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arXiv · 0804.1690

An efficient strategy to characterize alleles and complex haplotypes using DNA-markers

Rodrigo Labouriau·Poul Sørensen·Helle R. Juul-Madsen
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Abstract

We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is available but the values of neighbouring DNA-markers are at hand. We argue that the effects of the non-observable haplotypes of the genomic regions can and should be represented by factors representing disjoint groups of marker-alleles. A theoretical argument based on a hypothetical phylogenetic tree supports this general claim. The techniques described allow to identify and to infer the number of detectable haplotypes in the genomic region that are associated with a trait. The methods proposed use an exhaustive combinatorial search coupled with the maximization of a version of the likelihood function penalized for the number of parameters. This procedure can easily be implemented with standard statistical methods for a moderate number of marker-alleles.

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Rodrigo Labouriau, Poul Sørensen, Helle R. Juul-Madsen. 2008-04-10. An efficient strategy to characterize alleles and complex haplotypes using DNA-markers. https://arxiv.org/abs/0804.1690

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