A maximum likelihood based genetic algorithm for inferring haplotypes from genotypes

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.