scores using SOLAR v2.0.4 (Almasy and Blangero, 1998) Genhunter 2 (Kruglyak et al., 1996) and Merlin (http://www.sph.umich.edu/csg/abecasis/Merlin/) with similar results. Results are presented for SOLAR. Simulation analysis was used to estimate empirical LOD scores and make appropriate genome wide adjustments for non-normality when the trait was modeled as normally distributed trait (Blangero et al., 2000). Bivariate analyses of data on chromosome 12 for ASPD/CD and drinking severity, was performed using SOLAR (2.1.4). To test for pleiotropy, by excluding coincident linkage, the method proposed by Almasy et al. (1997) and as elaborated by North et al. (2005) was used. Briefly, the likelihood for the linkage model in which pq was estimated was compared to the likelihood for the linkage model in which pq was constrained to 1 (or −1 complete pleiotropy) or 0 (complete coincident linkage).
