Article

TreeDT: gene mapping by tree disequilibrium test

Authors:

Petteri Sevon,

Hannu T. T. Toivonen,

Vesa OllikainenAuthors Info & Claims

KDD '01: Proceedings of the seventh ACM SIGKDD international conference on Knowledge discovery and data mining

Pages 365 - 370

https://doi.org/10.1145/502512.502566

Published: 26 August 2001 Publication History

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Abstract

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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H. Toivonen, P. Onkamo, K. Vasko, V. Ollikainen, P. Sevon, H. Mannila, and J. Kere. Gene Mapping by Haplotype Pattern Mining. Proc. Bio-lnformatics and Biomedical Engineering, pp 99-108, Arlington, VA, November 8-10, 2000.

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Sevon PToivonen HOllikainen V(2006)TreeDTIEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)10.1109/TCBB.2006.283:2(174-185)Online publication date: 1-Apr-2006
https://dl.acm.org/doi/10.1109/TCBB.2006.28
Polvi APolvi TSevon PPetäys THaahtela TLaitinen LKere JLaitinen T(2002)Physical map of an asthma susceptibility locus in 7p15-p14 and an association study of TCRGEuropean Journal of Human Genetics10.1038/sj.ejhg.520086110:10(658-665)Online publication date: 2-Oct-2002
https://doi.org/10.1038/sj.ejhg.5200861

Index Terms

TreeDT: gene mapping by tree disequilibrium test

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Published In

KDD '01: Proceedings of the seventh ACM SIGKDD international conference on Knowledge discovery and data mining

August 2001

493 pages

ISBN:158113391X

DOI:10.1145/502512

Conference Chair:
Doheon Lee
Chonnam National University, Korea
,
General Chair:
Mario Schkolnick
SGI
,
Program Chairs:
Foster Provost
New York University
,
Ramakrishnan Srikant
IBM Almaden Research Center

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 26 August 2001

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KDD01: ACM SIGKDD International Conference on Knowledge Discovery and Data Mining

August 26 - 29, 2001

California, San Francisco

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KDD '01 Paper Acceptance Rate 31 of 237 submissions, 13%;

Overall Acceptance Rate 1,133 of 8,635 submissions, 13%

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Cited By

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Sevon PToivonen HOllikainen V(2006)TreeDTIEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)10.1109/TCBB.2006.283:2(174-185)Online publication date: 1-Apr-2006
https://dl.acm.org/doi/10.1109/TCBB.2006.28
Polvi APolvi TSevon PPetäys THaahtela TLaitinen LKere JLaitinen T(2002)Physical map of an asthma susceptibility locus in 7p15-p14 and an association study of TCRGEuropean Journal of Human Genetics10.1038/sj.ejhg.520086110:10(658-665)Online publication date: 2-Oct-2002
https://doi.org/10.1038/sj.ejhg.5200861

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TreeDT: Tree Pattern Mining for Gene Mapping

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