Haplotype Block Partitioning and TagSNP Selection on Human Chromosome 21

A Single Nucleotide Polymorphism or SNP is a DNA sequence variation occurring when a single nucleotide in the genome differs between members of species. Recent research reveals that SNPs within certain haplotype blocks induce only a few distinct common haplotypes in the majority of the population. The existence of haplotype block structures has serious implications for association-based methods in mapping of disease genes. In this paper, we propose and implement several efficient algorithms for identifying haplotype blocks in the genome. For dealing with missing data, which often appears in real biomedical data, we develop methods that assign missing data to specific alleles such that the resulting diversity is minimized. Our developed system is used for analyzing chromosome 21 haplotype data provided by Patil et al. [11]. In contrast to previous partition methods, the haplotype blocks and tagSNPs identified by our methods are longer and fewer, yet still retaining the desired expressing