APOE and Alzheimer disease: We tested three possible explanations for this finding: 1) the people who get AD without an E4 allele have more AD risk alleles, i.e. alleles at other loci have bigger effects in the absence of E4; 2) the effects of APOE and other risk SNPs are independent; 3) the results are driven by inflation due to the overlap between the discovery (IGAP) and test (E3 homozygote pathologically confirmed AD cases and controls) datasets.