A novel efficient dynamic programming algorithm for haplotype block partitioning.

In this paper, a new efficient algorithm is presented for haplotype block partitioning based on haplotype diversity. In this algorithm, finding the largest meaningful block that satisfies the diversity condition is the main goal as an optimization problem. The algorithm can be performed in polynomial time complexity with regard to the number of haplotypes and SNPs. We apply our algorithm on three biological data sets from chromosome 21 in three different population data sets from HapMap data bulk; the obtained results show the efficiency and better performance of our algorithm in comparison with three other well known methods.

[1]  Lon R. Cardon,et al.  A first-generation linkage disequilibrium map of human chromosome 22 , 2002, Nature.

[2]  Ting Chen,et al.  Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. , 2004, Genome research.

[3]  M. Daly,et al.  High-resolution haplotype structure in the human genome , 2001, Nature Genetics.

[4]  D Saur,et al.  A neuronal nitric oxide synthase (NOS-I) haplotype associated with schizophrenia modifies prefrontal cortex function , 2006, Molecular Psychiatry.

[5]  Fengzhu Sun,et al.  Haplotype block structure and its applications to association studies: power and study designs. , 2002, American journal of human genetics.

[6]  Kui Zhang,et al.  Hapblock: Haplotype Block Partitioning and Tag Snp Selection Software Using a Set of Dynamic Programming Algorithms , 2022 .

[7]  R. Hudson,et al.  Statistical properties of the number of recombination events in the history of a sample of DNA sequences. , 1985, Genetics.

[8]  Dan Geiger,et al.  High density linkage disequilibrium mapping using models of haplotype block variation , 2004, ISMB/ECCB.

[9]  A. Goate,et al.  SNP analysis to dissect human traits , 2001, Current Opinion in Neurobiology.

[10]  E. Urcelay,et al.  DRB1-TNF-α-TNF-β Haplotype is Strongly Associated With Severe Aortoiliac Occlusive Disease, A Clinical Form of Atherosclerosis , 2005 .

[11]  Peter J. Tonellato,et al.  Analysis of concordance of different haplotype block partitioning algorithms , 2005, BMC Bioinformatics.

[12]  S. Gabriel,et al.  The Structure of Haplotype Blocks in the Human Genome , 2002, Science.

[13]  Javad Zahiri,et al.  Tag SNP selection via a genetic algorithm , 2010, J. Biomed. Informatics.

[14]  Frank Dudbridge,et al.  Haplotype tagging for the identification of common disease genes , 2001, Nature Genetics.

[15]  S. P. Fodor,et al.  Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21 , 2001, Science.

[16]  Yan Shen,et al.  htSNPer1.0: software for haplotype block partition and htSNPs selection , 2005, BMC Bioinformatics.

[17]  J. Akey,et al.  Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. , 2002, American journal of human genetics.

[18]  J. Wall,et al.  Assessing the performance of the haplotype block model of linkage disequilibrium. , 2003, American journal of human genetics.

[19]  I. Gray,et al.  Single nucleotide polymorphisms as tools in human genetics. , 2000, Human molecular genetics.

[20]  Marek Kimmel,et al.  Haplotype and linkage disequilibrium architecture for human cancer-associated genes. , 2002, Genome research.