Browse > Article
http://dx.doi.org/10.3745/KIPSTA.2006.13A.1.079

MarSel : LD based tagSNP Selection System for Large-scale SNP Haplotype Dataset  

Kim Sang-Jun (중앙대학교 컴퓨터공학부)
Yeo Sang-Soo (중앙대학교 컴퓨터공학부)
Kim Sung-Kwon (중앙대학교 컴퓨터공학부)
Publication Information
The KIPS Transactions:PartA / v.13A, no.1, 2006 , pp. 79-86 More about this Journal
Abstract
Recently the tagSNP selection problem has been researched for reducing the cost of association studies between human's diversities and SNPs. General approach for this problem is that all of SNPs are separated into appropriate blocks and then tagSNPs are chosen in each block. Marsel in this paper is the system that involved the concept of linkage disequilibrium for overcoming the problem that the existing block partitioning approaches have short of biological meanings. In most approaches, the contiguous regions, which recombinations have LD coefficient |D'| and then tagSNP selection step is performed. And MarSel guarantees the minimum tagSNP selection using entropy-based optimal selection algorithm when tagSNPs are chosen in each block, and enables chromosome-level association studies using efficient memory management technique when input is very large-scale dataset that is impossible to be processed in the existing systems.
Keywords
SNP; Dynamic Programming; Haplotype; tagSNP Selection; Linkage Disequilibrium;
Citations & Related Records
연도 인용수 순위
  • Reference
1 N. Patil, A. J. Berno, D. A. Hinds, W. A. Barrett, J. M. Doshi, C. R. Hacker, C. R. Kautzer, D. H. Lee, C. Marjoribanks, D. P. McDonough, B. T. N. Nguyen, M. C. Norris, J. B. Sheehan, N. Shen, D. Stern, R. P. Stokowski, D. J Thomas, M. O. Trulson, K. R. Vyas, K. A. Frazer, S. P. A. Fodor, D. R. Cox, 'Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21,' Science, Vol.294, pp.1719-1723, 2001   DOI   ScienceOn
2 K. Zhang, M. Deng, T. Chen, M. S. Waterman and F. Sun, 'A Dynamic Programming Algorithm For Haplotype Block Partitioning,' Proceedings of the National Academy of Sciences (PNAS), Vol.99, No.11, pp.7335-7339, 2002   DOI   ScienceOn
3 M. J. Daly, J. D. Rioux, S. F. Schaffner, T. J. Hudson and E. S. Lander, 'High-Resolution Haplotype Structure in the Human Genome,' Nature Genetics, Vol.29, No.2, pp.151-158, 2001
4 K. Zhang and L. Jin, 'HaploBlockFinder: Haplotype Block Analyses,' Bioinformatics, Vol.19, No.10, pp.1300-1301, 2003   DOI   ScienceOn
5 J. I. Bell, 'Single Nucleotide Polymorphisms and Disease Gene Mapping,' Arthritis Research, Vol.4, pp.s273-s278, 2002   DOI
6 K. Zhang, Z. Qin, T. Chen, J. S.. Liu, M. S. Waterman and F. Sun, 'HapBlock: Haplotype Block Partitioning and Tag SNP Selection Software using a Set of Dynamic Programming Algorithms,' Bioinformatics, Vol.21(1), pp.131-134, 2003   DOI   ScienceOn
7 R. Mott, 'Marker Selection by Maximum Entropy,' http://www.well.ox.ac.uk/~rmott/SNPS, Wellcome Trust Centre for Human Genetics, University of Oxford, 2003
8 R. C. Lewontin, 'The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models,' Genetics, Vol.49, pp.49-67, 1964