title: Cloud computing-based TagSNP selection algorithm for human genome data.
abstract: Single nucleotide polymorphisms (SNPs) play a fundamental role in human genetic variation and are used in medical diagnostics, phylogeny construction, and drug design. They provide the highest-resolution genetic fingerprint for identifying disease associations and human features. Haplotypes are regions of linked genetic variants that are closely spaced on the genome and tend to be inherited together. Genetics research has revealed SNPs within certain haplotype blocks that introduce few distinct common haplotypes into most of the population. Haplotype block structures are used in association-based methods to map disease genes. In this paper, we propose an efficient algorithm for identifying haplotype blocks in the genome. In chromosomal haplotype data retrieved from the HapMap project website, the proposed algorithm identified longer haplotype blocks than an existing algorithm. To enhance its performance, we extended the proposed algorithm into a parallel algorithm that copies data in parallel via the Hadoop MapReduce framework. The proposed MapReduce-paralleled combinatorial algorithm performed well on real-world data obtained from the HapMap dataset; the improvement in computational efficiency was proportional to the number of processors used.
authors.affiliation: Department of Computer Science and Communication Engineering, Providence University, Taichung 43301, Taiwan. clhung@pu.edu.tw.
authors.forename: Che-Lun
authors.initials: CL
authors.lastname: Hung
authors.affiliation: Department of Applied Chemistry, Providence University, Taiwan 43301, Taiwan. g1016008@pu.edu.tw.
authors.forename: Wen-Pei
authors.initials: WP
authors.lastname: Chen
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan. gt758215@gmail.com.
authors.forename: Guan-Jie
authors.initials: GJ
authors.lastname: Hua
authors.affiliation: School of Computing and Mathematics, University of Ulster, Newtownabbey BT37 0QB, UK. h.zheng@ulster.ac.uk.
authors.forename: Huiru
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Department of Applied Chemistry, Providence University, Taiwan 43301, Taiwan. sjtsai@pu.edu.tw.
authors.forename: Suh-Jen Jane
authors.initials: SJ
authors.lastname: Tsai
authors.affiliation: Department of Applied Chemistry, Providence University, Taiwan 43301, Taiwan. yllin@pu.edu.tw.
authors.forename: Yaw-Ling
authors.initials: YL
authors.lastname: Lin
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide