Large recurrent microdeletions associated with schizophrenia.
Open accessAbstract
Reduced fecundity, associated with severe mental disorders, places negative selection pressure on risk alleles and may explain, in part, why common variants have not been found that confer risk of disorders such as autism, schizophrenia and mental retardation. Thus, rare variants may account for a larger fraction of the overall genetic risk than previously assumed. In contrast to rare single nucleotide mutations, rare copy number variations (CNVs) can be detected using genome-wide single nucleotide polymorphism arrays. This has led to the identification of CNVs associated with mental retardation and autism. In a genome-wide search for CNVs associating with schizophrenia, we used a population-based sample to identify de novo CNVs by analysing 9,878 transmissions from parents to offspring. The 66 de novo CNVs identified were tested for association in a sample of 1,433 schizophrenia cases and 33,250 controls. Three deletions at 1q21.1, 15q11.2 and 15q13.3 showing nominal association with schizophrenia in the first sample (phase I) were followed up in a second sample of 3,285 cases and 7,951 controls (phase II). All three deletions significantly associate with schizophrenia and related psychoses in the combined sample. The identification of these rare, recurrent risk variants, having occurred independently in multiple founders and being subject to negative selection, is important in itself. CNV analysis may also point the way to the identification of additional and more prevalent risk variants in genes and pathways involved in schizophrenia.
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Deletion of 15q11.2(BP1-BP2) leads to a two- to fourfold increase in the risk for schizophrenia, autism and intellectual disability.
“Deletion of 15q11.2(BP1–BP2) leads to a two to fourfold increase in the risk for schizophrenia, autism and intellectual disability [1–5].”
From Linking haploinsufficiency of the autism- and schizophrenia-associated gene Cyfip1 with striatal-limbic-cortical network dysfunction and cognitive inflexibility (2024) · cites this paper as [1]
The paper’s 15q11.2 passage (section labeled Abstract; page unavailable) reports the deletion in 0.55% of schizophrenia and related-psychosis cases versus 0.19% of controls, consistent with an approximately threefold association. It discusses autism and intellectual impairment in particular syndromes or a previously reported case, but does not establish a two- to fourfold risk increase for autism or intellectual disability from this deletion. (LLM, conf=0.88)
Experimental — accuracy not yet measuredAbout 0.25% of controls (n=66,462) are found with the 15q11.2 BP1-BP2 microdeletion.
“a review of reported data from control cohorts (n = 66,462 subjects) summarized to date show that about 0.25% of controls are found with the 15q11.2 BP1–BP2 microdeletion [18,27,28,29,30,31].”
From The 15q11.2 BP1–BP2 Microdeletion Syndrome: A Review (2015) · cites this paper as [31]
The paper’s 15q11.2 results (section labeled Abstract; page unavailable) report the deletion in controls, supporting its inclusion among the cited control-cohort data. But this paper reports 79 of 41,194 controls (0.19%), not the citing sentence’s pooled 66,462 controls (about 0.25%). (LLM, conf=0.88)
Experimental — accuracy not yet measuredCopy number variation at the 15q11.2 region is a significant risk locus for neurological and neuropsychiatric conditions such as schizophrenia and autism spectrum disorder.
“Copy number variation (CNV) at the 15q11.2 region has been identified as a significant risk locus for neurological and neuropsychiatric conditions such as schizophrenia (SCZ) and autism spectrum disorder (ASD).”
From The autism and schizophrenia associated gene CYFIP1 is critical for the maintenance of dendritic complexity and the stabilization of mature spines (2014) · cites this paper as [5]
The paper reports a significant association between the 15q11.2 deletion and schizophrenia or related psychoses (Abstract; page unavailable). It also discusses autistic features in Angelman syndrome cases with larger deletions that include 15q11.2, but does not establish the 15q11.2 CNV itself as a significant risk locus for autism spectrum disorder. (LLM, conf=0.85)
Experimental — accuracy not yet measuredCopy number variation of CYFIP1 within 15q11.2 is linked to both autism spectrum disorder and schizophrenia.
“Copy number variation of one gene within 15q11.2, coding for the cytoplasmic FMRP-interacting protein 1 (CYFIP1), has been linked to both ASD and SCZ.5,8,9”
From The autism and schizophrenia associated gene CYFIP1 is critical for the maintenance of dendritic complexity and the stabilization of mature spines (2014) · cites this paper as [5]
The paper reports an association between a 15q11.2 deletion and schizophrenia, and identifies CYFIP1 as the gene most likely to contribute to both that phenotype and autistic features in Angelman syndrome (passages [8] and [1], section labelled Abstract; no page supplied). But the deletion spans several genes, and the autism evidence concerns features in Angelman syndrome rather than a demonstrated association between CYFIP1-specific copy-number variation and ASD. (LLM, conf=0.84)
Experimental — accuracy not yet measuredAltered levels of CYFIP1 are associated with several neurological disorders including SCZ and ASD.
