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Genes 2018, 9(12), 608; https://doi.org/10.3390/genes9120608

Gene-Based Nonparametric Testing of Interactions Using Distance Correlation Coefficient in Case-Control Association Studies

1
School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China
2
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
3
Department of Mathematics, Rutgers University, Piscataway, NJ 08854, USA
4
Beijing Key Laboratory of Intelligent Processing for Building Big Data, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
*
Authors to whom correspondence should be addressed.
Received: 6 November 2018 / Revised: 24 November 2018 / Accepted: 27 November 2018 / Published: 5 December 2018
PDF [3190 KB, uploaded 5 December 2018]

Abstract

Among the various statistical methods for identifying gene–gene interactions in qualitative genome-wide association studies (GWAS), gene-based methods have recently grown in popularity because they confer advantages in both statistical power and biological interpretability. However, most of these methods make strong assumptions about the form of the relationship between traits and single-nucleotide polymorphisms, which result in limited statistical power. In this paper, we propose a gene-based method based on the distance correlation coefficient called gene-based gene-gene interaction via distance correlation coefficient (GBDcor). The distance correlation (dCor) is a measurement of the dependency between two random vectors with arbitrary, and not necessarily equal, dimensions. We used the difference in dCor in case and control datasets as an indicator of gene–gene interaction, which was based on the assumption that the joint distribution of two genes in case subjects and in control subjects should not be significantly different if the two genes do not interact. We designed a permutation-based statistical test to evaluate the difference between dCor in cases and controls for a pair of genes, and we provided the p-value for the statistic to represent the significance of the interaction between the two genes. In experiments with both simulated and real-world data, our method outperformed previous approaches in detecting interactions accurately.
Keywords: genome-wide association studies; qualitative trait; gene–gene interaction; distance correlation coefficient genome-wide association studies; qualitative trait; gene–gene interaction; distance correlation coefficient
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Guo, Y.; Wu, C.; Guo, M.; Liu, X.; Keinan, A. Gene-Based Nonparametric Testing of Interactions Using Distance Correlation Coefficient in Case-Control Association Studies. Genes 2018, 9, 608.

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