1. A maximum likelihood based genetic algorithm for inferring haplotypes from genotypes
- Author
-
Priyadarshini Lakshminarasimhan, Dongsheng Che, Robert E. Marmelstein, Qi Liu, and Mary G DeVito
- Subjects
Computer science ,Heuristic (computer science) ,Haplotype ,Inference ,Single-nucleotide polymorphism ,computer.software_genre ,ComputingMethodologies_PATTERNRECOGNITION ,Chromosome (genetic algorithm) ,TheoryofComputation_ANALYSISOFALGORITHMSANDPROBLEMCOMPLEXITY ,Genetic algorithm ,Statistics ,SNP ,Data mining ,Haplotype estimation ,computer - Abstract
A haplotype is a set of single nucleotide polymorphisms (SNPs) from a given chromosome, and provides valuable information about complex diseases. Current practices that the inferring of large scale SNP haplotypes from raw SNP data (genotypes) using computational approaches has gained a lot of attention, but it presents a grand challenges as it is inherently a NP-Hard problem. In this paper, we propose a heuristic approach, Genetic Algorithm (GA) model for the haplotypes inference method, based on the maximum-likelihood estimates of haplotype frequencies under the assumption of Hardy-Weinberg proportions. The goal of the genetic algorithm method is to obtain high prediction accuracy within a reasonable computing time. The performance of our model was evaluated on both simulated datasets and real datasets, and these results are promising, indicating that our model is a potential computational tool for haplotype inferences.
- Published
- 2010
- Full Text
- View/download PDF