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True and false positive peaks in genomewide scans: The long and the short of it
Author(s) -
Visscher Peter,
Haley Chris
Publication year - 2001
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/gepi.1010
Subject(s) - linkage (software) , false positive paradox , statistic , identity by descent , linkage disequilibrium , genome scan , locus (genetics) , quantitative trait locus , test statistic , genetics , biology , trait , genetic linkage , chromosome , genetic association , statistics , statistical hypothesis testing , evolutionary biology , mathematics , haplotype , computer science , allele , gene , single nucleotide polymorphism , genotype , microsatellite , programming language
When performing a genome scan in linkage or linkage disequilibrium studies to detect loci underlying complex or quantitative traits, it is important to attempt to distinguish between true and false positives using the appropriate statistical methods. There has been some controversy in the literature regarding the use of the length of a positive peak, i.e., the length of a chromosome region displaying identity‐by‐descent in linkage studies among affected individuals or the length of a continuous chromosome region for which the test statistic is above a certain threshold. We show in this study, by reasoning and by simulation studies, that conditional on the strength of evidence for a locus affecting a trait of interest, i.e., conditional on the peak height of a test statistic, there is no information in the length of the peak. Our finding has implications for linkage and association studies. Genet. Epidemiol. 20:409–414, 2001. © 2001 Wiley‐Liss, Inc.