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Gene mapping by haplotype pattern mining

H.T.T. Toivonen, P. Onkamo, K. Vasko, V. Ollikainen, P. Sevon, H. Mannila, J. Kere
Proceedings IEEE International Symposium on Bio-Informatics and Biomedical Engineering  
We describe a new method for linkage disequilibrium mapping, Haplotype Pattern Mining (HPM). The method is based on discovering recurrent patterns, inspired by data mining methods.  ...  The haplotypes are ordered by their strength of association to the phenotype, and all haplotypes exceeding a given threshold level are used for prediction of disease susceptibility gene location.  ...  This research has been funded by the Academy of Finland, Graduate School in Computational Biology, Bioinformatics, and Biometry (ComBi), and Helsinki Graduate School in Computer Science and Engineering  ... 
doi:10.1109/bibe.2000.889596 dblp:conf/bibe/ToivonenOVOSMK00 fatcat:xbdd5sxz3bb6fer2ejoo3qdftm

Data Mining for Gene Mapping [chapter]

2011 Next Generation of Data-Mining Applications  
From a data mining perspective, gene mapping can then be cast as a pattern discovery and analysis task: which genetically motivated marker patterns help to separate affected individuals from healthy ones  ...  We describe and illustrate data mining approaches to gene mapping using haplotypes: association analysis, similarity analysis, and clustering.  ...  Haplotype pattern mining Like practically any application of data mining or machine learning, the gene mapping problem requires careful engineering of the types of patterns to be used, i.e., feature construction  ... 
doi:10.1109/9780471696650.ch12 fatcat:tuhbmxsisbdhhm5m77bhhuxahq

Development of Knowledge-based System for Personalized Medicine by Utilizing Haplotype Gene Mapping

Sesdika Sansani, G. A. Putri Saptawati
2013 Procedia Technology - Elsevier  
The system is called KeBHap that is developed by integrating haplotype gene mapping into previous KBS called KBSNP which works based on SNP.  ...  After that, we develop KBS for supporting personalized medicine by integrating gene mapping to the systems.  ...  Haplotype Pattern Mining Data mining is an important approach in gene mapping and it is so called Haplotype Pattern Mining (HPM) [10, 11] .  ... 
doi:10.1016/j.protcy.2013.12.310 fatcat:6khx4dmytfbabjr6dpygtfulru

A survey of data mining methods for linkage disequilibrium mapping

Päivi Onkamo, Hannu Toivonen
2006 Human Genomics  
Data mining methods areg aining more interesta sp otential tools in mapping and identification of complex disease loci.  ...  Here, the current data mining-based methods for linkage disequilibrium mapping and phenotype analyses are reviewed.  ...  Discovery of frequent patterns The most popular data mining method applied to gene mappingh as been the discovery of typicalh aplotypes (or haplotype patterns) and analysiso ft heir associationsw ith the  ... 
doi:10.1186/1479-7364-2-5-336 pmid:16595078 pmcid:PMC3500183 fatcat:7qwqfnldtbbojodbeujhyc26ci

Data Mining Applied to Linkage Disequilibrium Mapping

Hannu T.T. Toivonen, Päivi Onkamo, Kari Vasko, Vesa Ollikainen, Petteri Sevon, Heikki Mannila, Mathias Herr, Juha Kere
2000 American Journal of Human Genetics  
We introduce a new method for linkage disequilibrium mapping: haplotype pattern mining (HPM). The method, inspired by data mining methods, is based on discovery of recurrent patterns.  ...  The haplotypes are ordered by their strength of association with the phenotype, and all haplotypes exceeding a given threshold level are used for prediction of disease susceptibility-gene location.  ...  In this study, we introduce haplotype pattern mining (HPM), a technique that uses data mining methods in LD-based gene mapping.  ... 
doi:10.1086/302954 pmid:10848493 pmcid:PMC1287071 fatcat:caic7dsavze23ngmvb3dp6hg7y

