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R/qtlDesign: inbred line cross experimental design

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Abstract

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.

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Acknowledgments

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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Authors and Affiliations

  1. Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, 94143, USA

    Śaunak Sen

  2. Department of Epidemiology and Biostatistics, Memorial Sloan Ketterning Cancer Center, New York, New York, 10021, USA

    Jaya M. Satagopan

  3. Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, 21205, USA

    Karl W. Broman

  4. The Jackson Laboratory, Bar Harbor, Maine, 04609, USA

    Gary A. Churchill

Authors
  1. Śaunak Sen
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  2. Jaya M. Satagopan
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  3. Karl W. Broman
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  4. Gary A. Churchill
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Correspondence to Śaunak Sen.

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Sen, Ś., Satagopan, J.M., Broman, K.W. et al. R/qtlDesign: inbred line cross experimental design. Mamm Genome 18, 87–93 (2007). https://doi.org/10.1007/s00335-006-0090-y

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  • DOI: https://doi.org/10.1007/s00335-006-0090-y

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