Empirical evaluation of genome scans for linkage of a quantitative trait associated with a complex disorder

Nonparametric sib-pair analysis (Haseman-Elston) was used to search for evidence of linkage between a putative locus for a complex quantitative trait Q1 and genome-wide markers (367 markers from 10 chromosomes) for the first 100 replicates of nuclear family data. The characteristics of the statistically positive linkage results [the magnitude of p-values (p), the number of supporting flanking markers, and the percentage of positive replicates] were compared for true linkage (major and minor genes) and false positive evidence for linkage. Discriminant analysis was used to evaluate which characteristics of these statistically positive linkage results are good indicators to discriminate true linkage from false positive evidence for linkage. Sensitivity and false positive rates of several proposed criteria for linkage, as well as the criteria based on our results were evaluated. The relationship between the map location of the marker with the lowest p-value and the map location of the true underlying gene was also evaluated, which provided useful information for fine mapping and replication studies.