HLODs, trait models, and ascertainment: implications of admixture for parameter estimation and linkage detection

Human Heredity
Veronica J Vieland, Mark W Logue

Abstract

Maximizing the homogeneity lod is known to be an appropriate procedure for estimating parameters of the trait model in an approximately 'ascertainment assumption free' (AAF) manner. We have investigated whether this same property also holds for the heterogeneity lod (HLOD). We show that, when the genetic models at linked and unlinked loci differ, HLODs are not AAF, and maximizing the HLOD yields parameter estimates that are for all practical purposes meaningless; indeed, the admixture parameter alpha does not even measure the proportion of linked families within the sample, as is commonly supposed. In spite of this, our results confirm a large body of evidence supporting the use of HLODs as robust tools for linkage detection, and suggest further that maximizing the HLOD over both alpha and parameters of the trait model can improve accuracy in estimation of the recombination fraction theta;. These findings have important implications for the optimal handling of nuisance parameters in linkage analysis, particularly when evaluating the evidence for or against linkage based on multiple independent heterogeneous sets of data.

Citations

Mar 18, 2006·Current Diabetes Reports·Andrew D Paterson
Jul 10, 2007·Current Neurology and Neuroscience Reports·David A Greenberg, Deb K Pal
Sep 14, 2012·Epilepsia·David A Greenberg, William C L Stewart
Dec 23, 2011·Human Heredity·Veronica J VielandWilliam Valentine-Cooper
Dec 23, 2011·Human Heredity·Joan E Bailey-Wilson, Alexander F Wilson
Jun 27, 2008·BMC Bioinformatics·Manika GovilVeronica J Vieland
Oct 2, 2004·BMC Genetics·Shili Lin, Swati Biswas
Mar 26, 2008·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·E G HollidayD R Nyholt
Jun 5, 2008·International Journal of Andrology·Laura Rodriguez-Murillo, David A Greenberg
Aug 11, 2006·Statistics in Medicine·Robert C Elston, M Anne Spence
Feb 25, 2005·American Journal of Human Genetics·Christopher W BartlettVeronica J Vieland
May 20, 2008·American Journal of Human Genetics·Veronica J VielandYaron Tomer
Jan 16, 2002·American Journal of Human Genetics·Susan E HodgeDavid A Greenberg
Jul 24, 2004·American Journal of Human Genetics·J E Bailey-WilsonM W Anderson
Dec 11, 2003·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Steven P HamiltonJames A Knowles
Aug 5, 2003·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Mark W LogueRaymond R Crowe
Nov 24, 2006·Genetic Epidemiology·Christopher W Bartlett, Veronica J Vieland
Oct 2, 2014·Current Protocols in Human Genetics·Nicole D Dueker, Margaret A Pericak-Vance

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