Following quality control and the exclusion of some individuals after correction of pedigree inconsistencies, the final analytic sample included 2,322 genotyped individuals from 118 extended families, of which 1,786 individuals met phenotypic criteria for inclusion (Table 1). The average number of genotyped members per family was 19.6, with an average of 5.9 genotyped individuals per family meeting criteria for DSM-IVAD. A total of 707,557 autosomal SNPs passed quality review. 115,772 SNPs were excluded due to a low minor allele frequency (<5%). The final dataset consisted of 591,785 SNPs, yielding a genome-wide threshold of p=8.45 × 10−8. Since the phenotypes examined represent some facet of AD and additional Bonferroni correction of related phenotypes would be unnecessarily stringent, this p-value based on the number of SNPs was considered as the significance threshold.
