CLIP Test: a new fast, simple and powerful method to distinguish between linked or pleiotropic quantitative trait loci in linkage disequilibria analysis.

TitleCLIP Test: a new fast, simple and powerful method to distinguish between linked or pleiotropic quantitative trait loci in linkage disequilibria analysis.
Publication TypeJournal Article
Year of Publication2013
AuthorsDavid, I, Elsen, J-M, Concordet, D
JournalHeredity (Edinb)
Volume110
Issue3
Pagination232-8
Date Published2013 Mar
ISSN1365-2540
KeywordsAlgorithms, Animals, Chromosome Mapping, Computer Simulation, Female, Genetic Linkage, Genetic Pleiotropy, Humans, Livestock, Male, Models, Genetic, Phenotype, Quantitative Trait Loci, Quantitative Trait, Heritable
Abstract

An important question arises when mapping quantitative trait loci (QTLs) for genetically correlated traits: is the correlation due to pleiotropy (a single QTL affecting more than one trait) and/or close linkage (different QTLs that are physically close to each other and influence the traits)? In this article, we propose the Close Linkage versus Pleiotropism (CLIP) test, a fast, simple and powerful method to distinguish between these two situations. The CLIP test is based on the comparison of the square of the observed correlation between a combination of apparent effects at the marker level to the minimal value it can take under the pleiotropic assumption. A simulation study was performed to estimate the power and alpha risk of the CLIP test and compare it to a test that evaluated whether the confidence intervals of the two QTLs overlapped or not (CI test). On average, the CLIP test showed a higher power (68%) to detect close-linked QTLs than the CI test (43%) and a same alpha risk (4%).

DOI10.1038/hdy.2012.70
Alternate JournalHeredity (Edinb)
PubMed ID23250009
PubMed Central IDPMC3668649