Cited by 490Genetic Associations and EpidemiologyCognitive Abilities and TestingGenetic Mapping and Diversity in Plants and Animals

Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence

Open access
Sniekers, Suzanne, Stringer, Sven, Watanabe, Kyoko, Jansen, Philip R, Coleman, Jonathan R I, Krapohl, Eva, Taskesen, Erdogan, Hammerschlag, Anke R +22 more·2017·Nature Genetics

Abstract

Danielle Posthuma and colleagues perform a large meta-analysis for intelligence and determine genetic overlap with several neuropsychiatric and metabolic traits. They find 15 new significant loci and implicate 40 new genes, most of which are predominantly expressed in the brain. Intelligence is associated with important economic and health-related life outcomes1. Despite intelligence having substantial heritability2 (0.54) and a confirmed polygenic nature, initial genetic studies were mostly underpowered3,4,5. Here we report a meta-analysis for intelligence of 78,308 individuals. We identify 336 associated SNPs (METAL P < 5 × 10−8) in 18 genomic loci, of which 15 are new. Around half of the SNPs are located inside a gene, implicating 22 genes, of which 11 are new findings. Gene-based analyses identified an additional 30 genes (MAGMA P < 2.73 × 10−6), of which all but one had not been implicated previously. We show that the identified genes are predominantly expressed in brain tissue, and pathway analysis indicates the involvement of genes regulating cell development (MAGMA competitive P = 3.5 × 10−6). Despite the well-known difference in twin-based heritability2 for intelligence in childhood (0.45) and adulthood (0.80), we show substantial genetic correlation (rg = 0.89, LD score regression P = 5.4 × 10−29). These findings provide new insight into the genetic architecture of intelligence.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/ng.3869

Cites

46 of 46 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Genome-wide association studies to date suggest that hundreds to thousands of genes additively influence variation in intelligence, with the effect of any one gene being very small.

    “Most genome-wide association studies (GWAS) to date have focused on intelligence or g [234–237], and suggest that hundreds to thousands of genes additively influence variation in intelligence, with the effect of any one gene being very small (typically in GWAS, a variant has r2 < 0.05% [238]).”

    From The role of prefrontal cortex in cognitive control and executive function (2022) · cites this paper as [235]

    The Abstract and letters section describe intelligence as polygenic, and the study identifies 52 associated genes through its SNP and gene-based analyses. Our copy does not establish that hundreds to thousands of genes influence intelligence, that their effects are additive, or that each gene’s effect is very small. The numerical variant-effect estimate is separately cited in the citing sentence. (LLM, conf=0.86)

    Experimental — accuracy not yet measured
  • Recent genome-wide meta-analyses have identified 24 genomic loci linked to variation in intelligence.

    “Recent genome-wide metaanalyses have identified 24 genomic loci linked to variation in intelligence 3-7”

    From Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence (2018) · cites this paper as [5]

    The Letters section reports that this genome-wide meta-analysis identified loci associated with intelligence, supporting the general point. It reports 18 independent significant loci, not 24; the cited paper alone therefore does not substantiate the sentence’s total across multiple studies. No page number is supplied in our copy. (LLM, conf=0.88)

    Experimental — accuracy not yet measured
  • GWAS of educational attainment was conducted in a non-overlapping European subset of UKB (n = 188,435) who did not complete the intelligence measure.

    “We conducted GWAS of educational attainment, an outcome with a high genetic correlation with intelligence 5 , in a non-overlapping European subset of the UKB sample (n = 188,435) who did not complete the intelligence measure.”
  • The correlation of ASD PRS with higher educational attainment and IQ is opposite to what has been reported for PRS of other neurodevelopmental disorders.

    “Surprisingly, multiple studies have found that PRS for ASD correlates with higher educational attainment and IQ in the population (Brainstorm Consortium et al., 2018), opposite to what has been reported for PRS of other neurodevelopmental disorders (Niemi et al., 2018; Sniekers et al., 2017).”

