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1: Mamm Genome. 2007 Feb;18(2):87-93. Epub 2007 Mar 8.Click here to read Click here to read Links

R/qtlDesign: inbred line cross experimental design.

Sen S, Satagopan JM, Broman KW, Churchill GA.

Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA. sen@biostat.ucsf.edu

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 .

PMID: 17347894 [PubMed - indexed for MEDLINE]

PMCID: PMC2366108