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Originally published as Genetics Published Articles Ahead of Print on August 24, 2007.
Genetics, Vol. 177, 1963-1966, November 2007, Copyright © 2007
doi:10.1534/genetics.107.080093
Significance Thresholds for Quantitative Trait Locus Mapping Under Selective Genotyping
Ani Manichaikul*,
Abraham A. Palmer
,
aunak Sen
and
Karl W. Broman*,1
* Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland 21205, Departments of Human Genetics and Psychiatry, University of Chicago, Chicago, Illinois 60637 and Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94107
1 Corresponding author: Department of Biostatistics and Medical Informatics, University of Wisconsin, 6770 Medical Sciences Center, 1300 University Ave., Madison, WI 53706.
E-mail: kbroman{at}biostat.wisc.edu
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.