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Cognitive Performance Among Carriers of Pathogenic Copy Number Variants: Analysis of 152,000 UK Biobank Subjects
Open accessAbstract
Background The UK Biobank is a unique resource for biomedical research, with extensive phenotypic and genetic data on half a million adults from the general population. We aimed to examine the effect of neurodevelopmental copy number variants (CNVs) on the cognitive performance of participants.Methods We used Affymetrix Power Tools and PennCNV-Affy software to analyze Affymetrix microarrays of the first 152,728 genotyped individuals. We annotated a list of 93 CNVs and compared their frequencies with control datasets. We analyzed the performance on seven cognitive tests of carriers of 12 CNVs associated with schizophrenia (n = 1087) and of carriers of another 41 neurodevelopmental CNVs (n = 484).Results The frequencies of the 93 CNVs in the Biobank subjects were remarkably similar to those among 26,628 control subjects from other datasets. Carriers of schizophrenia-associated CNVs and of the group of 41 other neurodevelopmental CNVs had impaired performance on the cognitive tests, with nine of 14 comparisons remaining statistically significant after correction for multiple testing. They also had lower educational and occupational attainment (p values between 10-7 and 10-18). The deficits in cognitive performance were modest (Z score reductions between 0.01 and 0.51), compared with individuals with schizophrenia in the Biobank (Z score reductions between 0.35 and 0.90).Conclusions This is the largest study on the cognitive phenotypes of CNVs to date. Adult carriers of neurodevelopmental CNVs from the general population have significant cognitive deficits. The UK Biobank will allow unprecedented opportunities for analysis of further phenotypic consequences of CNVs.
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“The deletion is significantly enriched in the SJCHU (OR 1.9, 95% CI 1.5 to 2.4) and OUH CMA database (OR 3.1, 95% CI 1.6 to 5.7), compared with the deletion prevalence from the UK BIOBANK (0.36%, 544/151619)16 (table 2).”
From Estimating the effect size of the 15Q11.2 BP1–BP2 deletion and its contribution to neurodevelopmental symptoms: recommendations for practice (2019) · cites this paper as [16]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The deletion is significantly enriched in the SJCHU (OR 1.9, 95% CI 1.5 to 2.4) and OUH CMA database (OR 3.1, 95% CI 1.6 to 5.7), compared with the deletion prevalence from the UK BIOBANK (0.36%, 544/151619)16 (table 2).”
From Estimating the effect size of the 15Q11.2 BP1–BP2 deletion and its contribution to neurodevelopmental symptoms: recommendations for practice (2019) · cites this paper as [16]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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“We used data on CNV frequency from the UK BIOBANK (151 619 individuals),16 which is an unselected population.”
From Estimating the effect size of the 15Q11.2 BP1–BP2 deletion and its contribution to neurodevelopmental symptoms: recommendations for practice (2019) · cites this paper as [16]
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In the citing paper
“The reciprocal duplication is not enriched in both the SJCHU and OUH cohorts (table 2) when using the prevalence in an unselected population provided by the UK BIOBANK (0.5%, 762/151619)16 and is therefore used as a control neutral CNV throughout the rest of this study.”
From Estimating the effect size of the 15Q11.2 BP1–BP2 deletion and its contribution to neurodevelopmental symptoms: recommendations for practice (2019) · cites this paper as [16]
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“The reciprocal duplication is not enriched in both the SJCHU and OUH cohorts (table 2) when using the prevalence in an unselected population provided by the UK BIOBANK (0.5%, 762/151619)16 and is therefore used as a control neutral CNV throughout the rest of this study.”
From Estimating the effect size of the 15Q11.2 BP1–BP2 deletion and its contribution to neurodevelopmental symptoms: recommendations for practice (2019) · cites this paper as [16]
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“There is, however, no significant enrichment 1.55 (95% CI 0.97 to 2.48) if the UK BIOBANK population frequency of 0.36% is used as the control group.”
From Estimating the effect size of the 15Q11.2 BP1–BP2 deletion and its contribution to neurodevelopmental symptoms: recommendations for practice (2019) · cites this paper as [16]
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“Currently, the best estimates range from 0.36% (UK BIOBANK)16 to 0.24% (Icelandic population).41”
From Estimating the effect size of the 15Q11.2 BP1–BP2 deletion and its contribution to neurodevelopmental symptoms: recommendations for practice (2019) · cites this paper as [16]
Experimental — accuracy not yet measuredIn the citing paper
“penetrance can be highly variable, ranging from subtle effects detectable by neuropsychological tests to mild degrees of anxiety/ADHD to co-occurrence of severe psychiatric disorders (Kendall et al., 2017; Stefansson et al., 2014; Ulfarsson et al., 2017)”
From Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders (2019) · cites this paper as Kendall et al., 2017
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Citations
Cites
Schizophrenia: A Concise Overview of Incidence, Prevalence, and Mortality
McGrath, J., Saha, S., Chant, D., & Welham, J. (2008) · Epidemiologic Reviews · doi:10.1093/epirev/mxn001 · Cited by 2,280
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Rare chromosomal deletions and duplications increase risk of schizophrenia
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What makes UK Biobank special?
