Multiobjective multifactor dimensionality reduction to detect SNP-SNP interactions

Bioinformatics
Cheng-Hong YangYu-Da Lin

Abstract

Single-nucleotide polymorphism (SNP)-SNP interactions (SSIs) are popular markers for understanding disease susceptibility. Multifactor dimensionality reduction (MDR) can successfully detect considerable SSIs. Currently, MDR-based methods mainly adopt a single-objective function (a single measure based on contingency tables) to detect SSIs. However, generally, a single-measure function might not yield favorable results due to potential model preferences and disease complexities. This study proposes a multiobjective MDR (MOMDR) method that is based on a contingency table of MDR as an objective function. MOMDR considers the incorporated measures, including correct classification and likelihood rates, to detect SSIs and adopts set theory to predict the most favorable SSIs with cross-validation consistency. MOMDR enables simultaneously using multiple measures to determine potential SSIs. Three simulation studies were conducted to compare the detection success rates of MOMDR and single-objective MDR (SOMDR), revealing that MOMDR had higher detection success rates than SOMDR. Furthermore, the Wellcome Trust Case Control Consortium dataset was analyzed by MOMDR to detect SSIs associated with coronary artery disease. Availability and im...Continue Reading

References

Jun 8, 2007·Nature·UNKNOWN Wellcome Trust Case Control Consortium
Jan 8, 2010·Bioinformatics·Jason H MooreScott M Williams
Mar 29, 2011·Briefings in Bioinformatics·Kristel Van Steen
Oct 7, 2011·Annals of Human Genetics·Adan NiuQiuying Sha
Sep 11, 2012·Bioinformatics·Seungyeoun LeeTaesung Park
Nov 26, 2013·Briefings in Bioinformatics·Jiahan LiRongling Wu
Jul 18, 2014·Genome Medicine·Trudy Fc Mackay, Jason H Moore
Jun 26, 2015·Briefings in Bioinformatics·Damian GolaInke R König

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Citations

Apr 11, 2020·BMC Bioinformatics·Christian Ponte-FernándezMaría J Martín
Sep 24, 2021·Methods : a Companion to Methods in Enzymology·Xin WangMaozu Guo

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