all selection processes (e.g., selecting the most significant SNPs to represent each gene and selecting the most significant genes to represent each gene set) need to be accounted for in the final gene set analysis. For example, when a gene is represented by the signal of a single SNP from the gene region, the potential effects of multiple association signals for the gene may be missed. Furthermore, because longer genes are more likely to have nominally significant P-values, choosing the most significant SNP to represent each gene may inflate the association test statistic for gene sets that have many long genes. Several recent studies assessed the impact of gene length on gene set analysis results and proposed new resampling based strategies for the correction of such bias [48,49].
