scholarly journals Tag SNP selection in genotype data for maximizing SNP prediction accuracy

2005 ◽  
Vol 21 (Suppl 1) ◽  
pp. i195-i203 ◽  
Author(s):  
E. Halperin ◽  
G. Kimmel ◽  
R. Shamir
Keyword(s):  
Prediction Accuracy ◽  
Genotype Data ◽  
Tag Snp ◽  
Tag Snp Selection

New multilocus linkage disequilibrium measure for tag SNP selection

2017 ◽  
Vol 15 (01) ◽  
pp. 1750001 ◽  
Author(s):  
Bo Liao ◽  
Xiangjun Wang ◽  
Wen Zhu ◽  
Xiong Li ◽  
Lijun Cai ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Prediction Accuracy ◽  
Single Nucleotide ◽  
Tag Snps ◽  
Tag Snp ◽  
Linkage Disequilibria ◽  
Linkage Disequilibrium Measure ◽  
Tag Snp Selection ◽  
The Cost ◽  
The Relationship

Numerous approaches have been proposed for selecting an optimal tag single-nucleotide polymorphism (SNP) set. Most of these approaches are based on linkage disequilibrium (LD). Classical LD measures, such as D′ and r2, are frequently used to quantify the relationship between two marker (pairwise) linkage disequilibria. Despite of their successful use in many applications, these measures cannot be used to measure the LD between multiple-marker. These LD measures need information about the frequencies of alleles collected from haplotype dataset. In this study, a cluster algorithm is proposed to cluster SNPs according to multilocus LD measure which is based on information theory. After that, tag SNPs are selected in each cluster optimized by the number of tag SNPs, prediction accuracy and so on. The experimental results show that this new LD measure can be directly applied to genotype dataset collected from the HapMap project, so that it saves the cost of haplotyping. More importantly, the proposed method significantly improves the efficiency and prediction accuracy of tag SNP selection.

scholarly journals Imputation-Aware Tag SNP Selection To Improve Power for Large-Scale, Multi-ethnic Association Studies

2018 ◽  
Vol 8 (10) ◽  
pp. 3255-3267 ◽  
Author(s):  
Genevieve L. Wojcik ◽  
Christian Fuchsberger ◽  
Daniel Taliun ◽  
Ryan Welch ◽  
Alicia R Martin ◽  
...  
Keyword(s):  
Large Scale ◽  
Association Studies ◽  
Tag Snp ◽  
Tag Snp Selection

scholarly journals Increasing the Power of Association Studies by Imputation-based Sparse Tag SNP Selection

2009 ◽  
Vol 9 (3) ◽  
pp. 269-282 ◽  
Author(s):  
Ofir Davidovich ◽  
Eran Halperin ◽  
Gad Kimmel ◽  
Ron Shamir
Keyword(s):  
Association Studies ◽  
Tag Snp ◽  
Tag Snp Selection

Tag SNP selection using clonal selection and majority voting algorithms

2016 ◽  
Vol 16 (4) ◽  
pp. 290
Author(s):  
N.A. �° ◽  
lhan �° ◽  
N.A. lhan ◽  
Gülay Tezel
Keyword(s):  
Clonal Selection ◽  
Majority Voting ◽  
Tag Snp ◽  
Tag Snp Selection

scholarly journals Efficient Association Study Design Via Power-Optimized Tag SNP Selection

2008 ◽  
Vol 72 (6) ◽  
pp. 834-847 ◽  
Author(s):  
B. Han ◽  
H. M. Kang ◽  
M. S. Seo ◽  
N. Zaitlen ◽  
E. Eskin
Keyword(s):  
Association Study ◽  
Study Design ◽  
Tag Snp ◽  
Tag Snp Selection
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