The Pascal gene scoring method consists of the following steps (Fig 1A). First, we assign SNPs to genes if they are located within a given window around the gene body. For the experiments reported in this paper, we used windows extending 50kb up and downstream from the gene. A reference population is required to estimate the correlation structure between Z-scores of SNP association values. Here, we used the European population of the 1000 Genomes Project (1KG)[22], which allows us to apply our approach flexibly to summary statistics from diverse panels (HapMap, 1KG imputed, metaboChip or ImmunoChip).
