Psychiatric Genomics Consortium Schizophrenia Datasets
The Psychiatric Genomics Consortium (PGC) sent their full sample schizophrenia GWAS results, individual quality controlled genotypes, and individual level dosage data (from an imputation model) for a subset of the full sample (i.e., "deposited data") to the NIMH Repository for distribution to qualified investigators. The PGC was founded in 2007 to conduct meta-analyses of genome wide data on psychiatric disorders. A major goal of the PGC is sharing data with the international scientific community. More information on the PGC may be found at their website (https://www.med.unc.edu/pgc).
PGC Schizophrenia Datasets
The PGC sent summary statistics for the full schizophrenia sample, n=22,127. In addition, subject-level data (original and imputed dosage genotypes) is provided for a subset of n=15,691 individuals, which excludes subjects from four samples (studies) due to restrictions on data sharing (see Table). The dosage genotype data is the result of an imputation model where fully observed snps are coded 0, 1, 2 and imputed snps have a single dosage on the interval [0,2]. The studies in the PGC that also have blood samples and/or phenotype data in the NIMH Repository are CATIE and MGS. Files available for download by authorized users include plots (Manhattan and QQ), a list of the top 1,000 SNPs, PLINK files of genotype data for individual datasets, and imputed dosage data for 2.4 M SNPs.
| Sample | Ancestry | Cases | Controls | Platform |
|---|---|---|---|---|
| Cardiff UK | UK | 472 | 2,934 | Affymetrix 500K (Only case data is distributed through NIMH) |
| Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) | United States | 402 | 309 | Affymetrix 500K |
| International Schizophrenia Consortium (ISC-Aberdeen) | UK | 720 | 698 | Affymetrix 5.0 |
| International Schizophrenia Consortium (ISC-Cardiff) | Bulgaria | 527 | 609 | Affymetrix 6.0 |
| International Schizophrenia Consortium (ISC-Dublin) | Ireland | 270 | 860 | Affymetrix 6.0 |
| Interational Schizophrenia Consortium (ISC-Edinburgh) | UK | 368 | 284 | Affymetrix 6.0 |
| International Schizophrenia Consortium (ISC-London) | UK | 518 | 491 | Affymetrix 500K/5.0 |
| International Schizophrenia Consortium (ISC-Portugal) | Portugal | 346 | 215 | Affymetrix 5.0 |
| International Schizophrenia Consortium, Sweden 1 (ISC-SW1) | Sweden | 168 | 167 | Affymetrix 5.0 |
| International Schizophrenia Consortium, Sweden 2 (ISC-SW2) | Sweden | 390 | 229 | Affymetrix 6.0 |
| Molecular Genetics of Schizophrenia (MGS) | United States, Australia | 2,679 | 2,653 | Affymetrix 6.0 |
| Schizophrenia Genetics Consortium (SGENE-Bonn) | Germany | 474 | 1,304 | Not distributed through NIMH |
| Schizophrenia Genetics Consortium (SGENE-Copenhagen) | Denmark | 482 | 457 | Not distributed through NIMH |
| Schizophrenia Genetics Consortium (SGENE-Munich) | Germany | 434 | 351 | Not distributed through NIMH |
| Schizophrenia Genetics Consortium, Thematic Organized Psychoses Research 3 (SGENE-TOP3) | Norway | 248 | 351 | Affymetrix 6.0 |
| Schizophrenia Genetics Consortium, University of California at Los Angeles (SGENE-UCLA) | The Netherlands | 704 | 631 | Illumina 550K |
| Zucker Hillside | United States | 192 | 190 | Affymetrix 500K |