Adjusted P Values for Genome-Wide Scans

Genome-wide scans for quantitative trait loci (QTL) have traditionally been summarized with plots of logarithm of odds (LOD) scores. A valuable modification is to supplement such plots with an additional vertical axis displaying quantiles of adjusted P values and labeling local maxima of the LOD sco...

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Bibliographic Details
Published inGenetics (Austin) Vol. 164; no. 4; pp. 1683 - 1687
Main Author Lystig, Theodore C
Format Journal Article
LanguageEnglish
Published United States Genetics Soc America 01.08.2003
Genetics Society of America
Subjects
Algorithms
Animals
Chromosome Mapping
Chromosomes - genetics
Computer Simulation
Crosses, Genetic
Data analysis
Epistasis, Genetic
Genetic Markers
Genetic Variation
Genetics
Genome
Lod Score
Probability
Quantitative Trait, Heritable
Rats
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Summary:Genome-wide scans for quantitative trait loci (QTL) have traditionally been summarized with plots of logarithm of odds (LOD) scores. A valuable modification is to supplement such plots with an additional vertical axis displaying quantiles of adjusted P values and labeling local maxima of the LOD scores with location-specific adjusted P values. This provides a visible gradation of genome-wide significance for the LOD score curve, instead of the stark dichotomy that a single threshold yields. Adjusted P values give genome-wide significance of individual LOD scores and are obtained through a straightforward modification of the familiar algorithm for generating permutation-based thresholds.
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ISSN:0016-6731
1943-2631
1943-2631
DOI:10.1093/genetics/164.4.1683