Gene-Gene Interaction Analysis for the Survival Phenotype Based on the Kaplan-Meier Median Estimate
Open Access
- 9 May 2020
- journal article
- research article
- Published by Hindawi Limited in BioMed Research International
- Vol. 2020, 1-10
- https://doi.org/10.1155/2020/5282345
Abstract
In this study, we propose a simple and computationally efficient method based on the multifactor dimensional reduction algorithm to identify gene-gene interactions associated with the survival phenotype. The proposed method, referred to as KM-MDR, uses the Kaplan-Meier median survival time as a classifier. The KM-MDR method classifies multilocus genotypes into a binary attribute for high- or low-risk groups using median survival time and replaces balanced accuracy with log-rank test statistics as a score to determine the best model. Through intensive simulation studies, we compared the power of KM-MDR with that of Surv-MDR, Cox-MDR, and AFT-MDR. It was found that KM-MDR has a similar power to that of Surv-MDR, with less computing time, and has comparable power to that of Cox-MDR and AFT-MDR, even when there is a covariate effect. Furthermore, we apply KM-MDR to a real dataset of ovarian cancer patients from The Cancer Genome Atlas (TCGA).Funding Information
- Ministry of Health and Welfare (2016R1D1A1B03934908, 2017R1A2B4011504, HI16C2037)
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