title: Haplotype estimation from fuzzy genotypes using penalized likelihood.
abstract: The Composite Link Model is a generalization of the generalized linear model in which expected values of observed counts are constructed as a sum of generalized linear components. When combined with penalized likelihood, it provides a powerful and elegant way to estimate haplotype probabilities from observed genotypes. Uncertain ("fuzzy") genotypes, like those resulting from AFLP scores, can be handled by adding an extra layer to the model. We describe the model and the estimation algorithm. We apply it to a data set of accurate human single nucleotide polymorphism (SNP) and to a data set of fuzzy tomato AFLP scores.
authors.affiliation: Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands. h.uh@lumc.nl
authors.forename: Hae-Won
authors.initials: HW
authors.lastname: Uh
authors.forename: Paul H C
authors.initials: PH
authors.lastname: Eilers
mesh_terms: D000465:Algorithms; D054458:Amplified Fragment Length Polymorphism Analysis; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D005260:Female; D017143:Fuzzy Logic; D005819:Genetic Markers / Q000235:genetics; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D016013:Likelihood Functions; D018551:Solanum lycopersicum / Q000235:genetics; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D011336:Probability; D002583:Uterine Cervical Neoplasms / Q000235:genetics
chemical_list: D005819:Genetic Markers