Measuring and estimating the effect sizes of copy number variants on general intelligence in community-based samples
Open accessAbstract
Importance;: Copy number variants (CNVs) classified as pathogenic are identified in 10% to 15% of patients referred for neurodevelopmental disorders. However, their effect sizes on cognitive traits measured as a continuum remain mostly unknown because most of them are too rare to be studied individually using association studies. Objective: To measure and estimate the effect sizes of recurrent and nonrecurrent CNVs on IQ. Design, Setting, and Participants: This study identified all CNVs that were 50 kilobases (kb) or larger in 2 general population cohorts (the IMAGEN project and the Saguenay Youth Study) with measures of IQ. Linear regressions, including functional annotations of genes included in CNVs, were used to identify features to explain their association with IQ. Validation was performed using intraclass correlation that compared IQ estimated by the model with empirical data. Main Outcomes and Measures: Performance IQ (PIQ), verbal IQ (VIQ), and frequency of de novo CNV events. Results: The study included 2090 European adolescents from the IMAGEN study and 1983 children and parents from the Saguenay Youth Study. Of these, genotyping was performed on 1804 individuals from IMAGEN and 977 adolescents, 445 mothers, and 448 fathers (484 families) from the Saguenay Youth Study. We observed 4928 autosomal CNVs larger than 50 kb across both cohorts. For rare deletions, size, number of genes, and exons affect IQ, and each deleted gene is associated with a mean (SE) decrease in PIQ of 0.67 (0.19) points (P = 6 × 10-4); this is not so for rare duplications and frequent CNVs. Among 10 functional annotations, haploinsufficiency scores best explain the association of any deletions with PIQ with a mean (SE) decrease of 2.74 (0.68) points per unit of the probability of being loss-of-function intolerant (P = 8 × 10-5). Results are consistent across cohorts and unaffected by sensitivity analyses removing pathogenic CNVs. There is a 0.75 concordance (95% CI, 0.39-0.91) between the effect size on IQ estimated by our model and IQ loss calculated in previous studies of 15 recurrent CNVs. There is a close association between effect size on IQ and the frequency at which deletions occur de novo (odds ratio, 0.86; 95% CI, 0.84-0.87; P = 2.7 × 10-88). There is a 0.76 concordance (95% CI, 0.41-0.91) between de novo frequency estimated by the model and calculated using data from the DECIPHER database. Conclusions and Relevance: Models trained on nonpathogenic deletions in the general population reliably estimate the effect size of pathogenic deletions and suggest omnigenic associations of haploinsufficiency with IQ. This represents a new framework to study variants too rare to perform individual association studies and can help estimate the cognitive effect of undocumented deletions in the neurodevelopmental clinic.
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The 15q11.2 deletion decreases IQ by 4.3 points (95% CI 6.5 to 2.03).
“The deletion decreases IQ by 4.3 points.”
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 [33]
The Conclusions figure caption identifies 15q11.2 among recurrent CNVs assessed for predicted IQ loss, and the Characteristics of Autosomal Deletion Contents That Affect IQ section describes comparing predictions with measured IQ loss. Neither passage gives a 4.3-point decrease or the stated 95% confidence interval (searched: 15q11.2, 4.3 points, and 6.5 to 2.03). Page numbers were not available in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measuredThe statistical model could underestimate the overall effect of the 15q11.2 deletion.
“Our statistical model estimates small effect sizes on IQ for CYFIP1, NIPA1, NIPA2, and TUBGCP5 (-2.72, –0.59, −1.33 and 0.0 points of IQ, respectively) and could underestimate the overall effect of the deletion.33”
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 [33]
The Discussion (page unavailable) says the model underestimates the IQ effects of 15q13.3 and 3q29 deletions, showing that underestimation is possible. The paper includes 15q11.2 among the recurrent deletions considered (figure caption in Conclusions, page unavailable), but our copy does not say its effect is underestimated. The claim applies a documented model limitation to a deletion for which the source does not establish it. (LLM, conf=0.82)
Experimental — accuracy not yet measuredClinical series are especially problematic for genetic variants with an effect size much smaller than the average referral criteria.
