Comparative analysis of algorithms for LD tagSNPs selection in a single population

To reduce genotyping costs, tagSNPs selection has gained lots of research interest and several algorithms have been proposed for LD tagSNPs selection. However, there is little understanding of benefits and drawbacks underlying the proposed approaches. In this paper, we broadly analyzed the existing algorithms for LD tagSNPs selection in a single population. It can be concluded that the original greedy algorithm is easy to implement and TAGster refines the selection steps of the original greedy algorithm. Results suggested that HTag can receive the highest tagging efficiency. In addition, we found that the precinct partitioning strategy can dramatically reduce the runtime of TAGster and HTag. Theoretical analysis revealed that unstable numbers of tagSNPs may be received by these methods sometimes.

[1]  Gudmundur A. Thorisson,et al.  The International HapMap Project Web site. , 2005, Genome research.

[2]  Mariza de Andrade,et al.  High-resolution whole-genome association study of Parkinson disease. , 2005, American journal of human genetics.

[3]  D. Clayton,et al.  Genome-wide association studies: theoretical and practical concerns , 2005, Nature Reviews Genetics.

[4]  M. Daly,et al.  Genome-wide association studies for common diseases and complex traits , 2005, Nature Reviews Genetics.

[5]  Jack A. Taylor,et al.  TAGster: efficient selection of LD tag SNPs in single or multiple populations , 2007, Bioinform..

[6]  C. Carlson,et al.  Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. , 2004, American journal of human genetics.

[7]  Timothy B. Stockwell,et al.  The Diploid Genome Sequence of an Individual Human , 2007, PLoS biology.

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

[9]  Zhaohui S. Qin,et al.  Bioinformatics Original Paper an Efficient Comprehensive Search Algorithm for Tagsnp Selection Using Linkage Disequilibrium Criteria , 2022 .

[10]  The eMERGE Clinical Annotation Working Group.  A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms , 2001 .

[11]  Zuping Zhang,et al.  A Refined and Heuristic Algorithm for LD tagSNPs Selection , 2011, 2011IEEE 10th International Conference on Trust, Security and Privacy in Computing and Communications.

[12]  M. Olivier.  A haplotype map of the human genome. , 2003, Nature.

[13]  Toshihiro Tanaka.  The International HapMap Project , 2003, Nature.

[14]  J. Pritchard,et al.  Linkage disequilibrium in humans: models and data. , 2001, American journal of human genetics.