Common genetic variants contribute to risk of rare severe neurodevelopmental disorders
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Abstract
There are thousands of rare human disorders that are caused by single deleterious, protein-coding genetic variants 1. However, patients with the same genetic defect can have different clinical presentations 2-4, and some individuals who carry known disease-causing variants can appear unaffected 5. Here, to understand what explains these differences, we study a cohort of 6,987 children assessed by clinical geneticists to have severe neurodevelopmental disorders such as global developmental delay and autism, often in combination with abnormalities of other organ systems. Although the genetic causes of these neurodevelopmental disorders are expected to be almost entirely monogenic, we show that 7.7% of variance in risk is attributable to inherited common genetic variation. We replicated this genome-wide common variant burden by showing, in an independent sample of 728 trios (comprising a child plus both parents) from the same cohort, that this burden is over-transmitted from parents to children with neurodevelopmental disorders. Our common-variant signal is significantly positively correlated with genetic predisposition to lower educational attainment, decreased intelligence and risk of schizophrenia. We found that common-variant risk was not significantly different between individuals with and without a known protein-coding diagnostic variant, which suggests that common-variant risk affects patients both with and without a monogenic diagnosis. In addition, previously published common-variant scores for autism, height, birth weight and intracranial volume were all correlated with these traits within our cohort, which suggests that phenotypic expression in individuals with monogenic disorders is affected by the same variants as in the general population. Our results demonstrate that common genetic variation affects both overall risk and clinical presentation in neurodevelopmental disorders that are typically considered to be monogenic.
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The genetic causes underlying NDDs are diverse, ranging from single gene mutations, copy number variations to whole-chromosome aberrations.
“The genetic causes underlying NDDs are diverse ranging from single gene mutations, copy number variations to whole‐chromosome aberrations [263].”
From Development of prefrontal cortex (2022) · cites this paper as [263]
The Abstract (page unavailable) describes severe neurodevelopmental disorders as typically monogenic and discusses rare single-gene variants alongside inherited common variation. It does not identify copy-number variations or whole-chromosome aberrations as causes of these disorders. The only CNV mention found is in a reference title about schizophrenia. (LLM, conf=0.86)
Experimental — accuracy not yet measuredEvidence suggests reduced SNP heritability for forms of ASD in which co-diagnosed ID is more common.
“Further, evidence suggests reduced SNP heritability for forms of ASD in which co-diagnosed ID is more common.15,25”
From The female protective effect against autism spectrum disorder (2022) · cites this paper as [25]
The genetic correlation between ID and ASD is not significantly different from zero as currently estimated.
“as currently estimated, the genetic correlation between ID and ASD is not significantly different from zero.25”
From The female protective effect against autism spectrum disorder (2022) · cites this paper as [25]
When directly examined, polygenic risk combines additively with major mutation burden.
“In the instances where this has been studied directly, polygenic risk acts additively with major mutational burdens (Gaugler et al., 2014; Niemi et al., 2018; Purcell et al., 2014; Weiner et al., 2017).”
From Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders (2019) · cites this paper as Niemi et al., 2018
Individuals with neurodevelopmental disorders carrying a reportable clinical diagnostic variant have significantly increased PRS.
“This study reported that individuals with NDDs who carry a reportable clinical diagnostic variant have a significantly increased PRS.”
From Getting to the cores of autism (2019) · cites this paper as Niemi et al., 2018
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 Niemi et al., 2018
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- Authors
- Niemi, M. E. K., Martin, H. C., Rice, D. L., Gallone, G., Gordon, S., Kelemen, M., McAloney, K., McRae, J., Radford, E. J., Yu, S., Gecz, J., Martin, N. G., Wright, C. F., Fitzpatrick, D. R., Firth, H. V., Hurles, M. E., & Barrett, J. C.
- Affiliations
- Wellcome Sanger Institute (GB)
- QIMR Berghofer Medical Research Institute (AU)
- University of Cambridge (GB)
- South Australia Pathology (AU)
- University of Exeter (GB)
- Western General Hospital (GB)
- Cambridge University Hospitals NHS Foundation Trust (GB)
- Corresponding author
- Barrett, Jeffrey C.
- ORCID
- Venue
- Nature
- Published
- 2018-09-26
- Volume
- 562
- Issue
- 7726
- Pages
- 268-271
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6726472
- OpenAlex
- W2952988698
- Cited by
- 340
- References
- 46
- Citations by year
- 2026: 20 · 2025: 45 · 2024: 39 · 2023: 41 · 2022: 54 · 2021: 52 · 2020: 41 · 2019: 41 · 2018: 7
- FWCI
- 21.62
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nd
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Open Research Exeter (University of Exeter) (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- Figshare (submittedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Apollo (University of Cambridge) (submittedVersion, cc-by-nc-nd)
- Apollo
- Funders
- University of Essex (ES/M008592/1)
- Wellcome Trust (HICF-1009-003, 091986, GEN/284/12, WT 098051, 10/H0305/83, 213422/Z/18/Z, 098051)
- Understanding Society
- National Institute for Health and Care Research (10/H0305/83, ACF-2015-14-007, HICF-1009-003, WT098051)
- Medical Research Council (MR/N01104X/1, MR/N01104X/2, WT098051, MC_UU_00007/3, Grant Number: MR/N01104X/1)
- Economic and Social Research Council (MR/N01104X/1, ES/M008592/1, ES/S008349/1)
- National Health and Medical Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- neurodevelopmental disorders, common genetic variants, monogenic disorders, global developmental delay, autism spectrum disorder, genetic burden, educational attainment, intelligence, schizophrenia risk, phenotypic expression, clinical heterogeneity, intracranial volume, birth weight, height
- MeSH terms
- Autistic Disorder, Birth Weight, Body Height, Developmental Disabilities, Female, Humans, Intelligence, Male, Phenotype, Schizophrenia, Genetic Variation, Cohort Studies, Linkage Disequilibrium, Case-Control Studies, Genetic Predisposition to Disease, Multifactorial Inheritance, Rare Diseases, Genome-Wide Association Study, Neurodevelopmental Disorders
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