Survey of computational haplotype determination methods for single individual

• DOI: 10.1007/s13258-015-0342-x
• Publication Date: 2015-10-14T22:21:45Z
• Authors: Je-Keun Rhee; Honglan Li; Je-Gun Joung; Kyu-Baek Hwang; Byoung-Tak Zhang; Soo-Yong Shin
• Keywords: 0206 medical engineering; 02 engineering and technology

Genome-wide association studies have expanded our understanding of the relationship between the human genome and disease. However, because of current technical limitations, it is still challenging to clearly resolve diploid sequences, that is, two copies for each chromosome. One copy of each chromosome is inherited from each parent and the genomic function is determined by the interplay between the alleles represented as genotypes in the diploid sequences. Thus, to understand the nature of genetic variation in biological processes, including disease, it is necessary to determine the complete genomic sequence of each haplotype. Although there are experimental approaches for haplotype sequencing that physically separate the chromosomes, these methods are expensive and laborious and require special equipment. Here, we review the computational approaches that can be used to determine the haplotype phase. Since 1990, many researchers have tried to reconstruct the haplotype phase using a variety of computational methods, and some researches have been successfully help to determine the haplotype phase. In this review, we investigate how the computational haplotype determination methods have been developed, and we present the remaining problems affecting the determination of the haplotype of single individual using next-generation sequencing methods.