Combined association and linkage analysis for general pedigrees and genetic models

Statistical Applications in Genetics and Molecular Biology
Ola Hössjer

Abstract

A combined score test for association and linkage analysis is introduced, based on a biologically plausible model with association between markers and causal genes and penetrance between phenotypes and the causal gene. The test is based on a retrospective likelihood of marker data given phenotypes, treating the alleles of the causal gene as hidden data. It is defined for arbitrary outbred pedigrees, a wide class of genetic models including polygenic and shared environmental effects and allows for missing marker data. It is multipoint, taking marker genotypes from several loci into account simultaneously. The score vector has one association and one linkage component, which can be used to define separate tests for association and linkage. For complete marker data, we give closed form expressions for the efficiency of the linkage, association and combined tests. These are examplified for binary and quantitative phenotypes with or without polygenic effects. The conclusion is that association tests are comparatively more efficient than linkage tests for strong association, weak penetrance models, small families and non-extreme phenotypes, whereas the linkage test is more efficient for weak association, strong penetrance models, lar...Continue Reading

Citations

Nov 15, 2006·Proceedings of the National Academy of Sciences of the United States of America·Michael C OldhamDaniel H Geschwind
Dec 17, 2009·Proceedings of the National Academy of Sciences of the United States of America·Katja NowickLisa Stubbs
Dec 27, 2005·Bioinformatics·Johannes TuikkalaTero Aittokallio
Aug 4, 2009·Bioinformatics·Verena Zuber, Korbinian Strimmer
Nov 17, 2009·Bioinformatics·Ramon Xulvi-Brunet, Hongzhe Li
Jan 3, 2012·Nucleic Acids Research·Stephanie SchneiderUlla Hansen
Jan 23, 2010·Science·Jill P Mesirov
Aug 24, 2007·EURASIP Journal on Bioinformatics & Systems Biology·Jianhua XuanEric Hoffman
Apr 23, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Yuanhui XiaoAndrei Yakovlev
May 17, 2008·Genetic Epidemiology·Azra Kurbasic, Ola Hössjer
Apr 18, 2008·Human Heredity·Lars AngquistLeif Groop

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