Microduplications of 16p11.2 are associated with schizophrenia
Open accessAbstract
Recurrent microdeletions and microduplications of a 600-kb genomic region of chromosome 16p11.2 have been implicated in childhood-onset developmental disorders. We report the association of 16p11.2 microduplications with schizophrenia in two large cohorts. The microduplication was detected in 12/1,906 (0.63%) cases and 1/3,971 (0.03%) controls (P = 1.2 x 10(-5), OR = 25.8) from the initial cohort, and in 9/2,645 (0.34%) cases and 1/2,420 (0.04%) controls (P = 0.022, OR = 8.3) of the replication cohort. The 16p11.2 microduplication was associated with a 14.5-fold increased risk of schizophrenia (95% CI (3.3, 62)) in the combined sample. A meta-analysis of datasets for multiple psychiatric disorders showed a significant association of the microduplication with schizophrenia (P = 4.8 x 10(-7)), bipolar disorder (P = 0.017) and autism (P = 1.9 x 10(-7)). In contrast, the reciprocal microdeletion was associated only with autism and developmental disorders (P = 2.3 x 10(-13)). Head circumference was larger in patients with the microdeletion than in patients with the microduplication (P = 0.0007).
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Deletions and duplications of 16p11.2 have highly pleiotropic phenotypic effects, with strong links to ASD, ID, motor/developmental delay, dysmorphic features, and epilepsy/seizures.
“Deletions and duplications of 16p11.2 have highly pleiotropic phenotypic effects, with strong links to ASD [8–19], ID [8, 10, 12, 14–16, 19–21], motor/developmental delay [8–10, 12, 13, 15–19, 22], dysmorphic features [8, 12, 16, 17, 22], and epilepsy/seizures [10, 12, 17].”
From 16p11.2 Copy Number Variations and Neurodevelopmental Disorders (2020) · cites this paper as [9]
Schizophrenia appears to be associated more strongly with 16p11.2 duplications than with deletions.
“Schizophrenia (SZ) appears to be associated more strongly with 16p11.2 duplications [9, 25–27].”
From 16p11.2 Copy Number Variations and Neurodevelopmental Disorders (2020) · cites this paper as [9]
Bipolar disorder is reported in 16p11.2 duplication carriers.
“Bipolar disorder is also reported in 16p11.2 duplication carriers [9, 14, 24].”
From 16p11.2 Copy Number Variations and Neurodevelopmental Disorders (2020) · cites this paper as [9]
In a 2009 study, 21 duplications and 1 deletion were detected among 5,877 schizophrenia patients, indicating a 14.5-fold increased SZ risk in 16p11.2 duplication patients.
“In a 2009 study, 21 duplications and 1 deletion were detected among 5,877 schizophrenia (SZ) patients, indicating a 14.5-fold increased SZ risk in 16p11.2 duplication patients [9].”
From 16p11.2 Copy Number Variations and Neurodevelopmental Disorders (2020) · cites this paper as [9]
Evidence from the present work and earlier research indicates that 16p11.2 CNVs have much stronger effects than any common variant for complex common disorders.
“there is clear evidence from this and prior studies (McCarthy et al., 2009) that 16p11.2 CNVs carry much larger effects than any common variant contributing to complex common disorders”
From Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism (2011) · cites this paper as McCarthy et al., 2009
Recurrent ASD-associated CNVs such as 16p11.2 are linked not only to ASD but also to schizophrenia, epilepsy, ADHD, and obesity.
“Variability of phenotype is also characteristic of recurrent ASD-associated CNVs, such as 16p11.2, which has been linked not only to ASD but also to schizophrenia, epilepsy, ADHD, and obesity (Mccarthy et al., 2009; Shinawi et al., 2010; Walters et al., 2010; Weiss et al., 2008).”
From Using Whole-Exome Sequencing to Identify Inherited Causes of Autism (2013) · cites this paper as Mccarthy et al., 2009
Very few CNVs contributing to schizophrenia are also associated with bipolar disorder, with possible exceptions being 16p11.2 microduplications and 3q29 microdeletions.
“Notably, very few of the CNVs that contribute to risk for schizophrenia are also associated with bipolar disorder, the possible exceptions being microduplications of 16p11.2 (McCarthy et al., 2009) and microdeletions of 3q29 (Clayton-Smith et al., 2010; Malhotra et al., 2011), which have been reported in multiple cases (Table 1).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as McCarthy et al., 2009
Deletions and duplications of 1q21.1 and 16p11.2 have contrasting effects on head size and psychiatric features.
“Furthermore, deletions and duplications of each region have contrasting effects on head size and psychiatric features (McCarthy et al., 2009) (Table 1).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as McCarthy et al., 2009
16p11.2 microduplications are associated with autism, schizophrenia, or bipolar disorder.
