%0 Journal Article
%T Analysis of concordance of different haplotype block partitioning algorithms
%A Amit R Indap
%A Gabor T Marth
%A Craig A Struble
%A Peter Tonellato
%A Michael Olivier
%J BMC Bioinformatics
%D 2005
%I BioMed Central
%R 10.1186/1471-2105-6-303
%X We simulated 1000 haplotypes using the standard coalescent for three world populations ¨C European, African American, and East Asian ¨C and applied three classes of block partitioning algorithms ¨C diversity based, LD based, and information theoretic. We assessed algorithm differences in number, size, and coverage of blocks inferred under different conditions of SNP density, allele frequency, and sample size.Each algorithm inferred blocks differing in number, size, and coverage under different density and allele frequency conditions. Different partitions had few if any matching block boundaries. However they still overlapped and a high percentage of total chromosomal region was common to all methods. This percentage was generally higher with a higher density of SNPs and when rarer markers were included.A gold standard definition of a haplotype block is difficult to achieve, but collecting haplotypes covered with a high density of SNPs, partitioning them with a variety of block algorithms, and identifying regions common to all methods may be the best way to identify genomic regions that harbor SNP variants that cause disease.Single Nucleotide Polymorphisms (SNPs) are single base pair differences between individuals in a population. The recent completion of the Human Genome Project has helped facilitate the discovery of millions of SNPs and their use in genetic association studies for human disease [1]. Association studies work on the premise that SNP genotypes are correlated with a disease phenotype. Individual SNPs are genotyped and the frequency of alleles are compared between groups of affected and un-affected individuals. SNPs that are tested for association either must be the causative allele or be in linkage disequilibrium (LD) with the causative allele. LD is the non-random association of alleles between adjacent loci [2]. SNPs that are in LD with causative allele serve as a proxy and the association with the disease phenotype is maintained.Numerous studies have
%U http://www.biomedcentral.com/1471-2105/6/303