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Originally published as Genetics Published Articles Ahead of Print on August 3, 2006.

Genetics, Vol. 174, 1063-1068, October 2006, Copyright © 2006
doi:10.1534/genetics.106.059469

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Assessing the Significance of Quantitative Trait Loci in Replicable Mapping Populations

Fei Zou*,1, Zongli Xu{dagger} and Todd Vision{ddagger}

* Department of Biostatistics and {ddagger} Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599 and {dagger} Epidemiology Branch, NIEHS, Research Triangle Park, North Carolina 27709

1 Corresponding author: Department of Biostatistics, University of North Carolina, 3107D McGavran–Greenberg Hall, CB 7420, Chapel Hill, NC 27599.
E-mail: fzou{at}bios.unc.edu

Replicable populations, such as panels of recombinant inbred or doubled haploid lines, are convenient resources for the mapping of QTL. To increase mapping power, replications are often collected within each RI line and a common way to analyze such data is to include in the QTL model only a single measurement from each line that represents the average among the replicates (a line means model). An obvious, but seldom explored, alternative, is to include every replicate in the model (a full data model). Here, we use simulations to compare these two approaches. Further, we propose an extension of the standard permutation procedure that is required to correctly control the type I error in mapping populations with nested structure.




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G. A. Churchill and R. W. Doerge
Naive Application of Permutation Testing Leads to Inflated Type I Error Rates
Genetics, January 1, 2008; 178(1): 609 - 610.
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