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Original Investigation
May 2016

Association of DNA Methylation Differences With Schizophrenia in an Epigenome-Wide Association Study

Author Affiliations
  • 1Medical Scientist Training Program and Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
  • 2Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
  • 3Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
  • 4Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
  • 5Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
  • 6Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
  • 7Department of Epidemiology, University of Alabama at Birmingham, Birmingham
  • 8Rutgers University Cell and DNA Repository, Piscataway, New Jersey
  • 9 Stanley Division of Developmental Neurovirology, Johns Hopkins School of Medicine, Baltimore, Maryland
  • 10Department of Psychiatry and Behavioral Sciences, Keck School of Medicine of University of Southern California, Los Angeles
  • 11Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
  • 12Department of Psychiatry, University of California San Diego School of Medicine, La Jolla
  • 13VISN22, Mental Illness Research, Education, and Clinical Center, VA Veterans Affairs San Diego Healthcare System, San Diego, California
  • 14Departments of Medicine and Biomedical Engineering, Johns Hopkins University School of Medicine and Whiting School of Engineering, Baltimore, Maryland
JAMA Psychiatry. 2016;73(5):506-514. doi:10.1001/jamapsychiatry.2016.0144

Importance  DNA methylation may play an important role in schizophrenia (SZ), either directly as a mechanism of pathogenesis or as a biomarker of risk.

Objective  To scan genome-wide DNA methylation data to identify differentially methylated CpGs between SZ cases and controls.

Design, Setting, and Participants  Epigenome-wide association study begun in 2008 using DNA methylation levels of 456 513 CpG loci measured on the Infinium HumanMethylation450 array (Illumina) in a consortium of case-control studies for initial discovery and in an independent replication set. Primary analyses used general linear regression, adjusting for age, sex, race/ethnicity, smoking, batch, and cell type heterogeneity. The discovery set contained 689 SZ cases and 645 controls (n = 1334), from 3 multisite consortia: the Consortium on the Genetics of Endophenotypes in Schizophrenia, the Project among African-Americans To Explore Risks for Schizophrenia, and the Multiplex Multigenerational Family Study of Schizophrenia. The replication set contained 247 SZ cases and 250 controls (n = 497) from the Genomic Psychiatry Cohort.

Main Outcomes and Measures  Identification of differentially methylated positions across the genome in SZ cases compared with controls.

Results  Of the 689 case participants in the discovery set, 477 (69%) were men and 258 (37%) were non–African American; of the 645 controls, 273 (42%) were men and 419 (65%) were non–African American. In our replication set, cases/controls were 76% male and 100% non–African American. We identified SZ-associated methylation differences at 923 CpGs in the discovery set (false discovery rate, <0.2). Of these, 625 showed changes in the same direction including 172 with P < .05 in the replication set. Some replicated differentially methylated positions are located in a top-ranked SZ region from genome-wide association study analyses.

Conclusions and Relevance  This analysis identified 172 replicated new associations with SZ after careful correction for cell type heterogeneity and other potential confounders. The overlap with previous genome-wide association study data can provide potential insights into the functional relevance of genetic signals for SZ.