Covariate-based affected relative pair linkage analysis using single-point identity-by-descent (IBD) probabilities and a general conditional logistic model was performed as implemented in GENIBD and LODPAL of S.A.G.E. v4.6 [6,7,11] on the microsatellite genotype data across the entire genome. In LODPAL, all affected relative pairs are treated as independent observations, and a single covariate value is calculated for each affected relative pair as the sum of the covariate values for the two affected relatives in the pair. The trait selected was ALDX1, defined as alcoholism based on both the DSM-III-R [12] and the Feighner criteria [13]. Covariates considered were age at interview (age_int), sex, maximum number of drinks (maxdrinks), smoking status (smoker), and ttth1, an electrophysiological measurement of brain activity. Additionally five different propensity scores were defined, and their corresponding regression coefficients are listed in Table 2. LOD scores were calculated by incorporating into the analysis no covariates, each covariate alone (including the different single covariate PS definitions), and all covariates simultaneously.
