Genotyping for the addiction array was performed using the Illumina GoldenGate genotyping protocols on 96-well format SentrixR arrays. All pre-PCR processing was performed using a TECAN liquid handling robot and arrays were imaged using an Illumina Beadstation GX500. The data were analyzed using GenCall v6.2.0.4 and GTS Reports software v5.1.2.0 (Illumina). Full details of array genotyping and post-experiment QC are described elsewhere 18. In brief, a total of 1105 unique samples were genotyped. After screening for poor performing SNPs based on technical metrics from the GX500 and assessment of Hardy-Weinberg equilibrium, the data available for this sample included 1286/1350 (95.3%) of gene SNPs and 176/186 (94.6%) AIM markers. Markers which passed QC metrics were then assessed for Hardy-Weinberg equilibrium, and those with p < 0.001 were discarded. Those SNPs or individuals in which more than 10% values were missing were dropped from further analysis. Any SNPs with minor allele frequency less than 5% were also discarded.
