ArticleAmerican journal of human genetics2000
Data mining applied to linkage disequilibrium mapping.
Article in American journal of human genetics, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 135 citations in OpenAlex.
- Imputation without doing imputation: a new method for the detection of non-genotyped causal variants.Genetic epidemiology · 2014Article
- Path-counting formulas for generalized kinship coefficients and condensed identity coefficients.Computational and mathematical methods in medicine · 2014Article
- Efficient path-based computations on pedigree graphs with compact encodings.BMC bioinformatics · 2012Article
- Simple strategies for haplotype analysis of the X chromosome with application to age-related macular degeneration.European journal of human genetics : EJHG · 2011Article
- Sequential Support Vector Regression with Embedded Entropy for SNP Selection and Disease Classification.Statistical analysis and data mining · 2011Article
- A novel approach for haplotype-based association analysis using family data.BMC bioinformatics · 2010Article
- Identification of MAMDC1 as a candidate susceptibility gene for systemic lupus erythematosus (SLE).PloS one · 2009Article
- A variable-sized sliding-window approach for genetic association studies via principal component analysis.Annals of human genetics · 2009Article
- The limits of fine-scale mapping.Genetic epidemiology · 2009Article
- A fast algorithm for genome-wide haplotype pattern mining.BMC bioinformatics · 2009Article
- TreeQA: quantitative genome wide association mapping using local perfect phylogeny trees.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2009Article
- Association mapping by generalized linear regression with density-based haplotype clustering.Genetic epidemiology · 2009Article
- Type 2 diabetes whole-genome association study in four populations: the DiaGen consortium.American journal of human genetics · 2007Article
- Association mapping via regularized regression analysis of single-nucleotide-polymorphism haplotypes in variable-sized sliding windows.American journal of human genetics · 2007Article
- The genetics of chronic obstructive pulmonary disease.Respiratory research · 2006Review
- Whole genome association mapping by incompatibilities and local perfect phylogenies.BMC bioinformatics · 2006Article
- Haplotype-based quantitative trait mapping using a clustering algorithm.BMC bioinformatics · 2006Article
- A survey of data mining methods for linkage disequilibrium mapping.Human genomics · 2006Review
- Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data.Human genetics · 2006Article
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Corrections and comments
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Authors and funding
8 authors at 3 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. We define a class of useful haplotype patterns in genetic case-control data and use the algorithm for finding disease-associated haplotypes. 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. The method is model-free, in the sense that it does not require (and is unable to utilize) any assumptions about the inheritance model of the disease. The statistical model is nonparametric. The haplotypes are allowed to contain gaps, which improves the method's robustness to mutations and to missing and erroneous data. Experimental studies with simulated microsatellite and SNP data show that the method has good localization power in data sets with large degrees of phenocopies and with lots of missing and erroneous data. The power of HPM is roughly identical for marker maps at a density of 3 single-nucleotide polymorphisms/cM or 1 microsatellite/cM. The capacity to handle high proportions of phenocopies makes the method promising for complex disease mapping. An example of correct disease susceptibility-gene localization with HPM is given with real marker data from families from the United Kingdom affected by type 1 diabetes. The method is extendable to include environmental covariates or phenotype measurements or to find several genes simultaneously.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.