Yan et al. (2014) used the SAGE EA and COGA EA datasets to conduct risk profile scoring analyses for both a set of candidate gene SNPs and SNPs from the GWAS using various P-value thresholds. In the first analysis, using a set of 21 SNPs associated with AD from candidate gene studies in the family-based COGA dataset to predict AD, they found no association with AD in either the COGA or SAGE samples. In a second analysis, they combined the SAGE and COGA datasets and randomly split it equally into case and control groups. The GWAS datasets were pruned for LD and genetic risk scores were computed in the target sample at several P-value thresholds. Here, in contrast to their results from candidate gene SNPs, they observed significant prediction of AD in the target sample for all thresholds with P ≥ 0.01, supporting a polygenic model of AD risk.
