Significance thresholds for quantitative trait locus mapping under selective genotyping.

@article{Manichaikul2007SignificanceTF,
  title={Significance thresholds for quantitative trait locus mapping under selective genotyping.},
  author={Ani Manichaikul and Abraham A Palmer and Saunak Sen and Karl W. Broman},
  journal={Genetics},
  year={2007},
  volume={177 3},
  pages={1963-6}
}
In the case of selective genotyping, the usual permutation test to establish statistical significance for quantitative trait locus (QTL) mapping can give inappropriate significance thresholds, especially when the phenotype distribution is skewed. A stratified permutation test should be used, with phenotypes shuffled separately within the genotyped and ungenotyped individuals. 
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