Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan.
Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
Bioinformatics. 2018 Jul 1;34(13):2228-2236. doi: 10.1093/bioinformatics/bty076.
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 implementation: MOMDR is freely available at https://goo.gl/M8dpDg.
Supplementary data are available at Bioinformatics online.
单核苷酸多态性 (SNP)-SNP 相互作用 (SSI) 是理解疾病易感性的流行标志物。多因子降维 (MDR) 可成功检测到大量 SSI。目前，基于 MDR 的方法主要采用单目标函数（基于列联表的单一度量）来检测 SSI。然而，由于潜在的模型偏好和疾病复杂性，单一度量函数可能无法产生有利的结果。
本研究提出了一种基于 MDR 列联表的多目标 MDR（MOMDR）方法作为目标函数。MOMDR 考虑了包含的度量标准，包括正确分类和似然率，以检测 SSI，并采用集合理论通过交叉验证一致性预测最有利的 SSI。MOMDR 能够同时使用多个度量标准来确定潜在的 SSI。
进行了三项模拟研究，以比较 MOMDR 和单目标 MDR（SOMDR）的检测成功率，结果表明 MOMDR 的检测成功率高于 SOMDR。此外，还通过 MOMDR 对与冠心病相关的 SSI 进行了 Wellcome Trust Case Control Consortium 数据集的分析。
MOMDR 可在 https://goo.gl/M8dpDg 上免费获得。
补充数据可在生物信息学在线获得。
