JS-MA: A Jensen-Shannon Divergence Based Method for Mapping Genome-Wide Associations on Multiple Diseases

Frontiers in Genetics
Xuan Guo

Abstract

Taking advantage of the high-throughput genotyping technology of Single Nucleotide Polymorphism (SNP), Genome-Wide Association Studies (GWASs) have been successfully implemented for defining the relative role of genes and the environment in disease risk, assisting in enabling preventative and precision medicine. However, current multi-locus-based methods are insufficient in terms of computational cost and discrimination power to detect statistically significant interactions with different genetic effects on multifarious diseases. Statistical tests for multi-locus interactions (≥2 SNPs) raise huge analytical challenges because computational cost increases exponentially as the growth of the cardinality of SNPs in an interaction module. In this paper, we develop a simple, fast, and powerful method, named JS-MA, based on Jensen-Shannon divergence and agglomerative hierarchical clustering, to detect the genome-wide multi-locus interactions associated with multiple diseases. From the systematical simulation, JS-MA is more powerful and efficient compared with the state-of-the-art association mapping tools. JS-MA was applied to the real GWAS datasets for two common diseases, i.e., Rheumatoid Arthritis and Type 1 Diabetes. The results s...Continue Reading

References

Mar 29, 2005·Nature Genetics·Jonathan MarchiniLon R Cardon
Jun 8, 2007·Nature·UNKNOWN Wellcome Trust Case Control Consortium
Aug 28, 2007·Nature Genetics·Yu Zhang, Jun S Liu
May 21, 2008·International Journal of Bioinformatics Research and Applications·Jing Li
Apr 17, 2009·The New England Journal of Medicine·Peter Kraft, David J Hunter
May 13, 2009·Nature Reviews. Genetics·Heather J Cordell
Sep 8, 2010·American Journal of Human Genetics·Xiang WanWeichuan Yu
Nov 3, 2010·Bioinformatics·Qianchuan He, Dan-Yu Lin
Aug 7, 2012·BMC Research Notes·Yining WangGuohui Lin
Apr 23, 2013·Journal of Bioinformatics and Computational Biology·Hadi SabaaGuohui Lin
Oct 7, 2015·Frontiers in Genetics·Clément NielGhislain Rocheleau
Feb 18, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xuan GuoYi Pan
Jul 8, 2017·American Journal of Human Genetics·Peter M VisscherJian Yang

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Methods Mentioned

BETA
genotyping
dissection

Software Mentioned

AM
DAM
SNPRuler
BOOST
SEE
MA
JS

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