A Refined and Heuristic Algorithm for LD tagSNPs Selection

Author

Chen, Hailin ; Zhang, Zuping ; Xia, Jing

Author_Institution

Sch. of Inf. Sci. & Eng., Central South Univ., Changsha, China

fYear

2011

fDate

16-18 Nov. 2011

Firstpage

1691

Lastpage

1694

Abstract

Single Nucleotide Polymorphisms (SNPs) play an important role in Genome-wide Association Studies. To reduce genotyping costs, several LD tagSNPs selection algorithms have been proposed. In this paper, the advantages and disadvantages of current LD tagSNPs selection algorithms are analyzed. And a refined and heuristic algorithm HTag for LD tagSNPs selection is developed: (1) The tagSNPs selection procedure of Xu et al. is modified to improve selection performance. (2) A strategy to optimize the selection result is proposed. Using data downloaded from the HapMap Project, the performance of these methods is evaluated and our algorithm shows improvements in tagging efficiency.

Keywords

biology computing; genomics; greedy algorithms; HapMap Project; LD tagSNP selection algorithm; genome-wide association studies; heuristic algorithm HTag; single nucleotide polymorphisms; Algorithm design and analysis; Bioinformatics; Couplings; Educational institutions; Genomics; Greedy algorithms; Partitioning algorithms; LD; SNPs; tagSNPs selection;

fLanguage

English

Publisher

ieee

Conference_Titel

Trust, Security and Privacy in Computing and Communications (TrustCom), 2011 IEEE 10th International Conference on

Conference_Location

Changsha

Print_ISBN

978-1-4577-2135-9

Type

conf

DOI

10.1109/TrustCom.2011.234

Filename

6121031