A survey of data mining methods for linkage disequilibrium mapping

Data mining methods are gaining more interest as potential tools in mapping and identification of complex disease loci. The methods are well suited to large numbers of genetic marker loci produced by high-throughput laboratory analyses, but also might be useful for clarifying the phenotype definitions prior to more traditional mapping analyses. Here, the current data mining-based methods for linkage disequilibrium mapping and phenotype analyses are reviewed.

[1]  J. Ott,et al.  Mathematical multi-locus approaches to localizing complex human trait genes , 2003, Nature Reviews Genetics.

[2]  P. Marjoram,et al.  Fine-scale mapping of disease genes with multiple mutations via spatial clustering techniques. , 2003, American journal of human genetics.

[3]  J. Zurada,et al.  NEW GENERATION OF DATA MINING APPLICATIONS , 2003 .

[4]  David M. Reif,et al.  Integrated analysis of genetic, genomic and proteomic data , 2004, Expert review of proteomics.

[5]  Salvatore Torquato,et al.  Motivation and Overview , 2002 .

[6]  E. Zeggini,et al.  0021-972X/04/$15.00/0 The Journal of Clinical Endocrinology & Metabolism 89(2):892–897 Printed in U.S.A. Copyright © 2004 by The Endocrine Society doi: 10.1210/jc.2003-031235 Glucocorticoid Sensitivity Is Determined by a Specific , 2022 .

[7]  Hannu Toivonen,et al.  TreeDT: tree pattern mining for gene mapping , 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[8]  N. Cook,et al.  Tree and spline based association analysis of gene–gene interaction models for ischemic stroke , 2004, Statistics in medicine.

[9]  S. Young,et al.  Recursive partitioning analysis of complex disease pharmacogenetic studies. I. Motivation and overview. , 2005, Pharmacogenomics.

[10]  P. Bork,et al.  Association of genes to genetically inherited diseases using data mining , 2002, Nature Genetics.

[11]  Hannu Toivonen,et al.  Gene Mapping by Pattern Discovery , 2005, Data Mining in Bioinformatics.

[12]  V. Ollikainen,et al.  Data mining and multiparameter analysis of lung surfactant protein genes in bronchopulmonary dysplasia. , 2004, Human molecular genetics.

[13]  D. Tregouet,et al.  Automated detection of informative combined effects in genetic association studies of complex traits. , 2003, Genome research.

[14]  J. Kere,et al.  A novel low-penetrance locus for familial glioma at 15q23-q26.3. , 2002, Cancer research.

[15]  L. Wasserman,et al.  On the identification of disease mutations by the analysis of haplotype similarity and goodness of fit. , 2003, American journal of human genetics.

[16]  Heikki Mannila,et al.  Gene mapping by haplotype pattern mining , 2000, Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering.

[17]  Hongyu Zhao,et al.  On a Family-Based Haplotype Pattern Mining Method for Linkage Disequilibrium Mapping , 2001, Pacific Symposium on Biocomputing.

[18]  Tao Jiang,et al.  Genetics and population analysis Haplotype-based linkage disequilibrium mapping via direct data mining , 2005 .

[19]  J. Kere,et al.  Data mining applied to linkage disequilibrium mapping. , 2000, American journal of human genetics.

[20]  David Page,et al.  Predicting cancer susceptibility from single-nucleotide polymorphism data: a case study in multiple myeloma , 2005, BIOKDD.

[21]  P Sevon,et al.  Association analysis for quantitative traits by data mining: QHPM , 2002, Annals of human genetics.

[22]  Jason H Moore,et al.  Computational analysis of gene-gene interactions using multifactor dimensionality reduction , 2004, Expert review of molecular diagnostics.

[23]  C. Panhuysen,et al.  Empirically derived phenotypic subgroups – qualitative and quantitative trait analyses , 2003, BMC Genetics.

[24]  Jurg Ott,et al.  Genetic dissection of diseases: design and methods. , 2004, Current opinion in genetics & development.

[25]  Thomas J. Hudson,et al.  Characterization of a Common Susceptibility Locus for Asthma-Related Traits , 2004, Science.

[26]  Jozef Zurada,et al.  Data Mining for Gene Mapping , 2005 .

[27]  Petteri Sevon.  Algorithms for Association-Based Gene Mapping , 2004 .

[28]  P. Bork,et al.  G2D: a tool for mining genes associated with disease , 2005, BMC Genetics.

[29]  J. H. Moore,et al.  Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. , 2001, American journal of human genetics.

[30]  Andrew P Morris,et al.  Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes. , 2004, American journal of human genetics.

[31]  Heikki Mannila,et al.  Fast Discovery of Association Rules , 1996, Advances in Knowledge Discovery and Data Mining.