Genetics, Vol 143, 1013-1020, Copyright © 1996

INVESTIGATIONS

Confidence Intervals in QTL Mapping by Bootstrapping

P. M. Visscher, R. Thompson and C. S. Haley
Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, Scotland

The determination of empirical confidence intervals for the location of quantitative trait loci (QTLs) was investigated using simulation. Empirical confidence intervals were calculated using a bootstrap resampling method for a backcross population derived from inbred lines. Sample sizes were either 200 or 500 individuals, and the QTL explained 1, 5, or 10% of the phenotypic variance. The method worked well in that the proportion of empirical confidence intervals that contained the simulated QTL was close to expectation. In general, the confidence intervals were slightly conservatively biased. Correlations between the test statistic and the width of the confidence interval were strongly negative, so that the stronger the evidence for a QTL segregating, the smaller the empirical confidence interval for its location. The size of the average confidence interval depended heavily on the population size and the effect of the QTL. Marker spacing had only a small effect on the average empirical confidence interval. The LOD drop-off method to calculate empirical support intervals gave confidence intervals that generally were too small, in particular if confidence intervals were calculated only for samples above a certain significance threshold. The bootstrap method is easy to implement and is useful in the analysis of experimental data.


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C. M. Lebreton, P. M. Visscher, C. S. Haley, A. Semikhodskii, and S. A. Quarrie
A Nonparametric Bootstrap Method for Testing Close Linkage vs. Pleiotropy of Coincident Quantitative Trait Loci
Genetics, October 1, 1998; 150(2): 931 - 943.
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Q. Zhang, D. Boichard, I. Hoeschele, C. Ernst, A. Eggen, B. Murkve, M. Pfister-Genskow, L. A. Witte, F. E. Grignola, P. Uimari, et al.
Mapping Quantitative Trait Loci for Milk Production and Health of Dairy Cattle in a Large Outbred Pedigree
Genetics, August 1, 1998; 149(4): 1959 - 1973.
[Abstract] [Full Text] [PDF]

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T. Mitchell-Olds and D. Pedersen
The Molecular Basis of Quantitative Genetic Variation in Central and Secondary Metabolism in Arabidopsis
Genetics, June 1, 1998; 149(2): 739 - 747.
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S. A. Knott, L. Marklund, C. S. Haley, K. Andersson, W. Davies, H. Ellegren, M. Fredholm, I. Hansson, B. Hoyheim, K. Lundstrom, et al.
Multiple Marker Mapping of Quantitative Trait Loci in a Cross Between Outbred Wild Boar and Large White Pigs
Genetics, June 1, 1998; 149(2): 1069 - 1080.
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A. E. Melchinger, H. F. Utz, and C. C. Schon
Quantitative Trait Locus (QTL) Mapping Using Different Testers and Independent Population Samples in Maize Reveals Low Power of QTL Detection and Large Bias in Estimates of QTL Effects
Genetics, May 1, 1998; 149(1): 383 - 403.
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M. J. Sillanpaa and E. Arjas
Bayesian Mapping of Multiple Quantitative Trait Loci From Incomplete Inbred Line Cross Data
Genetics, March 1, 1998; 148(3): 1373 - 1388.
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Empirical Nonparametric Bootstrap Strategies in Quantitative Trait Loci Mapping: Conditioning on the Genetic Model
Genetics, January 1, 1998; 148(1): 525 - 536.


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K. J. Buck, P. Metten, J. K. Belknap, and J. C. Crabbe
Quantitative Trait Loci Involved in Genetic Predisposition to Acute Alcohol Withdrawal in Mice
J. Neurosci., May 15, 1997; 17(10): 3946 - 3955.
[Abstract] [Full Text] [PDF]

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 Physiol. GenomicsHome page
D. W. HEYEN, J. I. WELLER, M. RON, M. BAND, J. E. BEEVER, E. FELDMESSER, Y. DA, G. R. WIGGANS, P. M. VANRADEN, and H. A. LEWIN
A genome scan for QTL influencing milk production and health traits in dairy cattle
Physiol Genomics, November 11, 1999; 1(3): 165 - 175.
[Abstract] [Full Text] [PDF]