The framework starts with the training of prediction models for gene expression traits followed by a selection of high-performing models. Next, a mathematical operation is performed to compute the association between each gene and the downstream complex trait. Additional adjustment for the uncertainty in the prediction model can be added. To avoid capturing LD-contaminated associations, which can occur when expression predictor SNPs and phenotype causal SNPs are different but in LD, we use colocalization methods that estimate the probability of shared or independent signals.