“Clinical series are especially problematic for genetic variants with an effect size much smaller than the average referral criteria (ie, 16p13.11, 1q21.1 TAR, 17q12, 16p11.2 Distal (SH2B1), 1q21.1 Distal (Class I) and 15q13.3).33”
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 [33]
The Discussion (page unavailable) says IQ effects for 15q13.3 and 3q29 deletions may be overestimated because carriers are often referred to clinics for behavioral or neurologic symptoms. This supports a concern about clinical ascertainment, but the paper does not establish that clinical series are especially problematic for every listed variant or compare their effects with an average referral criterion. (LLM, conf=0.82)
Experimental — accuracy not yet measuredThe sum of pLI of genes included in a deletion is tightly correlated to its effect size on cognition.
“Our previous study suggests that the sum of pLI of genes included in a deletion is tightly correlated to its effect size on cognition.33”
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 [33]
Our estimate of the effect size on IQ is concordant with the frequency of de novo occurrence observed in deletion carriers (8.3%).
“Our estimate of the effect size on IQ is concordant with the frequency of de novo occurrence observed in deletion carriers (8.3%), which is tightly related to the effect size of deletions on IQ.33”
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 [33]
The statistical model estimates effect sizes on IQ for CYFIP1, NIPA1, NIPA2, and TUBGCP5 of -2.72, -0.59, -1.33, and 0.0 IQ points, respectively.
“Our statistical model estimates small effect sizes on IQ for CYFIP1, NIPA1, NIPA2, and TUBGCP5 (-2.72, –0.59, −1.33 and 0.0 points of IQ, respectively) and could underestimate the overall effect of the deletion.33”
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 [33]
The Characteristics Underlying the Associations of Deletions With IQ section describes a model estimating gene-level effects on performance IQ, but it does not give estimates for CYFIP1, NIPA1, NIPA2, or TUBGCP5. Searches for those genes and the four stated values found no passage in our copy that verifies the gene-specific figures. (LLM, conf=0.74)
Experimental — accuracy not yet measuredRare, large-effect variants that increase risk for neurodevelopmental and neuropsychiatric disorders are also associated with deleterious effects on cognition, and ASD is no exception.
“Rare, large-effect variants that increase risk for neurodevelopmental and neuropsychiatric disorders are also associated with deleterious effects on cognition,28, 29, 30 and ASD is no exception.”
From Insufficient Evidence for “Autism-Specific” Genes (2020) · cites this paper as [29]
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- Authors
- Huguet, G., Schramm, C., Douard, E., Jiang, L., Labbe, A., Tihy, F., Mathonnet, G., Nizard, S., Lemyre, E., Mathieu, A., Poline, J.-B., Loth, E., Toro, R., Schumann, G., Conrod, P., Pausova, Z., Greenwood, C., Paus, T., Bourgeron, T., Jacquemont, S., & for the IMAGEN Consortium
- Affiliations
- Centre Hospitalier Universitaire Sainte-Justine (CA)
- Jewish General Hospital (CA)
- HEC Montréal (CA)
- Centre National de la Recherche Scientifique (FR)
- University of California, Berkeley (US)
- King's College London (GB)
- Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, England
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Rotman Research Institute, Baycrest, Toronto, Ontario, Canada
- Corresponding author
- Jacquemont, Sébastien
- ORCID
- Venue
- JAMA Psychiatry
- Publisher
- American Medical Association (AMA)
- Published
- 2018-05-01
- Volume
- 75
- Issue
- 5
- Pages
- 447
- ISSN
- 2168-622X (ISSN-L)
- PMC
- PMC5875373
- OpenAlex
- W2789286209
- Cited by
- 96
- References
- 48
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 10 · 2023: 9 · 2022: 16 · 2021: 23 · 2020: 15 · 2019: 7 · 2018: 3
- FWCI
- 7.36
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- JAMA Psychiatry (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Research Portal (King's College London) (submittedVersion, other-oa)
- Funders
- Wellcome Trust
- Canadian Institutes of Health Research
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- copy number variation, general intelligence, IQ, effect size estimation, recurrent CNVs, de novo CNVs, haploinsufficiency, loss-of-function intolerance, gene dosage, performance IQ, verbal IQ, neurodevelopmental disorders, functional annotation, Imagen, community sample, adolescents, parents and children, gene-gene interaction
- MeSH terms
- Loss of Function Mutation, Adolescent, Child, Chromosome Aberrations, Europe, Exons, Female, Genotype, Genetic Carrier Screening, Humans, Intelligence, Male, Models, Genetic, Quebec, Sampling Studies, Cohort Studies, Gene Deletion, DNA Copy Number Variations, Haploinsufficiency, Neurodevelopmental Disorders
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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