Table 1 Overview of tools and different subsequent protocols in use. Study designs enlist three stages of analysis
Tool in use | Statistic used | Statistical model in use | Default pre-selection criteria for interaction test | Study design | No. of tests performed | Bonferroni adjusted genome-wide level of significance (< 1% FDR) | No. of risk loci pairs discovered |
|---|---|---|---|---|---|---|---|
CASSI | Wellek-Zeigler statistic | Logistic regression; fixed effects weighted model | Single marker test P value < 10−3 | Discovery study | 2.8 × 107 | 5 × 10− 10 | 561 |
Follow up study | 4.4 × 105 | 5 × 10−10 | 352 | ||||
Replication study | 8.2 × 106 | 5 × 10−10 | 23 | ||||
INTERSNP | Chi square statistic | Full log-linear model | Top 5000 variants of single marker test | Discovery study | 1.25 × 107 | 8 × 10−10 | none |