The art of computer programming, volume 3: (2nd ed.) sorting and searching
The art of computer programming, volume 3: (2nd ed.) sorting and searching
TreeDT: gene mapping by tree disequilibrium test
Proceedings of the seventh ACM SIGKDD international conference on Knowledge discovery and data mining
Gene Mapping by Haplotype Pattern Mining
BIBE '00 Proceedings of the 1st IEEE International Symposium on Bioinformatics and Biomedical Engineering
Artificial Intelligence in Medicine
International Journal of Computational Intelligence in Bioinformatics and Systems Biology
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We describe TreeDT, a novel association-based gene mapping method. Given a set of disease-associated haplotypes and a set of control haplotypes, TreeDT predicts likely locations of a disease susceptibility gene. TreeDT extracts, essentially in the form of haplotype trees, information about historical recombinations in the population: A haplotype tree constructed at a given chromosomal location is an estimate of the genealogy of the haplotypes. TreeDT constructs these trees for all locations on the given haplotypes and performs a novel disequilibrium test on each tree: Is there a small set of subtrees with relatively high proportions of disease-associated chromosomes, suggesting shared genetic history for those and a likely disease gene location? We give a detailed description of TreeDT and the tree disequilibrium tests, we analyze the algorithm formally, and we evaluate its performance experimentally on both simulated and real data sets. Experimental results demonstrate that TreeDT has high accuracy on difficult mapping tasks and comparisons to other methods (EATDT, HPM, TDT) show that TreeDT is very competitive.