linkage disequilibrium. Beecham et al. (2010) demonstrated this problem by pooling two case-control GWA studies for Alzheimer disease which had been genotyped on different chips, and testing for associations in the APOE gene, which is known to be strongly associated with risk. They used imputation to produce commensurable data sets, and filtered out SNPs according to imputation quality. They found that even though each study separately found strong associations in the APOE gene, there was no association in the pooled analysis, because many SNPs had been excluded due to low imputation quality measures caused by weak linkage disequilibrium in the region.
