Haplotype estimation from fuzzy genotypes using penalized likelihood.
basic_science · Level V
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- Record sourced from PubMed, PMID 21931662.
- Also identified by DOI 10.1371/journal.pone.0024219 and PMC identifier PMC2760579.
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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.