“Altered levels of CYFIP1 are associated with several neurological disorders including SCZ and ASD.4,5,10”
From The autism and schizophrenia associated gene CYFIP1 is critical for the maintenance of dendritic complexity and the stabilization of mature spines (2014) · cites this paper as [5]
The paper reports an association between a 15q11.2 deletion containing CYFIP1 and schizophrenia, and proposes CYFIP1 as the gene most likely to explain autistic features associated with related deletions (Abstract; page unavailable). It also notes reduced CYFIP1 expression in fragile X syndrome. It does not establish that altered CYFIP1 levels themselves are associated with both schizophrenia and ASD. (LLM, conf=0.84)
Experimental — accuracy not yet measured
The BP1-BP2 deletion is associated with phenotypic variability and has been reported in individuals with neurodevelopmental disorders, schizophrenia, ASD, and epilepsy.
“The BP1-BP2 deletion is associated with phenotypic variability and has been reported in individuals with neurodevelopmental disorders [20], schizophrenia [53], [60], ASD [44]–[46], [49], and epilepsy [61].”
From Genetic and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism Spectrum Disorders (2012) · cites this paper as [53]
The most compelling candidate in the deleted region is CYFIP1, which codes for a binding partner of FMRP, the protein responsible for fragile X syndrome.
“However, the most compelling candidate in the deleted region is CYFIP1 [45], [53], which codes for a binding partner of FMRP, the protein responsible for fragile X syndrome.”
From Genetic and Functional Analyses of SHANK2 Mutations Suggest a Multiple Hit Model of Autism Spectrum Disorders (2012) · cites this paper as [53]
Inherited CNVs detected in this study included a 1q21.1 duplication in a bipolar disorder subject and a duplication and a deletion at 15q13.3 in bipolar disorder and schizophrenia subjects, respectively.
“Notably, inherited CNVs detected in this study included variants at loci that have been previously linked to schizophrenia (International Schizophrenia Consortium, 2008 and Stefansson et al., 2008), including a duplication at 1q21.1 in a subject with bipolar disorder and a duplication and a deletion at 15q13.3 detected in subjects with bipolar disorder and schizophrenia, respectively (Document S2,”
From High frequencies of de novo CNVs in bipolar disorder and schizophrenia (2011) · cites this paper as Stefansson et al., 2008
The size difference between SD-mediated and non-SD-mediated de novo CNVs is consistent with prior studies linking CNV size to mutational mechanism.
“Notably, the median size of SD and non-SD-mediated de novo CNVs was 722 kb and 67 kb respectively, consistent with previous studies that have found differences in CNV size related to the underlying mutational mechanism (Itsara et al., 2010 and Stefansson et al., 2008).”
From High frequencies of de novo CNVs in bipolar disorder and schizophrenia (2011) · cites this paper as Stefansson et al., 2008
Structural variants have been associated with autism, schizophrenia, and Crohn's disease.
“SVs have already been associated with diverse diseases, including autism2,3, schizophrenia4,5 and Crohn’s disease6,7.”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [4]
Such CNVs must frequently occur as recurrent de novo mutations.
“Accordingly, such CNVs must frequently occur as recurrent de novo mutations.”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [7]
Several individual CNV loci have been strongly implicated as risk factors for schizophrenia.
“several individual CNV loci have been strongly implicated as risk factors for schizophrenia with high degrees of statistical confidence. These include deletions at 1q21.1, NRXN1, 3q29, 15q11.2, 15q13.3, 22q11.2 and duplications at VIPR2, 16p11.2, 16p13.1 and 15q11-q13.2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [7]
Those mutations that occur in multiple unrelated individuals are likely to do so through independent de novo mutations.
“those that occur in multiple unrelated individuals are likely to do so through independent de novo mutations.7, 22, 23, 24”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [7]
There is strong published evidence for deletions at 15q11.2 being relevant to schizophrenia.
“Although there is strong published evidence for deletions at this locus being relevant to schizophrenia,3, 7”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [7]
The TAR syndrome 1q21.1 deletion does not overlap the known 1q21.1 schizophrenia locus.
“(which does not overlap the known 1q21.1 schizophrenia locus2, 7)”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [7]
Recurrent CNVs initially observed in ID or ASD are also found in adults with epilepsy, bipolar disorder, or schizophrenia, suggesting genetic overlap among these disorders.
“many of these same recurrent CNVs observed initially in patients with ID [15] or ASD [16] have been identified in adults with epilepsy [17], bipolar disorder [18], or schizophrenia [19,20], suggesting overlap in the genetic etiology of these disorders.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [19]
Five percent of schizophrenia cases and five percent of autism cases have been attributed to CNVs at fewer than six genomic locations.
“Five percent of cases of schizophrenia and of autism have each been attributed to CNVs at fewer than a half dozen genomic locations46–48.”
