Significance thresholds for quantitative trait loc...[Genetics. 2007]

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1: Genetics. 2007 Nov;177(3):1963-6. Epub 2007 Aug 24. Links

Significance thresholds for quantitative trait locus mapping under selective genotyping.

Manichaikul A, Palmer AA, Sen S, Broman KW.

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

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.

PMID: 17720902 [PubMed - indexed for MEDLINE]

PMCID: PMC2147971

A likelihood approach for quantitative-trait-locus mapping with selected pedigrees. [Biometrics. 2005]
Quantitative trait locus study design from an information perspective. [Genetics. 2005]
The full EM algorithm for the MLEs of QTL effects and positions and their estimated variances in multiple-interval mapping. [Biometrics. 2005]
Maximum likelihood analysis of quantitative trait loci under selective genotyping. [Heredity. 2000]
Sequential quantitative trait locus mapping in experimental crosses. [Stat Appl Genet Mol Biol. 2007]
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Significance thresholds for quantitative trait locus mapping under selective genotyping.

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