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| GenADA is a multi-site collaborative study, involving GlaxoSmithKline Inc. and nine medical centers in Canada, to develop a dataset containing 1000 Alzheimer’s disease patients and 1000 ethnically-matched controls in order to associate DNA sequence (allelic) variations in candidate genes with Alzheimer’s disease phenotypes. The analysis presented here was performed with the specific goal of re-calling genotypes from the original Affymetrix CEL files using the CRLMM algorithm, and performing a general QC on the resulting data. Following QC filtering of samples and markers, Fisher’s Exact tests for association of nominal case-control AD status were performed using a genotypic model on all samples which passed QC, first using all markers and then using only passing markers. Odds ratio was calcuated based on the single-copy change of an testing allele. Two SNPs in the APOE gene were included with the GWAS data for these tests. The tests demonstrated little evidence of batch effects as shown in QQ plots. The second set of tests resulted in two markers with genome-wide significance. No further association testing was performed, and all of the analyzed data are provided as well as data from several samples excluded from analysis for QC reasons. |