Confidence intervals in QTL mapping by bootstrapping

A - Papers appearing in refereed journals

Visscher, P. M., Thompson, R. and Haley, C. S. 1996. Confidence intervals in QTL mapping by bootstrapping. Genetics. 143 (2), pp. 1013-1020.

AuthorsVisscher, P. M., Thompson, R. and Haley, C. S.
Abstract

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.

Year of Publication1996
JournalGenetics
Journal citation143 (2), pp. 1013-1020
PubMed ID8725246
Web address (URL)https://www.genetics.org/content/143/2/1013
Open accessPublished as bronze (free) open access
Funder project or code207
445
Project: 141433
Publisher's version
Output statusPublished
Publication dates
Print01 Jun 1996
Publication process dates
Accepted24 Feb 1996
Copyright licensePublisher copyright
PublisherGenetics Society of America (GSA)
ISSN0016-6731

Permalink - https://repository.rothamsted.ac.uk/item/87861/confidence-intervals-in-qtl-mapping-by-bootstrapping

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