London; Competence Network of Dementia (CND) and Department of Psychiatry, University of Bonn, Germany; the National Institute of Mental Health (NIMH)AD Genetics Initiative. 6,129 population controls were drawn from large existing cohorts with available GWAS data, including the 1958 British Birth Cohort (1958BC) (http://www.b58cgene.sgul.ac.uk), the KORA F4 Study and the Heinz Nixdorf Recall Study. All AD cases met criteria for either probable (NINCDS-ADRDA, DSM-IV) or definite (CERAD) AD. All elderly controls were screened for dementia using the MMSE or ADAS-cog, were determined to be free from dementia at neuropathological examination or had a Braak score of 2.5 or lower. Genotypes from all cases and 4,617 controls were previously included in the AD GWAS by Harold and colleagues (2009). Genotypes for the remaining 2,660 population controls were obtained from WTCCC2. Imputation of the dataset was performed using IMPUTE2 and the 1000 genomes (http://www.1000genomes.org/) Dec2010 reference panel (NCBI build 37.1). The imputed data was then analysed using logistic regression including covariates for country of origin, gender, age and 3 principal components obtained with EIGENSTRAT software based on individual genotypes for the GERAD study participants.
