Back to Search
Start Over
Data mining applied to linkage disequilibrium mapping
- Source :
- University of Helsinki
- Publication Year :
- 2000
-
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.
- Subjects :
- Male
Linkage disequilibrium
LOCI
DISEASE GENES
computer.software_genre
Linkage Disequilibrium
HLA Antigens
311 Basic medicine
Genetics(clinical)
Child
Genetics (clinical)
Genes, Dominant
Aged, 80 and over
0303 health sciences
EXAMPLE
Linkage Disequilibrium Mapping
030305 genetics & heredity
Chromosome Mapping
Articles
ASSOCIATION
Middle Aged
FINLAND
Founder Effect
Phenotype
Child, Preschool
TESTS
Microsatellite
POPULATIONS
Female
Data mining
Algorithms
Adult
Adolescent
education
Biology
Polymorphism, Single Nucleotide
Statistics, Nonparametric
LIKELIHOOD
03 medical and health sciences
Gene mapping
Genetics
Humans
Computer Simulation
Genetic Predisposition to Disease
Alleles
030304 developmental biology
Statistical hypothesis testing
Aged
Models, Genetic
COMPLEX TRAITS
Haplotype
Nonparametric statistics
Infant
Statistical model
United Kingdom
Diabetes Mellitus, Type 1
Haplotypes
Mutation
computer
Microsatellite Repeats
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- University of Helsinki
- Accession number :
- edsair.doi.dedup.....93ae210370744a6bd362d4afd8d6c1b0