorrected P = 1.38 × 10−7), and these results were consistent when using 2 alternative definitions of depression. This association was partially explained by physical health, educational attainment, social deprivation, smoking status, and alcohol consumption. A strong independent association remained between the neurodevelopmental CNVs and depression in analyses that incorporated these other measures (OR, 1.26; 95% CI, 1.11-1.43; P = 2.87 × 10−4). Eight individual CNVs were nominally associated with risk of depression, and 3 of these 8 CNVs (1q21.1 duplication, Prader-Willi syndrome duplication, and 16p11.2 duplication) survived Bonferroni correction for the 53 CNVs tested. After the exclusion of carriers of neurodevelopmental CNVs, no association was found between measures of CNV burden and depression.

Conclusions and Relevance  Neurodevelopmental CNVs appear to be associated with depression, extending the spectrum of clinical phenotypes that are associated with CNV carrier status.