GWAS controls consisted of 2509 samples, including 1297 self-reported Caucasian children of European ancestry recruited from CHOP Health Care Network and 1212 samples from the 1958 birth cohort genotyped by the WTCCC27. Although the controls were not selected for absence of neurodegenerative disease, the large size of the cohort relative to the low population frequency of FTLD overrides this potential concern. Furthermore, the minor allele frequencies at the 7p21 loci are very similar (<1-2% variation) between CHOP and WTCCC cohorts suggesting they accurately reflect the control allelic frequencies in the general population (Supplementary Table 9). To reduce the risk of population stratification all internal controls were screened using the STRUCTURE package19 at 220 AIMs. To improve clustering the samples were spiked with 90 CEPH, Yoruban and Chinese/Japanese individuals genotyped as part of the HapMap project. Cases were excluded if their inferred proportion of ancestry was less than 90% that of the CEU cluster.
