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Mukherjee S, Guha S, Ikeda M, Iwata N, Malhotra AK, Pe'er I, Darvasi A, Lencz T. Excess of homozygosity in the major histocompatibility complex in schizophrenia. Hum Mol Genet 2014; 23:6088-95. [PMID: 24943592 PMCID: PMC4204767 DOI: 10.1093/hmg/ddu308] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 04/11/2014] [Accepted: 06/12/2014] [Indexed: 01/20/2023] Open
Abstract
Genome-wide association studies (GWAS) in schizophrenia have focused on additive allelic effects to identify disease risk loci. In order to examine potential recessive effects, we applied a novel approach to identify regions of excess homozygosity in an ethnically homogenous cohort: 904 schizophrenia cases and 1640 controls drawn from the Ashkenazi Jewish (AJ) population. Genome-wide examination of runs of homozygosity identified an excess in cases localized to the major histocompatibility complex (MHC). To refine this signal, we used the recently developed GERMLINE algorithm to identify chromosomal segments shared identical-by-descent (IBD) and compared homozygosity at such segments in cases and controls. We found a significant excess of homozygosity in schizophrenia cases compared with controls in the MHC (P-value = 0.003). An independent replication cohort of 548 schizophrenia cases from Japan and 542 matched healthy controls demonstrated similar effects. The strongest case-control recessive effects (P = 8.81 × 10(-8)) were localized to a 53-kb region near HLA-A, in a segment encompassing three poorly annotated genes, TRIM10, TRIM15 and TRIM40. At the same time, an adjacent segment in the Class I MHC demonstrated clear additive effects on schizophrenia risk, demonstrating the complexity of association in the MHC and the ability of our IBD approach to refine localization of broad signals derived from conventional GWAS. In sum, homozygosity in the classical MHC region appears to convey significant risk for schizophrenia, consistent with the ecological literature suggesting that homozygosity at the MHC locus may be associated with vulnerability to disease.
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Affiliation(s)
- Semanti Mukherjee
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA,
| | - Saurav Guha
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA
| | - Masashi Ikeda
- Fujita Health University School of Medicine, 1-98 Kutsukake-cho Dengakugakubo, Toyoake, Aichi 470-1192, Japan
| | - Nakao Iwata
- Fujita Health University School of Medicine, 1-98 Kutsukake-cho Dengakugakubo, Toyoake, Aichi 470-1192, Japan
| | - Anil K Malhotra
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA, Hofstra University School of Medicine, 500 Hofstra University, Hempstead, NY 11549, USA
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA and
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Todd Lencz
- The Zucker Hillside Hospital, Psychiatry Research, 75-59 263rd Street, Glen Oaks, NY 11004, USA, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY 11030, USA, Hofstra University School of Medicine, 500 Hofstra University, Hempstead, NY 11549, USA,
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