Significance thresholds for quantitative trait locus mapping under selective genotyping

Genetics. 2007 Nov;177(3):1963-6. doi: 10.1534/genetics.107.080093. Epub 2007 Aug 24.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Chromosome Mapping / methods*
  • Chromosome Mapping / statistics & numerical data
  • Genotype
  • Likelihood Functions
  • Lod Score
  • Models, Genetic
  • Phenotype
  • Quantitative Trait Loci*