DP Dataset 4.02 (GenRED)

Researchers who analyze data and biomaterials from the NIMH Depression Genetics Initiative will use the text specified in the Distribution Agreement to acknowledge the contribution of scientists who collected the data and biomaterials.  Researchers who analyze the genetic analysis data available on this page will use the following additional text to acknowledge, in any and all oral and written presentations, disclosures, and publications, the contribution of scientists who generated the genetic analysis data.

Shi J, Potash JB, Knowles JA, Weissman MM, Coryell W, Scheftner WA, Lawson WB, DePaulo JR Jr., Gejman PV, Sanders AR, Johnson JK, Adams P, Chaudhury S, Jancic D, Evgrafov O, Zvinyatskovskiy A, Ertman N, Gladis M, Neimanas K, Goodell M, Hale N, Ney N, Verma R, Mirel D, Holmans P, Levinson DF.  Genome-wide association study of recurrent early-onset major depressive disorder.  Mol Psychiatry 2010 Feb 2.  PMID: 20125088

Data are provided by Douglas F. Levinson, M.D.

There are 2 directories:

1) CEL_FILES/ : contains 1,103 cel files (Affymetrix 6.0 platform; genotyped at Broad Institute lab of Stacey Gabriel and Daniel Mirel).  These are listed in the file CEL_FILES_list.txt in the top directory.

2) PLINK_FILES/ : contains the plink files and related files.  These are listed in the file PLINK_FILES_list.txt in the top directory.

Please note that the data in these files are only for GenRED cases.  The controls in our association analyses are from the Gejman et al. Molecular Genetics of Schizophrenia dataset.  We selected 1,636 MGS controls who passed GWAS QC and whose self-report responses to an online lifetime version of the CIDI-SF diagnostic instrument revealed no lifetime major depression.  Some of the control subjects were genotyped by the GAIN project, and some were genotyped by a grant from NIMH to the MGS project ("NONGAIN" subjects).  Genotypes for these control subjects are available from dbGAP (http://www.ncbi.nlm.nih.gov/gap).  The proprietary period has expired for the GAIN subjects' genotypes, and these can be used as per dbGAP distribution specifications by investigators who access them through dbGAP.  The proprietary period for the NONGAIN controls is still in effect (see dbGAP for details).  GenRED used these control datasets during their proprietary periods through a collaboration with Dr. Gejman and MGS.

We are not permitted to distribute dbGAP genotypes.  Investigators who wish to replicate our case-control analysis or carry out additional analyses with the same dataset can apply to dbGAP for the control genotypes (the controls included in each of our datasets are listed in attached files), and then extract the SNPs listed in our case .bim files.  This will produce a post-QC control dataset identical to what we used.

Rutgers University Rutgers University USC Information Sciences Institute Washington University in St.Louis National Institute of Mental Health