Research on single nucleotide polymorphisms interaction detection from network perspective

PloS One
Lingtao SuLun Yan

Abstract

Single Nucleotide Polymorphisms (SNPs) found in Genome-Wide Association Study (GWAS) mainly influence the susceptibility of complex diseases, but they still could not comprehensively explain the relationships between mutations and diseases. Interactions between SNPs are considered so important for deeply understanding of those relationships that several strategies have been proposed to explore such interactions. However, part of those methods perform poorly when marginal effects of disease loci are weak or absent, others may lack of considering high-order SNPs interactions, few methods have achieved the requirements in both performance and accuracy. Considering the above reasons, not only low-order, but also high-order SNP interactions as well as main-effect SNPs, should be taken into account in detection methods under an acceptable computational complexity. In this paper, a new pairwise (or low-order) interaction detection method IG (Interaction Gain) is introduced, in which disease models are not required and parallel computing is utilized. Furthermore, high-order SNP interactions were proposed to be detected by finding closely connected function modules of the network constructed from IG detection results. Tested by a wide r...Continue Reading

References

Jan 15, 2003·BMC Bioinformatics·Gary D Bader, Christopher W V Hogue
Nov 5, 2004·Expert Review of Molecular Diagnostics·Jason H Moore
Nov 9, 2004·Genetic Epidemiology·Charles Kooperberg, Ingo Ruczinski
Jun 17, 2005·Nature·Caitlin Smith
Mar 29, 2006·Radiology·Yuan-Ya LiaoYu-Min Lin
May 5, 2006·BMC Cancer·Venüs Ummiye OnayHilmi Ozcelik
Jun 8, 2007·Nature·UNKNOWN Wellcome Trust Case Control Consortium
Nov 1, 2008·Bioinformatics·Andrew D JohnsonPaul I W de Bakker
Jan 30, 2009·Bioinformatics·Tong Tong WuKenneth Lange
May 14, 2009·Bioinformatics·Guimei LiuHon Nian Chua
Dec 17, 2009·Nature Biotechnology·William S Noble
Jan 8, 2010·Bioinformatics·Jason H MooreScott M Williams
Mar 27, 2010·Rheumatology International·Monica SinghTaranpal Kaur
Sep 8, 2010·American Journal of Human Genetics·Xiang WanWeichuan Yu
May 18, 2011·Nucleic Acids Research·Tomaz CurkBlaz Zupan
Jul 17, 2012·BMC Bioinformatics·Stacey J WinhamJoanna M Biernacka
Feb 16, 2013·Journal of Clinical Bioinformatics·Li-Yeh ChuangCheng-Hong Yang
Apr 23, 2013·Journal of Bioinformatics and Computational Biology·Sriganesh Srihari, Hon Wai Leong
Jun 24, 2014·Seminars in Cell & Developmental Biology·Siobhan S Mc MahonMichael P H Stumpf

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Citations

Oct 23, 2016·Briefings in Bioinformatics·Paola G Ferrario, Inke R König
Apr 9, 2021·BMC Bioinformatics·James M Kunert-GrafDavid J Galas

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Software Mentioned

Forest
Random
BOOST
RandomForest
MCODE
IG SNPsyn
IG
PLINK
SNPsyn

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