Psychiatric Genomics Consortium Depression Datasets
The Psychiatric Genomics Consortium (PGC) sent their full sample depression 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 Depression Datasets
The PGC sent summary statistics for the full depression sample, n=18,759. In addition, subject-level data (original and imputed dosage genotypes) is provided for a subset of n=10,409 individuals, which excludes 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 GAIN, GenRED, and STAR*D. 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 | Cases | Controls | Platform |
|---|---|---|---|
| GAIN | 1,696 | 1,765 | Not distributed through NIMH |
| GenRED | 1,030 | 1,253 | Affymetrix 6.0 |
| GSK | 887 | 864 | Not distributed through NIMH |
| MDD2000-QIMR_610 | 433 | 751 | Affymetrix 6.0 |
| MDD2000-QIMR_317 | 1,017 | 960 | Various |
| MPIP | 376 | 537 | Not distributed through NIMH |
| RADIANT + Bonn/Mann | 935 | 1,290 | Not distributed through NIMH |
| RADIANT UK | 1,625 | 1,588 | Illumina 610K |
| STAR*D | 1,241 | 511 | Affymetrix 500K/5.0 |