To evaluate the performance of MAGMA, the WTCCC Crohn’s Disease (CD) GWAS data [15] in conjunction with both WTCCC control samples was used. The data was cleaned according to the protocol described by Anderson [22], resulting in a sample of 1,694 cases and 2,917 controls with data for 403,227 SNPs. The European samples from the 1,000 Genomes data [23] and the HapMap 3 data [24] were used as reference data sets for the summary statistics gene analysis.