“Likewise microduplications of 16p11.2 are associated with autism, schizophrenia or bipolar disorder (McCarthy et al., 2009; Weiss et al., 2008).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as McCarthy et al., 2009
For some well-characterized genomic disorders, a relationship between CNV genotype and clinical phenotype is beginning to emerge.
“For some of the more well-characterized genomic disorders, a relationship between CNV genotype and clinical phenotype is beginning to emerge (Brunetti-Pierri et al., 2008; McCarthy et al., 2009).”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as McCarthy et al., 2009
Reciprocal deletion and duplication of 16p11.2 result in similar brain structural alterations in human and mouse, with deletion associated with brain overgrowth and duplication with reduced brain volume.
“For example reciprocal deletion and duplication of 16p11.2 result in similar brain structural alterations in human and mouse, the deletion associated with brain overgrowth and the duplication associated with reduced brain volume (Horev et al., 2011; McCarthy et al., 2009; Shinawi et al., 2010), and structural alterations appear to be widely distributed across multiple brain regions.”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as McCarthy et al., 2009
Structural alterations from 16p11.2 CNV appear to be widely distributed across multiple brain regions.
“For example reciprocal deletion and duplication of 16p11.2 result in similar brain structural alterations in human and mouse, the deletion associated with brain overgrowth and the duplication associated with reduced brain volume (Horev et al., 2011; McCarthy et al., 2009; Shinawi et al., 2010), and structural alterations appear to be widely distributed across multiple brain regions.”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as McCarthy et al., 2009
The three significant schizophrenia regions correspond to CNVs previously implicated in schizophrenia at 3q29, 7q36.3, and 16p11.2.
“In schizophrenia, three genomic regions were significant (Table S6B), all corresponding to CNVs that have been previously implicated in schizophrenia at 3q29 (Mulle et al., 2010), 7q36.3 (Vacic et al., 2011), and 16p11.2 (McCarthy et al., 2009).”
From High frequencies of de novo CNVs in bipolar disorder and schizophrenia (2011) · cites this paper as McCarthy et al., 2009
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 [5]
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 [12]
Many CNVs robustly implicated in schizophrenia are also implicated in neurodevelopmental disorders in which cognitive impairment is common.
“Many of the CNVs robustly implicated in schizophrenia are also implicated in neurodevelopmental disorders in which cognitive impairment is common.39, 40, 41”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [39]
16p11 duplications are observed in ASD, schizophrenia, and various forms of developmental delay.
“Such is certainly the case with 16p11 duplications, which are observed in ASD, schizophrenia, and various forms of developmental delay [37–39]”
From Genetics of autism spectrum disorders (2011) · cites this paper as [39]
Even the largest genome-wide scans, typically under 10,000 samples, remain underpowered to robustly confirm genetic association for most pathogenic CNVs reported so far, particularly those with low frequencies or intermediate effect sizes.
“yet even the largest genome-wide scans (sample sizes typically <10,000) remain under-powered to robustly confirm genetic association for the majority of pathogenic CNVs reported so far, particularly for those with low frequencies (<0.5% in cases) or intermediate effect sizes (odds ratios 2–10).”
From Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects (2017) · cites this paper as [7]
Identical mutations may be associated with highly divergent phenotype.
“identical mutations may be associated with highly divergent phenotype”
From Autism risk factors: genes, environment, and gene-environment interactions (2012) · cites this paper as [41]
Identical CNVs have been associated with autism and schizophrenia, notably 16p11 rearrangements.
“identical CNVs have been associated with autism and schizophrenia, notably 16p11 rearrangements”
From Autism risk factors: genes, environment, and gene-environment interactions (2012) · cites this paper as [41]
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Self-citation
- Authors
- Wellcome Trust Case Control Consortium, McCarthy, S. E., Makarov, V., Kirov, G., Addington, A. M., McClellan, J., Yoon, S., Perkins, D. O., Dickel, D. E., Kusenda, M., Krastoshevsky, O., Krause, V., Kumar, R. A., Grozeva, D., Malhotra, D., Walsh, T., Zackai, E. H., Kaplan, P., Ganesh, J., Krantz, I. D., Spinner, N. B., Roccanova, P., Bhandari, A., Pavon, K., Lakshmi, B., Leotta, A., Kendall, J., Lee, Y.-H., Vacic, V., Gary, S., Iakoucheva, L. M., Crow, T. J., Christian, S. L., Lieberman, J. A., Stroup, T. S., Lehtimäki, T., Puura, K., Haldeman-Englert, C., Pearl, J., Goodell, M., Willour, V. L., DeRosse, P., Steele, J., Kassem, L., Wolff, J., Chitkara, N., McMahon, F. J., Malhotra, A. K., Potash, J. B., Schulze, T. G., Nöthen, M. M., Cichon, S., Rietschel, M., Leibenluft, E., Kustanovich, V., Lajonchere, C. M., Sutcliffe, J. S., Skuse, D., Gill, M., Gallagher, L., Mendell, N. R., Craddock, N., Owen, M. J., O'Donovan, M. C., Shaikh, T. H., Susser, E., DeLisi, L. E., Sullivan, P. F., Deutsch, C. K., Rapoport, J., Levy, D. L., King, M.-C., & Sebat, J.
