Calculation of multipoint likelihoods using flanking marker data: a simulation study.
The calculation of multipoint likelihoods is computationally challenging, with the exact calculation of multipoint probabilities only possible on small pedigrees with many markers or large pedigrees with few markers. This paper explores the utility of calculating multipoint likelihoods using data on markers flanking a hypothesized position of the trait locus. The calculation of such likelihoods is often feasible, even on large pedigrees with missing data and complex structures. Performance characteristics of the flanking marker procedure are assessed through the calculation of multipoint heterogeneity LOD scores on data simulated for Genetic Analysis Workshop 14 (GAW14). Analysis is restricted to data on the Aipotu population on chromosomes 1, 3, and 4, where chromosomes 1 and 3 are known to contain disease loci. The flanking marker procedure performs well, even when missing data and genotyping errors are introduced.
George
Andrew W
AW
Program in Public Health Genetics, College of Public Health, University of Iowa, Iowa City, Iowa, USA. andrew-george@uiowa.edu
Mangin
LaVonne A
LA
Bartlett
Christopher W
CW
Logue
Mark W
MW
Segre
Alberto M
AM
Vieland
Veronica J
VJ
D002874:Chromosome Mapping; D002878:Chromosomes, Human, Pair 1 / Q000235:genetics; D003198:Computer Simulation; D030541:Databases, Genetic; D018740:Genetic Heterogeneity; D008040:Genetic Linkage; D005819:Genetic Markers; D005838:Genotype; D006801:Humans; D016013:Likelihood Functions; D008126:Lod Score; D040641:Quantitative Trait Loci / Q000235:genetics; D012984:Software
D005819:Genetic Markers