article

Searching high-order SNP combinations for complex diseases based on energy distribution difference

Editor: Ying Xu Authors:

Alex Zelikovsky,

Yi PanAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 12, Issue 3

Pages 695 - 704

https://doi.org/10.1109/TCBB.2014.2363459

Published: 01 May 2015 Publication History

Abstract

Single nucleotide polymorphisms, a dominant type of genetic variants, have been used successfully to identify defective genes causing human single gene diseases. However, most common human diseases are complex diseases and caused by gene-gene and gene-environment interactions. Many SNP-SNP interaction analysis methods have been introduced but they are not powerful enough to discover interactions more than three SNPs. The paper proposes a novel method that analyzes all SNPs simultaneously. Different from existing methods, the method regards an individual's genotype data on a list of SNPs as a point with a unit of energy in a multi-dimensional space, and tries to find a new coordinate system where the energy distribution difference between cases and controls reaches the maximum. The method will find different multiple SNPs combinatorial patterns between cases and controls based on the new coordinate system. The experiment on simulated data shows that the method is efficient. The tests on the real data of age-related macular degeneration (AMD) disease show that it can find out more significant multi-SNP combinatorial patterns than existing methods.

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Cited By

Sergeev RKavaliou ISataneuski UGabrielian ARosenthal ATartakovsky MTuzikov A(2019)Genome-Wide Analysis of MDR and XDR Tuberculosis from BelarusIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2017.272066916:4(1398-1408)Online publication date: 1-Jul-2019
https://dl.acm.org/doi/10.1109/TCBB.2017.2720669
Li SShang JChen QSun YLiu J(2016)A compressed sensing based two-stage method for detecting epistatic interactionsInternational Journal of Data Mining and Bioinformatics10.1504/IJDMB.2016.07582114:4(354-372)Online publication date: 1-Apr-2016
https://dl.acm.org/doi/10.1504/IJDMB.2016.075821

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Searching high-order SNP combinations for complex diseases based on energy distribution difference

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IEEE Computer Society Press

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Publication History

Published: 01 May 2015

Accepted: 06 October 2014

Revised: 31 August 2014

Received: 14 May 2014

Published in TCBB Volume 12, Issue 3

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Cited By

Sergeev RKavaliou ISataneuski UGabrielian ARosenthal ATartakovsky MTuzikov A(2019)Genome-Wide Analysis of MDR and XDR Tuberculosis from BelarusIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2017.272066916:4(1398-1408)Online publication date: 1-Jul-2019
https://dl.acm.org/doi/10.1109/TCBB.2017.2720669
Li SShang JChen QSun YLiu J(2016)A compressed sensing based two-stage method for detecting epistatic interactionsInternational Journal of Data Mining and Bioinformatics10.1504/IJDMB.2016.07582114:4(354-372)Online publication date: 1-Apr-2016
https://dl.acm.org/doi/10.1504/IJDMB.2016.075821

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