- Affiliations
- Cold Spring Harbor Laboratory (US)
- Cardiff University (GB)
- National Institutes of Health (US)
- University of Washington (US)
- University of North Carolina at Chapel Hill (US)
- McLean Hospital (US)
- University of Chicago (US)
- Children's Hospital of Philadelphia (US)
- Ontario Institute for Cancer Research (CA)
- Rockefeller University (US)
- Warneford Hospital (GB)
- Columbia University (US)
- Tampere University (FI)
- Johns Hopkins University (US)
- Zucker Hillside Hospital (US)
- University of Bonn (DE)
- Autism Speaks (US)
- Vanderbilt University (US)
- University College London (GB)
- Trinity College Dublin (IE)
- Stony Brook University (US)
- Harvard University (US)
- Corresponding author
- Sebat, Jonathan
- ORCID
- Makarov, Vladimir
- Kirov, George
- Addington, Anjene M
- McClellan, Jon
- Perkins, Diana O
- Dickel, Diane E
- Grozeva, Detelina
- Malhotra, Dheeraj
- Walsh, Tom
- Zackai, Elaine H
- Kaplan, Paige
- Ganesh, Jaya
- Krantz, Ian D
- Spinner, Nancy B
- Bhandari, Abhishek
- Lakshmi, B
- Vacic, Vladimir
- Iakoucheva, Lilia M
- Lieberman, Jeffrey A
- Stroup, T Scott
- Lehtimäki, Terho
- Puura, Kaija
- Pearl, Justin
- Willour, Virginia L
- DeRosse, Pamela
- McMahon, Francis J
- Malhotra, Anil K
- Potash, James B
- Schulze, Thomas G
- Nöthen, Markus M
- Cichon, Sven
- Rietschel, Marcella
- Leibenluft, Ellen
- Lajonchere, Clara M
- Sutcliffe, James S
- Skuse, David
- Gill, Michael
- Gallagher, Louise
- Craddock, Nick
- Owen, Michael J
- Shaikh, Tamim H
- Susser, Ezra
- DeLisi, Lynn E
- Sullivan, Patrick F
- Levy, Deborah L
- King, Mary-Claire
- Sebat, Jonathan
- Venue
- Nature Genetics
- Published
- 2009-10-25
- Volume
- 41
- Issue
- 11
- Pages
- 1223-1227
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC2951180
- OpenAlex
- W2160435411
- Cited by
- 711
- References
- 40
- Citations by year
- 2026: 12 · 2025: 23 · 2024: 22 · 2023: 25 · 2022: 15 · 2021: 42 · 2020: 32 · 2019: 34 · 2018: 29 · 2017: 43 · 2016: 38 · 2015: 55 · 2014: 51 · 2013: 75 · 2012: 79
- FWCI
- 41.53
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Wellcome Trust (076113)
- National Institutes of Health (2r01mh044245-06a1, 5r01mh071523-05, n01mh90001-21-0-0)
- U.S. Public Health Service (HF004222)
- National Institute of Mental Health (R01MH061009, R01MH077139, R00MH086756, U24MH081810, R01MH091350, MH44245, MH074027, MH 31340, N01 MH090001, MH076431, K99MH086756, ZIAMH002581, MH071523, MH081810, R01-MH071523, R01MH074027, R01MH031340, MH077139, MH061009, MH083989, R01MH083989, R01MH076431)
- National Institute of General Medical Sciences (R01GM081519, GM081519)
- National Institute of Dental and Craniofacial Research (DE016442, R42DE016442, R41DE016442)
- National Center for Research Resources (RR-000037, M01RR000037)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD-04147, P30HD004147)
- 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 › Genome Rearrangement Algorithms
- Keywords
- schizophrenia, bipolar disorder, autism spectrum disorder, developmental disorders, copy number variation, genetic risk, head circumference, mental illness
- MeSH terms
- Chromosomes, Human, Pair 16, Humans, Risk Factors, Schizophrenia, Genetic Predisposition to Disease, Gene Duplication
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.
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