Genome-wide case-control analyses were conducted by applying the WG-Permer software (http://www.mpipsykl.mpg.de/wg-permer/). For post-hoc analyses, applications in R-2.5.0 (http://cran.r-project.org) and SPSS for Windows (Releases 16, SPSS Inc., Chicago, Illinois 60606, USA) were used. SNPs with genotype distributions deviating from HWE at a significance level of 10−5 or 0.05 with a call rate below 98% or 95% in the GWAS or German replication sample, respectively, and SNPs with a MAF below 5% were excluded from statistical analysis. Autosomal SNPs were tested for association with unipolar depressive disorder in a case-control design using Chi-square test statistics under allelic and both alternative recessive-dominant modes of inheritance. The level of significance was set to 5% (family-wise error rate). Nominal p-values were corrected for multiple comparisons by the permutation-based minimum p method proposed by Westfall and Young (Westfall and Young, 1993; Westfall et al., 2001) under 104 permutations over the 3 performed genetic models and all SNPs tested per study. Empirical and nominal p-values for all reported associations did not deviate from each other. Moreover, sample demographic statistics and post-hoc tests on age, gender and German
