title: CLIP Test: a new fast, simple and powerful method to distinguish between linked or pleiotropic quantitative trait loci in linkage disequilibria analysis.
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%).
authors.affiliation: INRA UR631 SAGA, F-31326, Castanet-Tolosan, France. Ingrid.david@toulouse.inra.fr
authors.forename: I
authors.initials: I
authors.lastname: David
authors.forename: J-M
authors.initials: JM
authors.lastname: Elsen
authors.forename: D
authors.initials: D
authors.lastname: Concordet
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping; D003198:Computer Simulation; D005260:Female; D008040:Genetic Linkage; D058685:Genetic Pleiotropy; D006801:Humans; D058751:Livestock; D008297:Male; D008957:Models, Genetic; D010641:Phenotype; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable