NDLI: A Hierarchical Clustering Method of Selecting Kernel SNP to Unify Informative SNP and Tag SNP

Content Provider	IEEE Xplore Digital Library
Author	Bo Liao Xiong Li Lijun Cai Zhi Cao Haowen Chen
Copyright Year	2004
Abstract	Various strategies can be used to select representative single nucleotide polymorphisms (SNPs) from a large number of SNPs, such as tag SNP for haplotype coverage and informative SNP for haplotype reconstruction, respectively. Representative SNPs are not only instrumental in reducing the cost of genotyping, but also serve an important function in narrowing the combinatorial space in epistasis analysis. The capacity of kernel SNPs to unify informative SNP and tag SNP is explored, and inconsistencies are minimized in further studies. The correlation between multiple SNPs is formalized using multi-information measures. In extending the correlation, a distance formula for measuring the similarity between clusters is first designed to conduct hierarchical clustering. Hierarchical clustering consists of both information gain and haplotype diversity, so that the proposed approach can achieve unification. The kernel SNPs are then selected from every cluster through the top rank or backward elimination scheme. Using these kernel SNPs, extensive experimental comparisons are conducted between informative SNPs on haplotype reconstruction accuracy and tag SNPs on haplotype coverage. Results indicate that the kernel SNP can practically unify informative SNP and tag SNP and is therefore adaptable to various applications.
Sponsorship	IEEE Computer Society
Starting Page	113
Ending Page	122
Page Count	10
File Size	826986
File Format	PDF
ISSN	15455963
Volume Number	12
Issue Number	1
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-01-01
Publisher Place	U.S.A.
Access Restriction	One Nation One Subscription (ONOS)
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Kernel Entropy Accuracy Computational complexity Bioinformatics Correlation support vector machine Tag SNP informative SNP clustering
Content Type	Text
Resource Type	Article
Subject	Applied Mathematics Genetics Biotechnology

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