Bias in Estimates of Quantitative-Trait–Locus Effect in Genome Scans: Demonstration of the Phenomenon and a Method-of-Moments Procedure for Reducing Bias  David B. Allison, Jose R. Fernandez, Moonseong Heo, Shankuan Zhu, Carol Etzel, T. Mark Beasley, Christopher I. Amos  The American Journal of Human Genetics  Volume 70, Issue 3, Pages 575-585 (March 2002) DOI: 10.1086/339273 Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 1 Estimated versus true QTL effects, without selection of only significant results. All analyses included 200 independent sibling pairs and used HE2 to provide the QTL estimates. The American Journal of Human Genetics 2002 70, 575-585DOI: (10.1086/339273) Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 2 Estimated versus true QTL effects, with selection of only significant results. All analyses included 200 independent sibling pairs and used HE2 as the preliminary test with a one-tailed α level of 0.01. The American Journal of Human Genetics 2002 70, 575-585DOI: (10.1086/339273) Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 3 MOM estimates of QTL effect versus true QTL effect, with selection of only significant results from experiment 2. All analyses included 200 independent sibling pairs and used HE2 as the preliminary test with a one-tailed α level of 0.01. The American Journal of Human Genetics 2002 70, 575-585DOI: (10.1086/339273) Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 4 MOM estimates of QTL effect versus true QTL effect, with selection of only significant results from experiment 3. All analyses included 200 independent sibling pairs and used HE2 as the preliminary test with a one-tailed α level of 0.01. The American Journal of Human Genetics 2002 70, 575-585DOI: (10.1086/339273) Copyright © 2002 The American Society of Human Genetics Terms and Conditions

Figure 5 Simulations with nonadditive models, but with MOM estimates calculated assuming additivity. Note that the true QTL effects, as well as the preliminary (ordinary) estimates, include both the additive component and the dominance component. All analyses included 200 independent sibling pairs and used HE2 as the preliminary test with a one-tailed α level of 0.01. For details of nonadditive models, see the “Simulation Parameters and Methods” subsection. The American Journal of Human Genetics 2002 70, 575-585DOI: (10.1086/339273) Copyright © 2002 The American Society of Human Genetics Terms and Conditions