Abstract

One of the main topics in genomics is to determine the relevance of DNA variations with some genetic disease. Single nucleotide polymorphism (SNP) is the most frequent and important form of genetic variation which involves a single DNA base. The values of a set of SNPs on a particular chromosome copy define a haplotype. Because of its importance in the studies of complex disease association, haplotyping is one of the central problems in bioinformatics. There are two classes of in silico haplotyping problems, i.e., single individual haplotyping and population haplotyping. In this review paper, we give an overview on the existing models and algorithms on this topic, report the recent progresses from the computational viewpoint and further discuss the future research trends.

Keywords: Single nucleotide polymorphism (SNP), haplotype assembly, Minimum Fragment Removal (MFR), Hardy-Weinber equilibrium (HWE), Perfect Phylogeny Haplotyping