SNPHarvester

SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies. Motivation: Hundreds of thousands of single nucleotide polymorphisms (SNPs) are available for genome-wide association (GWA) studies nowadays. The epistatic interactions of SNPs are believed to be very important in determining individual susceptibility to complex diseases. However, existing methods for SNP interaction discovery either suffer from high computation complexity or perform poorly when marginal effects of disease loci are weak or absent. Hence, it is desirable to develop an effective method to search epistatic interactions in genome-wide scale. Results: We propose a new method SNPHarvester to detect SNP–SNP interactions in GWA studies. SNPHarvester creates multiple paths in which the visited SNP groups tend to be statistically associated with diseases, and then harvests those significant SNP groups which pass the statistical tests. It greatly reduces the number of SNPs. Consequently, existing tools can be directly used to detect epistatic interactions. By using a wide range of simulated data and a real genome-wide data, we demonstrate that SNPHarvester outperforms its recent competitor significantly and is promising for practical disease prognosis. Availability:http://bioinformatics.ust.hk/SNPHarvester.html


References in zbMATH (referenced in 6 articles )

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  1. Guan, Boxin; Zhao, Yuhai; Yin, Ying; Li, Yuan: A differential evolution based feature combination selection algorithm for high-dimensional data (2021)
  2. Wang, Lizhi; Nikouei Mehr, Maryam: An optimization approach to epistasis detection (2019)
  3. Wu, Jun; He, Zengyou; Gu, Feiyang; Liu, Xiaoqing; Zhou, Jianyu; Yang, Can: Computing exact permutation (p)-values for association rules (2016)
  4. Li, Jiahan; Zhong, Wei; Li, Runze; Wu, Rongling: A fast algorithm for detecting gene-gene interactions in genome-wide association studies (2014)
  5. Yang, Can; Wan, Xiang; Yang, Qiang; Xue, Hong; Yu, Weichuan: Identifying Main effects and epistatic interactions from large-scale SNP data via adaptive group lasso (2010) ioport
  6. Yang, Can; He, Zengyou; Wan, Xiang; Yang, Qiang; Xue, Hong; Yu, Weichuan: Snpharvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies (2009) ioport