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Study Description

This study is part of the Molecular Genetics of Schizophrenia (MGS) genome wide association study (GWAS) of 3,972 cases (2,686 EA and 1,286 AA) and 3,629 controls (2,656 EA and 973 AA) (analyzed sample remaining after quality control exclusions), comprised of European ancestry (EA) and African American (AA) samples. We genotyped about half of the EA sample and almost all of the AA sample under the auspices of the Genetic Association Information Network (GAIN) with the Affymetrix 6.0 platform at the Broad Institute. The remainder of the included sample was also genotyped with the Affymetrix 6.0 platform at the Broad Institute, and we refer to this component as the nonGAIN sample. Cases met criteria for schizophrenia (SCZ) or schizoaffective disorder (SA) per the Diagnostic and Statistical Manual of Mental Disorders version IV (DSM-IV) for all three collections (SGI, MGS1, and MGS2) comprising these cases. However, for the older SGI collection, codes for the secondary diagnoses refer to the older DSM-III-R version. Controls were screened briefly and excluded if they endorsed a history of these illnesses.

  • Study Type: Case-Control
  • dbGaP estimated ancestry components using GRAF-pop
  • Number of study subjects that have individual level data available through Authorized Access: 3029

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

Please refer to the following documents for detailed information: "Cases_Protocol.pdf" and "Controls_Protocol.pdf". Briefly, all subjects had to give informed consent, be at least 18 years old, and be able to communicate in English. Included cases had a consensus best estimate final diagnosis of DSM-IV SCZ or SA. Cases were excluded if they had worse than mild mental retardation, or if their psychotic illness was judged to be secondary to substance use or a neurological disorder. Some case parents were included to make trios that were only used for quality control purposes (e.g., Mendelian checks of SNPs). Controls were excluded if they did not deny all of the following psychosis screening questions: treatment for or diagnosis of schizophrenia or schizoaffective disorder; treatment for or diagnosis of bipolar disorder or manic-depression; treatment for or diagnosis of psychotic symptoms such as auditory hallucinations or persecutory delusions.

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Genome Genotyping Affymetrix AFFY_6.0 934940 52074
Study History

Samples were collected under the following grants: NIMH Schizophrenia Genetics Initiative U01s: MH46276, MH46289, and MH46318; and Molecular Genetics of Schizophrenia Part 1 (MGS1) and Part 2 (MGS2) R01s: MH67257, MH59588, MH59571, MH59565, MH59587, MH60870, MH60879, MH59566, MH59586, and MH61675. Genotyping and analyses were funded under the MGS U01s: MH79469 and MH79470.

Selected publications
Diseases/Traits Related to Study (MESH terms)
Links to Related Resources
Authorized Data Access Requests
Study Attribution