Collins, R. (2012) · The Lancet · doi:10.1016/s0140-6736(12)60404-8 · Cited by 1,128
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Kirov, G., Pocklington, A. J., Holmans, P., Ivanov, D., Ikeda, M., Ruderfer, D., Moran, J., Chambert, K., Toncheva, D., Georgieva, L., et al. (2012) · Molecular Psychiatry · doi:10.1038/mp.2011.154 · Cited by 844 · cited 4×
“Much less is known about the effects of these CNVs in adults from the general population (9, 10).”
InfluentialSelf-citationCoe, B. P., Witherspoon, K., Rosenfeld, J. A., van Bon, B. W. M., Vulto-van Silfhout, A. T., Bosco, P., Friend, K. L., Baker, C., Buono, S., Vissers, L. E. L. M., et al. (2014) · Nature Genetics · doi:10.1038/ng.3092 · Cited by 720
Microduplications of 16p11.2 are associated with schizophrenia
Wellcome Trust Case Control Consortium, McCarthy, S. E., Makarov, V., Kirov, G., Addington, A. M., McClellan, J., Yoon, S., Perkins, D. O., Dickel, D. E., Kusenda, M., et al. (2009) · Nature Genetics · doi:10.1038/ng.474 · Cited by 711
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Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders
Sullivan, P. F., & Geschwind, D. H. (2019) · Cell · doi:10.1016/j.cell.2019.01.015 · Cited by 452
Schizophrenia and the neurodevelopmental continuum:evidence from genomics
Owen, M. J., & O’Donovan, M. C. (2017) · World Psychiatry · doi:10.1002/wps.20440 · Cited by 339
Self-citationA large data resource of genomic copy number variation across neurodevelopmental disorders
Zarrei, M., Burton, C. L., Engchuan, W., Young, E. J., Higginbotham, E. J., MacDonald, J. R., Trost, B., Chan, A. J. S., Walker, S., Lamoureux, S., et al. (2019) · npj Genomic Medicine · doi:10.1038/s41525-019-0098-3 · Cited by 187
Li, Y., Sahakian, B. J., Kang, J., Langley, C., Zhang, W., Xie, C., Xiang, S., Yu, J., Cheng, W., & Feng, J. (2022) · Nature Aging · doi:10.1038/s43587-022-00210-2 · Cited by 185
Medical consequences of pathogenic CNVs in adults: analysis of the UK Biobank
Crawford, K., Bracher-Smith, M., Owen, D., Kendall, K. M., Rees, E., Pardiñas, A. F., Einon, M., Escott-Price, V., Walters, J. T. R., O’Donovan, M. C., et al. (2019) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2018-105477 · Cited by 175
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Metadata
- Authors
- Kendall, K. M., Rees, E., Escott-Price, V., Einon, M., Thomas, R., Hewitt, J., O’Donovan, M. C., Owen, M. J., Walters, J. T. R., & Kirov, G.
- Affiliations
- Cardiff University (GB)
- University Hospital Llandough (GB)
- Corresponding author
- Kirov, George
- ORCID
- Venue
- Biological Psychiatry
- Publisher
- Elsevier BV
- Published
- 2017-07
- Volume
- 82
- Issue
- 2
- Pages
- 103-110
- ISSN
- 0006-3223 (ISSN-L)
- OpenAlex
- W2513914028
- Cited by
- 226
- References
- 32
- Citations by year
- 2026: 18 · 2025: 14 · 2024: 23 · 2023: 29 · 2022: 36 · 2021: 30 · 2020: 18 · 2019: 31 · 2018: 19 · 2017: 8
- FWCI
- 15.60
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Biological Psychiatry (publishedVersion)
- PubMed (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion, cc-by-nc-nd)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- Wellcome Trust (201171/Z/16/Z)
- Cardiff University (MR/L010305/1, G0800509)
- Medical Research Council (MR/L023784/2, MR/P005748/1, MR/L010305/1, G0800509, MR/L023784/1, No. MR/L010305/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Health Sciences › Medicine › Psychiatry and Mental health › Schizophrenia research and treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- copy number variation, neurodevelopmental disorders, cognitive performance, schizophrenia, educational attainment, occupational attainment, UK Biobank, cognitive impairment
- MeSH terms
- Adult, Aged, Female, United Kingdom, Humans, Male, Middle Aged, Neuropsychological Tests, Schizophrenia, Biological Specimen Banks, DNA Copy Number Variations, Cognitive Dysfunction, Neurodevelopmental Disorders
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