R/qtlDesign: inbred line cross experimental design

An investigator planning a QTL (quantitative trait locus) experiment has to choose which strains to cross, the type of cross, genotyping strategies, and the number of progeny to raise and phenotype. To help make such choices, we have developed an interactive program for power and sample size calcula...

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Bibliographic Details
Published inMammalian genome Vol. 18; no. 2; pp. 87 - 93
Main Authors Sen, Śaunak, Satagopan, Jaya M, Broman, Karl W, Churchill, Gary A
Format Journal Article
LanguageEnglish
Published United States New York : Springer-Verlag 01.02.2007
Springer Nature B.V
Subjects
Animals
Animals, Inbred Strains - genetics
backcrossing
Chromosome Mapping
computer software
Crosses, Genetic
experimental design
Genetic Variation
genome
genotyping
inbred lines
loci
mammals
phenotype
Probability
progeny
Quantitative Trait Loci
variance
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Summary:An investigator planning a QTL (quantitative trait locus) experiment has to choose which strains to cross, the type of cross, genotyping strategies, and the number of progeny to raise and phenotype. To help make such choices, we have developed an interactive program for power and sample size calculations for QTL experiments, R/qtlDesign. Our software includes support for selective genotyping strategies, variable marker spacing, and tools to optimize information content subject to cost constraints for backcross, intercross, and recombinant inbred lines from two parental strains. We review the impact of experimental design choices on the variance attributable to a segregating locus, the residual error variance, and the effective sample size. We give examples of software usage in real-life settings. The software is available at http://www.biostat.ucsf.edu/sen/software.html.
Bibliography:http://dx.doi.org/10.1007/s00335-006-0090-y
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ISSN:0938-8990
1432-1777
DOI:10.1007/s00335-006-0090-y