Two linkage analysis programs (SIBPAL in S.A.G.E. v. 4.2 and GENEHUNTER v. 2.1) were used in the study. For the EM (expectation maximization) Haseman-Elston quantitative trait locus (QTL) regression method implemented in GENEHUNTER, we analyzed both log-transformed and categorized SR data sets. A detail description on the method can be found in Kruglyak et al. [7] and Kruglyak and Lander [8]. In SIBPAL, default options were used for all parameters in the trait regression method except that the options w3 (the weighted combination of squared trait difference and squared mean-corrected trait sum adjusting for the non-independence of sib pairs) and w4 (the non-independence of squared trait sums and differences) were examined [9]. Both options yielded essentially the same results on three data sets (i.e., SR, log-transformed SR and categorized SR). Sex and age were included as covariates for all analyses reported in this communication. The S-PLUS 6.1 and SAS 8.2 packages were used to prepare the data in the required format and to analyze the data generated from the linkage analysis programs.
