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 15q11.2 deletion is significantly enriched in the SJCHU CMA database (OR 1.9, 95% CI 1.5 to 2.4) compared with UK Biobank.
“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]
The Results report 151,659 UK Biobank samples passing quality control, and the CNV Calling Criteria include 15q11.2 deletions. But our copy does not give the cited deletion prevalence of 0.36% (544/151,619) or the SJCHU comparison and odds ratio; it directs readers to a separate Excel file for locus-specific frequencies (CNV Breakpoints and Frequencies, Table S2). The citation is attached to the UK Biobank baseline, not clearly to the citing authors’ enrichment calculation. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe 15q11.2 deletion is significantly enriched in the OUH CMA database (OR 3.1, 95% CI 1.6 to 5.7) compared with UK Biobank.
“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]
The Results and the section describing Table S2 establish that the paper measured CNV frequencies in UK Biobank, including the 15q11.2 deletion listed in the CNV Calling Criteria. Our copy does not give the cited deletion prevalence of 0.36% (544/151619), and it does not report an OUH CMA comparison or the stated odds ratio and confidence interval. In the citing sentence, the reference appears next to the UK Biobank prevalence, not the authors’ OUH enrichment result. (LLM, conf=0.83)
Experimental — accuracy not yet measuredThe UK Biobank data used as control is from an unselected population (151,619 individuals).
“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]
Methods and Materials says UK Biobank participants were recruited without exclusion criteria, supporting the description of an unselected sample. However, Methods and Materials and Results report 151,659 samples passing quality control, not 151,619. The Discussion also cautions that the sample is not fully representative of the general population. (LLM, conf=0.90)
Experimental — accuracy not yet measuredThe 15q11.2 duplication is used as a control neutral CNV throughout the study.
“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]
The reciprocal 15q11.2 duplication is not enriched in the SJCHU and OUH cohorts when using UK Biobank prevalence (0.5%).
“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]
There is no significant enrichment of CHD in 15q11.2 deletion carriers (OR 1.55, 95% CI 0.97 to 2.48) if the UK Biobank population frequency is used as control.
“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]
The Results and the section on CNV frequencies say the study measured copy-number-variant frequencies in UK Biobank, but the available text directs readers to an Excel supplement for the locus-specific figures. Searches for the 15q11.2 deletion frequency, CHD, and the stated odds ratio found no passage giving 0.36% or assessing CHD enrichment. Our copy therefore does not verify the claimed comparison. (LLM, conf=0.72)
Experimental — accuracy not yet measuredThe best estimates of the population frequency of the 15q11.2 deletion range from 0.36% (UK BIOBANK) to 0.24% (Icelandic population).
“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]
The Discussion says the authors established frequencies for 93 CNVs in UK Biobank, but the CNV Breakpoints and Frequencies section directs readers to Table S2 in a separate Excel file. Our copy does not give a 0.36% frequency for the 15q11.2 deletion (searched: 0.36%, 15q11.2 deletion frequency). The Icelandic estimate has a separate citation in the citing sentence and is not attributed to this paper. (LLM, conf=0.74)
Experimental — accuracy not yet measuredPenetrance of copy number variants can be highly variable, ranging from subtle effects detectable by neuropsychological tests to mild anxiety or ADHD to co-occurrence of severe psychiatric disorders.
“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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- 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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