A Tag SNP Selection Method Based on Haplotype Recognition

被引：0
|
作者：
Li, Xuedong [1 ,2 ]
Cao, Zhi [1 ]
Li, Xiong [1 ]
Chen, Juan [1 ]
Li, Gangcheng [2 ]
机构：
[1] Hunan Univ, Coll Informat Sci & Engn, Changsha 410082, Hunan, Peoples R China
[2] Hunan Coll Informat, Dept Informat Engn, Wang Cheng 410200, Hunan, Peoples R China
来源：
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE | 2014年 / 11卷 / 12期
基金：
国家教育部博士点专项基金资助;
关键词：
Single Nucleotide Polymorphism; Tag SNPs; Ant Colony Algorithm; Haplotype Recognition; GENE SELECTION; ALGORITHM;
D O I：
10.1166/jctn.2014.3667
中图分类号：
O6 [化学];
学科分类号：
0703 ;
摘要：
In association study based on Haplotype, some methods use a small amount of SNP to capture most variations of different samples' haplotypes which are known as Tag SNPs. Currently, there are many methods for tag SNP selection. However, these methods still exist deficiencies, mainly in these aspects: high time complexity and high compactness degree of tag SNP subsets which will lead to high cost in the following genetic association. In order to improve the efficiency of search space and attain the smallest number of tag SNPs, this paper not only designs the ant colony algorithm for path selection operator but also improves the heuristic function to seek the best combination of tag SNP subsets. The experimental results show that the method have certain advantages in the time complexity and compactness degree of tag SNP subsets.
引用
收藏
页码：2495 / 2498
页数：4
相关论文
共 50 条
  • [1] Fuzzy guided BPSO method for haplotype tag SNP selection
    Chuang, Li-Yeh
    Hou, Yu-Jen
    Yang, Cheng-Hong
    2009 IEEE INTERNATIONAL CONFERENCE ON FUZZY SYSTEMS, VOLS 1-3, 2009, : 1015 - +
  • [2] Haplotype block partitioning and tag SNP selection using genotype data.
    Zhang, K
    Qin, ZS
    Liu, JS
    Chen, T
    Waterman, MS
    Sun, F
    AMERICAN JOURNAL OF HUMAN GENETICS, 2003, 73 (05) : 422 - 422
  • [3] Dynamic programming algorithms for haplotype block partitioning and tag SNP selection using haplotype data or genotype data
    Zhang, K
    Chen, T
    Waterman, MS
    Qin, ZHS
    Liu, JS
    Sun, FZ
    COMPUTATIONAL METHODS FOR SNPS AND HAPLOTYPE INFERENCE, 2004, 2983 : 96 - 112
  • [4] Efficient Haplotype Block Partitioning and Tag SNP Selection Algorithms under Various Constraints
    Chen, Wen-Pei
    Hung, Che-Lun
    Lin, Yaw-Ling
    BIOMED RESEARCH INTERNATIONAL, 2013, 2013
  • [5] Tag SNP selection based on multivariate linear regression
    He, Jingwu
    Zelikovsky, Alex
    COMPUTATIONAL SCIENCE - ICCS 2006, PT 2, PROCEEDINGS, 2006, 3992 : 750 - 757
  • [6] Haplotype block partitioning and tag SNP selection using genotype data and their applications to associate studies
    Zhang, K
    Qin, ZHS
    Liu, JS
    Chen, T
    Waterman, MS
    Sun, FZ
    GENOME RESEARCH, 2004, 14 (05) : 908 - 916
  • [7] HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms
    Zhang, K
    Qin, ZH
    Chen, T
    Liu, JS
    Waterman, MS
    Sun, FZ
    BIOINFORMATICS, 2005, 21 (01) : 131 - 134
  • [8] Tag SNP selection for association studies
    Stram, DO
    GENETIC EPIDEMIOLOGY, 2004, 27 (04) : 365 - 374
  • [9] TAG SNP SELECTION USING CLONAL SELECTION ALGORITHM BASED ON SUPPORT VECTOR MACHINE
    Ilhan, Ilhan
    Goktepe, Yunus Emre
    Ozcan, Cengiz
    Kahramanli, Sirzat
    PROCEEDINGS OF THE 2011 3RD INTERNATIONAL CONFERENCE ON FUTURE COMPUTER AND COMMUNICATION (ICFCC 2011), 2011, : 47 - +
  • [10] Linear reduction methods for tag SNP selection
    He, JW
    Zelikovsky, A
    PROCEEDINGS OF THE 26TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-7, 2004, 26 : 2840 - 2843
12345