Mammalian Genome

, Volume 18, Issue 2, pp 87–93 | Cite as

R/qtlDesign: inbred line cross experimental design

  • Śaunak Sen
  • Jaya M. Satagopan
  • Karl W. Broman
  • Gary A. Churchill
Original Contributions


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


Quantitative Trait Locus Recombinant Inbred Line Effective Sample Size Quantitative Trait Locus Effect Quantitative Trait Locus Detection 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors thank two anonymous reviewers for helpful comments on this article and the software. They thank Cynthia Piontkowski for editorial assistance. Their work was supported by NIH grants GM060457 (JMS), GM074244 (KWB), and GM070683 (GAC).


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Copyright information

© Springer Science+Business Media, Inc. 2007

Authors and Affiliations

  • Śaunak Sen
    • 1
  • Jaya M. Satagopan
    • 2
  • Karl W. Broman
    • 3
  • Gary A. Churchill
    • 4
  1. 1.Department of Epidemiology and BiostatisticsUniversity of California San FranciscoSan FranciscoUSA
  2. 2.Department of Epidemiology and BiostatisticsMemorial Sloan Ketterning Cancer CenterNew YorkUSA
  3. 3.Department of BiostatisticsJohns Hopkins UniversityBaltimoreUSA
  4. 4.The Jackson LaboratoryBar HarborUSA

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