The MDD2000+ project comprises a total of 2431 cases with MDD and 3673 screened controls from different sources and genotyped on different platforms (Tables 1 and 2). Samples were provided by the Queensland Institute of Medical Research (QIMR, Australia), The Netherlands Study of Anxiety and Depression (NESDA), The Netherlands Twin Registry (NTR), the University of Edinburgh (UK), and the Molecular Genetics of Schizophrenia study (controls only, US). Genotyping was conducted on different Illumina and Affymetrix platforms and because the overlap in genotyped single-nucleotide polymorphisms (SNPs) is limited, association analysis is based on a set of >1 M imputed SNPs. The number of SNPs for each analysis set (Table 1), represents genotyped SNPs surviving all quality control (QC) criteria that were used for imputation.
