Whole genome association mapping by incompatibilities and local perfect phylogenies

Background: With current technology, vast amounts of data can be cheaply and efficiently produced in association studies, and to prevent data analysis to become the bottleneck of studies, fast and efficient analysis methods that scale to such data set sizes must be developed. Results: We present a fast method for accurate localisation of disease causing variants in high density case-control association mapping experiments with large numbers of cases and controls. The method searches for significant clustering of case chromosomes in the "perfect" phylogenetic tree defined by the largest region around each marker that is compatible with a single phylogenetic tree. This perfect phylogenetic tree is treated as a decision tree for determining disease status, and scored by its accuracy as a decision tree. The rationale for this is that the perfect phylogeny near a disease affecting mutation should provide more information about the affected/unaffected classification than random tr...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Thomas Mailund, Søren Besenbacher, Mikkel H. Schierup
• Keywords: BMCBI 2006, Decision Tree, Disease, Phylogenetic Tree