document: TreeDT : gene mapping by tree disequilibrium test We introduce and evaluate TreeDT , a novel gene mapping method which is based on discovering and assessing tree-like patterns in genetic marker data . Gene mapping aims at discovering a statistical connection from a particular disease or trait to a narrow region in the genome . In a typical case-control setting , data consists of genetic markers typed for a set of disease-associated chromosomes and a set of control chromosomes . A computer scientist would view this data as a set of strings . TreeDT extracts , essentially in the form of substrings and prefix trees , information about the historical recombinations in the population . This information is used to locate fragments potentially inherited from a common diseased founder , and to map the disease gene into the most likely such fragment . The method measures for each chromosomal location the disequilibrium of the prefix tree of marker strings starting from the location , to assess the distribution of disease-associated chromosomes . We evaluate experimentally the performance of TreeDT on realistic , simulated data sets , and comparisons to state of the art methods ( TDT , HPM ) show that TreeDT is very competitive .
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