Author/Authors :
Eslahchi، Changiz نويسنده , , Katanforoush، Ali نويسنده Faculty of Mathematical Sciences, Shahid Beheshti University, G.C., P.O. Box 198396-3113, Tehran, I.R. Iran , , Pezeshk، Hamid نويسنده School of Mathematics, Statistics and Computer Sciences, Center of Excellence in Biomathematics, College of Science, University of Tehran, P.O. Box 6455-14155, Tehran, I.R. Iran , , Afzaly، Narjes نويسنده School of Mathematics, Statistics and Computer Sciences, Center of Excellence in Biomathematics, College of Science, University of Tehran, P.O. Box 6455-14155, Tehran, I.R. Iran ,
Abstract :
Single Nucleotide Polymorphisms (SNPs) are the most usual form of polymorphism in human genome. Analyses of genetic variations have revealed that individual genomes share common SNP-haplotypes. The particular pattern of these common variations forms a block-like structure on human genome. In this work, we develop a new method based on the Perfect Phylogeny Model to identify haplotype blocks using samples of individual genomes. We introduce a rigorous definition of the quality of the partitioning of haplotypes into blocks and devise a greedy algorithm for finding the proper partitioning in case of perfect and semi-perfect phylogeny. It is shown that the minimum number of tagSNPs in a haplotype block of Perfect Phylogeny can be obtained by a polynomial time algorithm. We compare the performance of our algorithm on haplotype data of human chromosome 21 with other previously developed methods through simulations. The results demonstrate that our algorithm outperforms the conventional implementation of the Four Gamete Test approach which is the only available method for haplotype block partitioning based on Perfect Phylogeny.
