Comparison of variance components, ANOVA and regression of offspring on midparent (ROMP) methods for SNP markers

An extension of the traditional regression of offspring on midparent (ROMP) method was used to estimate the heritability of the trait, test for marker association, and estimate the heritability attributable to a marker locus. The fifty replicates of the Genetic Analysis Workshop (GAW) 12 simulated g eneral population data were used to compare the ROMP method with the varian ce components method as implemented in SOLAR as a test for marker associati on, and to a standard analysis of variance (ANOVA) method. Large sample sta tistical properties of the ROMP and ANOVA methods were compared using 2,000 replicates resampled from the families of the original 50 replicates. Over all, the power to detect a completely associated single nucleotide polymorp hism (SNP) marker was high, and the type I error rates were similar to nomi nal significance levels for all three methods. The standard deviations of t he estimates of the heritability of the trait were large for both SOLAR and ROMP, but the estimates were, on average, close to those of the generating model for both methods. However, on average, SOLAR overestimated the herit ability attributable to the associated SNP marker (by 256%) while ROMP unde restimated it (by 26%). (C) 2001 Wiley-Liss, Inc.