EFFICIENT MINING OF HAPLOTYPE PATTERNS FOR LINKAGE DISEQUILIBRIUM MAPPING

LI LIN, LIMSOON WONG, TZE-YUN LEONG, POH SAN LAI
2010 Journal of Bioinformatics and Computational Biology  
We compared our method with some leading methods in linkage disequilibrium mapping such as Hap-Miner, Blade, GeneRecon, and Haplotype Pattern Mining (HPM).  ...  Linkage disequilibrium mapping is the process of finding disease gene locations through comparisons of haplotype frequencies between disease chromosomes and normal chromosomes.  ...  Acknowledgments This research was supported in part by Singapore Agency for Science, Technology and Research grants SERC/072/101/0016 and BM/00/07, and an Academic Research Funding grant R-252-000-111-  ... 
doi:10.1142/s0219720010005142 pmid:21155024 fatcat:2z37jny7irejzolex3opuocqp4

TreeDT

Petteri Sevon, Hannu T. T. Toivonen, Vesa Ollikainen
2001 Proceedings of the seventh ACM SIGKDD international conference on Knowledge discovery and data mining - KDD '01  
We also compare the results to those obtained using TDT (transmission/disequilibrium test), an established method for gene mapping, and Haplotype Pattern Mining (HPM), an earlier data mining method.  ...  We introduce and evaluate TreeDT, a novel gene mapping method which is based on discovering and assessing tree-like patterns in genetic marker data.  ...  This research has been funded by Helsinki Graduate School in Computer Science and Engineering (HeCSE) and Graduate School in Computational Biology, Bioinformatics, and Biometry (ComBi).  ... 
doi:10.1145/502512.502566 fatcat:coxsks7455dytmov6xxntnlkei

Association analysis for quantitative traits by data mining: QHPM

P. ONKAMO, V. OLLIKAINEN, P. SEVON, H. T. T. TOIVONEN, H. MANNILA, J. KERE
2002 Annals of Human Genetics  
 Previously, we have presented a data mining-based algorithmic approach to genetic association analysis, Haplotype Pattern Mining.  ...  Comparison with quantitative trait TDT (QTDT) showed that QHPM has better localization accuracy when the gene effect is weak.  Interest in association analysis and LD mapping methods for complex  ...  Previously, we introduced a data mining inspired algorithmic approach, Haplotype Pattern Mining (HPM), for genetic association analysis of binary traits (Toivonen et al. 2000 ; Sevon et al. 2001) .  ... 
doi:10.1046/j.1469-1809.2002.00131.x pmid:12485474 fatcat:3bzalfia6fdrtf3y7jf6deh5he

ON A FAMILY-BASED HAPLOTYPE PATTERN MINING METHOD FOR LINKAGE DISEQUILIBRIUM MAPPING

SHUANGLIN ZHANG, KUI ZHANG, JINMING LI, HONGYU ZHAO
2001 Biocomputing 2002  
Acknowledgements Supported in part by grants GM59507 and HD36834 from NIH. We thank Dr. MacCluer for providing us the simulated data from GAW12. GAW is supported by NIH grant GM31575 from NIGMS.  ...  [1] proposed haplotype pattern mining (HPM), a technique that uses data mining methods in LD-based gene mapping.  ...  When a haplotype pattern P is studied, we treat P as one allele, denoted by A, and the other haplotype patterns as another allele, denoted by B.  ... 
doi:10.1142/9789812799623_0010 fatcat:pnssj5ez6regxegfjhlci2vtfu

Haplotype-based allele mining in the Japan-MAGIC rice population

Daisuke Ogawa, Eiji Yamamoto, Toshikazu Ohtani, Noriko Kanno, Hiroshi Tsunematsu, Yasunori Nonoue, Masahiro Yano, Toshio Yamamoto, Jun-ichi Yonemaru
2018 Scientific Reports  
The haplotype-based allele mining (HAM) proposed in this study is a promising approach to the detection of allelic variation in genes controlling agronomic traits in MAGIC populations.  ...  To obtain information on the haplotypes in the JAM lines, we predicted the haplotype blocks in the whole chromosomes using 16,345 SNPs identified via genotyping-by-sequencing analysis.  ...  Seeds of the founders were provided by Tohoku Agricultural Research Centre (BE),  ... 
doi:10.1038/s41598-018-22657-3 pmid:29531264 pmcid:PMC5847589 fatcat:gwtcgocv6jdifinbhyldcbpwqy

Linkage disequilibrium screening for multiple sclerosis implicates JAG1 and POU2AF1 as susceptibility genes in Europeans

