The QIMR Genetic Epidemiology Laboratory has collected a wide range of phenotypic variables and DNA samples as part of different projects. DNA samples were collected in accordance with standard protocols and submitted to different genotype centres using different SNP platforms (Illumina 317K, Illumina HumanCNV370-Quadv3, Illumina Human610-Quad, and Affymetrix 6.0). The quality control (QC) procedure we employed for the combined use of these Illumina and Affymetrix genotype data consisted of three steps (see Figure 1, Appendix I). Initial QC control - including checks for ancestry outliers, Hardy Weinberg Equilibrium, Mendelian errors, Minor Allele Frequency (MAF) - was applied separately to all different projects. Full details of these initial QC procedures for the Illumina and Affymetrix data are described in detail in Medland et al. (2009) and Wray et al. (submitted), respectively. As the individuals genotyped on the Affymetrix platform comprised a sample of major depressive disorder cases only, more stringent QC criteria were applied. We had 327 individuals genotyped on both the Illumina and the Affymetrix platform, allowing for cross project QC. These checks led us to a more stringent value
