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Analysis of copy number variations at 15 schizophrenia-associated loci

  • Elliott Rees (a1), James T. R. Walters (a1), Lyudmila Georgieva (a1), Anthony R. Isles (a1), Kimberly D. Chambert (a2), Alexander L. Richards (a1), Gerwyn Mahoney-Davies (a1), Sophie E. Legge (a1), Jennifer L. Moran (a2), Steven A. McCarroll (a2), Michael C. O'Donovan (a1), Michael J. Owen (a1) and George Kirov (a1)...



A number of copy number variants (CNVs) have been suggested as susceptibility factors for schizophrenia. For some of these the data remain equivocal, and the frequency in individuals with schizophrenia is uncertain.


To determine the contribution of CNVs at 15 schizophrenia-associated loci (a) using a large new data-set of patients with schizophrenia (n = 6882) and controls (n = 6316), and (b) combining our results with those from previous studies.


We used Illumina microarrays to analyse our data. Analyses were restricted to 520 766 probes common to all arrays used in the different data-sets.


We found higher rates in participants with schizophrenia than in controls for 13 of the 15 previously implicated CNVs. Six were nominally significantly associated (P<0.05) in this new data-set: deletions at 1q21.1, NRXN1, 15q11.2 and 22q11.2 and duplications at 16p11.2 and the Angelman/Prader–Willi Syndrome (AS/PWS) region. All eight AS/PWS duplications in patients were of maternal origin. When combined with published data, 11 of the 15 loci showed highly significant evidence for association with schizophrenia (P<4.1×10−4).


We strengthen the support for the majority of the previously implicated CNVs in schizophrenia. About 2.5% of patients with schizophrenia and 0.9% of controls carry a large, detectable CNV at one of these loci. Routine CNV screening may be clinically appropriate given the high rate of known deleterious mutations in the disorder and the comorbidity associated with these heritable mutations.

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Corresponding author

George Kirov, MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Hadyn Ellis Building, Cardiff University, Cardiff CF24 4HQ, UK. Email:


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The work at Cardiff University was funded by Medical Research Council (MRC) Centre (G0800509) and Program Grants (G0801418) and the European Community's Seventh Framework Programme (HEALTH-F2-2010-241909 (Project EU-GEI), and an MRC PhD Studentship to E.R. M.C.O'D., M.J.O. and G.K. have received funding from the MRC and the Wellcome Trust, UK. A.R.I. has received funding from the Biotechnology and Biological Sciences Research Council (UK), the Wellcome Trust and the Leverhulme Trust. This work was supported by a clinical research fellowship to J.T.R.W. from the MRC/Welsh Assembly Government and the Margaret Temple Award from the British Medical Association. The schizophrenia samples were genotyped at the Broad Institute, USA, and funded by a philanthropic gift to the Stanley Center for Psychiatric Research.

Declaration of interest




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Analysis of copy number variations at 15 schizophrenia-associated loci

  • Elliott Rees (a1), James T. R. Walters (a1), Lyudmila Georgieva (a1), Anthony R. Isles (a1), Kimberly D. Chambert (a2), Alexander L. Richards (a1), Gerwyn Mahoney-Davies (a1), Sophie E. Legge (a1), Jennifer L. Moran (a2), Steven A. McCarroll (a2), Michael C. O'Donovan (a1), Michael J. Owen (a1) and George Kirov (a1)...


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