We also combined the results from the family-based analysis with allele frequencies from control data from the Study on Addiction: Genetics and Environment (SAGE), also genotyped with the Illumina Human 1M-single Infinium BeadChip (23). Combining the AGP family-based transmission data with control data also yielded no new loci (see Supplementary Material). The peak association for MACROD2 remained at rs4141463 (Table 2 and Supplementary Material), but the P-value for association increased to 8.1 × 10−8 (strict diagnosis, European ancestry). For the loci identified by primary analyses of AGP data, the AGP, AGRE and control data taken together (Table 2) had little effect on the significance level for rs4141463 (P = 3.7 × 10−8 for strict diagnosis, European ancestry). In fact, the combined AGP, AGRE and control analyses showed similar results to those from the combined AGP and AGRE analysis (see Table 2), with the exception of rs4150167; the P-value for this SNP rises to 2.1 × 10−5. Looking over the entire genome, analysis of the combined data did not reveal compelling new loci (see Supplementary Material).
