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Copy number variation in schizophrenia in Sweden

Molecular Psychiatry volume 19, pages 762–773 (2014)Cite this article

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Abstract

Schizophrenia (SCZ) is a highly heritable neuropsychiatric disorder of complex genetic etiology. Previous genome-wide surveys have revealed a greater burden of large, rare copy number variations (CNVs) in SCZ cases and identified multiple rare recurrent CNVs that increase risk of SCZ although with incomplete penetrance and pleiotropic effects. Identification of additional recurrent CNVs and biological pathways enriched for SCZ CNVs requires greater sample sizes. We conducted a genome-wide survey for CNVs associated with SCZ using a Swedish national sample (4719 cases and 5917 controls). High-confidence CNV calls were generated using genotyping array intensity data, and their effect on risk of SCZ was measured. Our data confirm increased burden of large, rare CNVs in SCZ cases as well as significant associations for recurrent 16p11.2 duplications, 22q11.2 deletions and 3q29 deletions. We report a novel association for 17q12 duplications (odds ratio=4.16, P=0.018), previously associated with autism and mental retardation but not SCZ. Intriguingly, gene set association analyses implicate biological pathways previously associated with SCZ through common variation and exome sequencing (calcium channel signaling and binding partners of the fragile X mental retardation protein). We found significantly increased burden of the largest CNVs (>500 kb) in genes present in the postsynaptic density, in genomic regions implicated via SCZ genome-wide association studies and in gene products localized to mitochondria and cytoplasm. Our findings suggest that multiple lines of genomic inquiry—genome-wide screens for CNVs, common variation and exonic variation—are converging on similar sets of pathways and/or genes.

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Acknowledgements

We are deeply grateful for the participation of all subjects contributing to this research and to the team that conducted the fieldwork (Emma Flordal-Thelander, Ann-Britt Holmgren, Marie Hallin, Marie Lundin, Ann-Kristin Sundberg, Christina Pettersson, Radja Satgunanthan-Dawoud, Sonja Hassellund, Malin Rådstrom, Birgitta Ohlander, Leila Nyrén and Isabelle Kizling). Funding support was provided by NIMH R01 MH077139 (Sullivan), NIMH R01 MH095034 (Sklar), NIMH K01 MH093517 (Szatklewicz), the Stanley Center for Psychiatric Research, the Stanley Medical Research Institute, the Sylvan Herman Foundation, the Karolinska Institutet, Karolinska University Hospital, the Swedish Research Council, the Swedish County Council, the Söderström Königska Foundation and the Netherlands Scientific Organization (NWO 645-000-003). The work at UK was funded by Medical Research Council (MRC) Centre (G0800509) and Program Grants (G0801418), the European Community’s Seventh Framework Programme (HEALTH-F2-2010-241909 (Project EU-GEI), an MRC PhD Studentship to ER, a clinical research fellowship to JTRW from the MRC/Welsh Assembly Government and the Margaret Temple Award from the British Medical Association. The UK samples were genotyped at the Broad Institute, USA, funded by a philanthropic gift to the Stanley Center for Psychiatric Research. The funders had no role in study design, execution, analysis and manuscript preparation. We thank two anonymous reviewers for their helpful comments. All authors reviewed and approved the final version of the manuscript. The corresponding authors had access to the full data set.

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Author notes

  1. J P Szatkiewicz and C O'Dushlaine: The first two authors contributed equally to this work.

  2. S A McCarroll and P F Sullivan: The last two authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics, University of North Carolina, Chapel Hill, NC, USA

    J P Szatkiewicz, G Chen, Y Kim, J J Crowley & P F Sullivan

  2. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    C O'Dushlaine, K Chambert, J L Moran, B M Neale, S E Bergen, E Scolnick, S Purcell & S A McCarroll

  3. Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA

    M Fromer, D Ruderfer, P Sklar & S Purcell

  4. Department of Medical Epidemiology, Karolinska Institutet, Stockholm, Sweden

    S Akterin, S E Bergen, A Kähler, P K E Magnusson, C M Hultman & P F Sullivan

  5. MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK

    E Rees, G Kirov, M C O'Donovan, M J Owen & J Walters

  6. Department of Genetics, Harvard Medical School, Boston, MA, USA

    S A McCarroll

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  1. J P Szatkiewicz
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Correspondence to P F Sullivan.

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Competing interests

PFS was on the SAB of Expression Analysis (Durham, NC, USA). PS is on the Board of Directors of Catalytic, Inc. The other authors declare no conflict of interest.

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Szatkiewicz, J., O'Dushlaine, C., Chen, G. et al. Copy number variation in schizophrenia in Sweden. Mol Psychiatry 19, 762–773 (2014). https://doi.org/10.1038/mp.2014.40

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