2008/04/10 by Rodrigo Labouriau, Labouriau, Rodrigo, Poul Sørensen +4
Biochemistry, Genetics and Molecular Biology · Mathematics · #Applications (stat.AP) #FOS: Biological sciences #FOS: Computer and information sciences #Genetic Associations and Epidemiology #Genetic Mapping and Diversity in Plants and Animals #Genetic and phenotypic traits in livestock #Genomics (q-bio.GN) #q-bio.GN #stat.AP
paper · pdf · doi:10.48550/arxiv.0804.1690
21 pages, 7 figures
arxiv created 2008/04/10 · openalex publication_date 2008/04/10 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
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.