The GAMES Collaborative Group
2006 Journal of Neuroimmunology  
Association mapping across the candidate genes implicated by these markers in 937 UK trio families revealed modestly associated haplotypes in JAG1 (p = 0.019) on chromosome 20p12.2 and POU2AF1 (p = 0.003  ...  As might be expected five of these markers map within the Major Histocompatibility Complex (MHC) and are in LD with HLA-DRB1.  ...  Haplotype pattern mapping was then performed using the Haplotype Pattern Mining a These meta-analyses were based on analysis of the raw data without using the adapting factors suggested by Yeo et al.  ... 
doi:10.1016/j.jneuroim.2006.06.003 pmid:16934875 fatcat:zyvnoau54zcajows75l2sxp35i

A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea

Hari D. Upadhyaya, Deepak Bajaj, Shouvik Das, Maneesha S. Saxena, Saurabh Badoni, Vinod Kumar, Shailesh Tripathi, C. L. L. Gowda, Shivali Sharma, Akhilesh K. Tyagi, Swarup K. Parida
2015 Plant Molecular Biology  
The gene haplotype-based LD mapping discovered diverse novel natural allelic variants and haplotypes in eight genes with high trait association potential (41 % combined PVE) for flowering time differentiation  ...  The flower-specific expression, including differential up-and down-regulation (>three folds) of eight flowering time-associated genes (including six genes validated by QTL mapping) especially in early  ...  Acknowledgments The authors gratefully acknowledge the financial support by the core grant of National Institute of Plant Genome Research (NIPGR), New Delhi, India.  ... 
doi:10.1007/s11103-015-0377-z pmid:26394865 fatcat:fkq3buuhlvfvda27snekejhby4

Adaptation to heavy-metal contaminated environments proceeds via selection on pre-existing genetic variation [article]

Kevin M. Wright, Uffe Hellsten, Chenling Xu, Annie L. Jeong, Avinash Sreedasyam, Jarrod A. Chapman, Jeremy Schmutz, Graham Coop, Daniel S. Rokhsar, John H. Willis
2015 bioRxiv   pre-print
upon beneficial haplotypes that predates the existence of the copper mine habitat.  ...  We discover Tol1 candidate genes that exhibit significantly large differences in expression between tolerant and non-tolerant genotypes or in allele frequency between mine/off-mine population pairs.  ...  This pattern suggests 329 these core haplotypes predates the establishment of the mine populations.  ... 
doi:10.1101/029900 fatcat:ejxgf3bclvcn7piywoxk6p4i54

Genetic association with rheumatoid arthritis—Genetic Analysis Workshop 15: summary of contributions from Group 2

Marsha A. Wilcox, Zhong Li, Will Tapper
2007 Genetic Epidemiology  
In the pattern-based strategy (Pattern Examiner) developed by Li et al. [2007] , a pattern-based data mining method was used to exhaustively, yet efficiently, identify all patterns satisfying predefined  ...  Li et al. [2007] employed a pattern-based mining strategy to detect local markers in moderate or strong LD and global, unlinked markers, multi-locus genetic associations as well as gene-gene/geneenvironment  ... 
doi:10.1002/gepi.20276 pmid:18046771 fatcat:xaoaxu6asvfkzbdm7olupwnjza

An Integrated Genomic Strategy Delineates Candidate Mediator Genes Regulating Grain Size and Weight in Rice

Naveen Malik, Nidhi Dwivedi, Ashok K. Singh, Swarup K. Parida, Pinky Agarwal, Jitendra K. Thakur, Akhilesh K. Tyagi
2016 Scientific Reports  
This strategy was further integrated with traditional bi-parental mapping population validation, differential expression profiling and gene-based SNP haplotyping/LD (linkage disequilibrium) mapping to  ...  An integrated approach of SNP marker-based high resolution candidate gene-based association analysis, traditional QTL mapping, differential expression profiling and molecular haplotyping is well documented  ...  It would be thus interesting to constitute gene-specific haplotypes by targeting/combining other novel coding and non-coding SNP allelic variants mined from this OsMED4_2 gene and determine trait association  ... 
doi:10.1038/srep23253 pmid:27000976 pmcid:PMC4802383 fatcat:vnerh7tezfaoxfyilhydflvoxe
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