    From Getting to the cores of autism (2019) · cites this paper as Sniekers et al., 2017

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Sniekers, S., Stringer, S., Watanabe, K., Jansen, P. R., Coleman, J. R. I., Krapohl, E., Taskesen, E., Hammerschlag, A. R., Okbay, A., Zabaneh, D., Amin, N., Breen, G., Cesarini, D., Chabris, C. F., Iacono, W. G., Ikram, M. A., Johannesson, M., Koellinger, P., Lee, J. J., Magnusson, P. K. E., McGue, M., Miller, M. B., Ollier, W. E. R., Payton, A., Pendleton, N., Plomin, R., Rietveld, C. A., Tiemeier, H., van Duijn, C. M., & Posthuma, D.
Affiliations
  • Amsterdam Neuroscience (NL)
  • Erasmus MC (NL)
  • King's College London (GB)
  • New York University (US)
  • Union College (US)
  • University of Minnesota (US)
  • Stockholm School of Economics (SE)
  • Karolinska Institutet (SE)
  • University of Manchester (GB)
  • Manchester Academic Health Science Centre (GB)
  • Erasmus University Rotterdam (NL)
Venue
Nature Genetics
Published
2017-05-22
Volume
49
Issue
7
Pages
1107-1112
ISSN
  • 1061-4036 (ISSN-L)
  • 1546-1718
OpenAlex
W2940205897
Cited by
490
References
46
Citations by year
2026: 13 · 2025: 34 · 2024: 39 · 2023: 53 · 2022: 32 · 2021: 54 · 2020: 98 · 2019: 65 · 2018: 82 · 2017: 20
FWCI
9.32
Type
journal article
Language
en
Update notices
erratum (2017-10-01)
Open access
Locations
  • Nature Genetics (publishedVersion, other-oa)
  • PubMed (publishedVersion)
  • Pure Amsterdam UMC (publishedVersion, cc-by)
  • Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion)
  • EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
  • VU Research Portal (publishedVersion, other-oa)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • e-space (Manchester Metropolitan University) (acceptedVersion)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
  • Data Archiving and Networked Services (DANS) (submittedVersion)
  • EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
  • RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
  • Figshare (submittedVersion)
  • Research Portal (King's College London) (submittedVersion, other-oa)
  • Research Explorer (The University of Manchester) (submittedVersion)
  • Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
Funders
  • Vrije Universiteit Amsterdam
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek (480- 05-003, VICI 453-14-005, NWO VICI 453-14-005, 453-13-005, 453-14-005)
  • Medical Research Council (MR/K002279/1, MR/M021475/1)
  • Biotechnology and Biological Sciences Research Council (BB/F022441/1)
  • National Institute on Alcohol Abuse and Alcoholism (R01AA009367, R37AA009367, R01AA011886)
  • National Institute on Aging (T32AG000186)
  • National Institute of Mental Health (R01MH066140, T32MH016880)
  • National Institute on Drug Abuse (F31DA029377, R01DA013240, R01DA024417, R01DA005147, R01DA036216, R37DA005147)
  • National Institute of Diabetes and Digestive and Kidney Diseases (U01DK066134)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Social Sciences › Psychology › Experimental and Cognitive Psychology › Cognitive Abilities and Testing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords
intelligence, polygenic risk, genetic loci, single nucleotide polymorphisms, brain gene expression, neuropsychiatric traits, metabolic phenotypes, genetic correlation, heritability, cell development, genetic architecture
MeSH terms
Adolescent, Adult, Aged, Brain, Child, Child, Preschool, Female, Humans, Infant, Intelligence, Male, Middle Aged, Nerve Tissue Proteins, Linkage Disequilibrium, Polymorphism, Single Nucleotide, White People, Genome-Wide Association Study, Young Adult

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 ›

Are you an author, or do you see a problem with this page? Request a review