Association mapping through heuristic evolutionary history reconstruction-application to GAW15 Problem 3

This paper presents a novel method of identifying phenotypically important regions of the genome. It involves a form of association mapping that works by summarizing properties of the ancestral recombination graph (ARG) of a sample of unrelated phenotyped and genotyped individuals. By breaking the sample into many small sub-samples and averaging the results, it becomes computationally tractable to measure the degree to which the evolutionary history of any locus is consistent with the distribution of the phenotypes in the sample. Analysis of simulated rheumatoid arthritis data demonstrates the efficiency and effectiveness of this method in identifying loci of large phenotypic effect.