From Rare and common variants: twenty arguments (2012) · cites this paper as [46]
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- Authors
- GROUP, Stefansson, H., Rujescu, D., Cichon, S., Pietiläinen, O. P. H., Ingason, A., Steinberg, S., Fossdal, R., Sigurdsson, E., Sigmundsson, T., Buizer-Voskamp, J. E., Hansen, T., Jakobsen, K. D., Muglia, P., Francks, C., Matthews, P. M., Gylfason, A., Halldorsson, B. V., Gudbjartsson, D., Thorgeirsson, T. E., Sigurdsson, A., Jonasdottir, A., Jonasdottir, A., Bjornsson, A., Mattiasdottir, S., Blondal, T., Haraldsson, M., Magnusdottir, B. B., Giegling, I., Möller, H.-J., Hartmann, A., Shianna, K. V., Ge, D., Need, A. C., Crombie, C., Fraser, G., Walker, N., Lonnqvist, J., Suvisaari, J., Tuulio-Henriksson, A., Paunio, T., Toulopoulou, T., Bramon, E., Di Forti, M., Murray, R., Ruggeri, M., Vassos, E., Tosato, S., Walshe, M., Li, T., Vasilescu, C., Mühleisen, T. W., Wang, A. G., Ullum, H., Djurovic, S., Melle, I., Olesen, J., Kiemeney, L. A., Franke, B., Sabatti, C., Freimer, N. B., Gulcher, J. R., Thorsteinsdottir, U., Kong, A., Andreassen, O. A., Ophoff, R. A., Georgi, A., Rietschel, M., Werge, T., Petursson, H., Goldstein, D. B., Nöthen, M. M., Peltonen, L., Collier, D. A., St Clair, D., & Stefansson, K.
- Affiliations
- deCODE Genetics (Iceland) (IS)
- University of Bonn (DE)
- University Medical Center Utrecht (NL)
- University of Copenhagen (DK)
- GlaxoSmithKline (Italy) (IT)
- GlaxoSmithKline (United Kingdom) (GB)
- National University Hospital of Iceland (IS)
- Ludwig-Maximilians-Universität München (DE)
- Duke University (US)
- University of Aberdeen (GB)
- King's College London (GB)
- University of Verona (IT)
- Amager Hospital (DK)
- University of Oslo (NO)
- Glostrup Hospital (DK)
- Radboud University Medical Center (NL)
- University of California, Los Angeles (US)
- Heidelberg University (DE)
- Sankt Hans Hospital (DK)
- Broad Institute (US)
- ORCID
- Rujescu, Dan
- Cichon, Sven
- Pietiläinen, Olli P. H.
- Steinberg, Stacy
- Hansen, Thomas
- Muglia, Pierandrea
- Francks, Clyde
- Matthews, Paul M.
- Gylfason, Arnaldur
- Gudbjartsson, Daniel
- Thorgeirsson, Thorgeir E.
- Haraldsson, Magnus
- Giegling, Ina
- Möller, Hans-Jürgen
- Hartmann, Annette
- Ge, Dongliang
- Need, Anna C.
- Suvisaari, Jaana
- Paunio, Tiina
- Bramon, Elvira
- Murray, Robin
- Ruggeri, Mirella
- Vassos, Evangelos
- Tosato, Sarah
- Walshe, Muriel
- Li, Tao
- Mühleisen, Thomas W.
- Wang, August G.
- Ullum, Henrik
- Djurovic, Srdjan
- Melle, Ingrid
- Olesen, Jes
- Kiemeney, Lambertus A.
- Franke, Barbara
- Sabatti, Chiara
- Freimer, Nelson B.
- Kong, Augustine
- Andreassen, Ole A.
- Ophoff, Roel A.
- Georgi, Alexander
- Rietschel, Marcella
- Werge, Thomas
- Goldstein, David B.
- Nöthen, Markus M.
- Peltonen, Leena
- Collier, David A.
- Venue
- Nature
- Published
- 2008-09
- Volume
- 455
- Issue
- 7210
- Pages
- 232-236
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2687075
- OpenAlex
- W1997031801
- Cited by
- 1,745
- References
- 32
- Citations by year
- 2026: 11 · 2025: 21 · 2024: 28 · 2023: 32 · 2022: 34 · 2021: 51 · 2020: 41 · 2019: 62 · 2018: 61 · 2017: 62 · 2016: 80 · 2015: 118 · 2014: 115 · 2013: 159 · 2012: 173
- FWCI
- 130.32
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Lirias (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- Hirsla (Landspítali University Hospital) (submittedVersion)
- Funders
- Wellcome Trust (089061)
- National Institute for Health and Care Research (PDA/02/06/016)
- Bundesministerium für Bildung und Forschung
- Alfried Krupp von Bohlen und Halbach-Stiftung
- National Institute of Mental Health (R01MH071425, R01MH078075, R01MH71425-01A1)
- 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
- schizophrenia, copy number variation, de novo copy number variants, 1q21.1, 15q11.2, 15q13.3, chromosome 1, chromosome 15, rare variants, negative selection, fecundity, psychosis, genetic association, founder effect
- MeSH terms
- China, Chromosomes, Human, Pair 1, Chromosomes, Human, Pair 15, Europe, Genotype, Humans, Models, Genetic, Psychotic Disorders, Schizophrenia, Genome, Human, Sequence Deletion, Gene Dosage, Loss of Heterozygosity, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide
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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