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Statistics in Biosciences

, Volume 7, Issue 2, pp 262–281 | Cite as

An Adaptive Genetic Association Test Using Double Kernel Machines

  • Xiang ZhanEmail author
  • Michael P. Epstein
  • Debashis Ghosh
Article

Abstract

Recently, gene set-based approaches have become very popular in gene expression profiling studies for assessing how genetic variants are related to disease outcomes. Since most genes are not differentially expressed, existing pathway tests considering all genes within a pathway suffer from considerable noise and power loss. Moreover, for a differentially expressed pathway, it is of interest to select important genes that drive the effect of the pathway. In this article, we propose an adaptive association test using double kernel machines (DKM), which can both select important genes within the pathway as well as test for the overall genetic pathway effect. This DKM procedure first uses the garrote kernel machines test for the purposes of subset selection and then the least squares kernel machine test for testing the effect of the subset of genes. An appealing feature of the kernel machine framework is that it can provide a flexible and unified method for multi-dimensional modeling of the genetic pathway effect allowing for both parametric and nonparametric components. This DKM approach is illustrated with application to simulated data as well as to data from a neuroimaging genetics study.

Keywords

Double kernel machine Garrote kernel machine Least squares kernel machine Subset testing Thresholding 

Notes

Acknowledgments

This research was supported by NIH grants CA129102. The authors thank the reviewers for helpful comments.

Conflict of interest

The authors declare that they have no conflict of interest.

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Copyright information

© International Chinese Statistical Association 2014

Authors and Affiliations

  • Xiang Zhan
    • 1
    Email author
  • Michael P. Epstein
    • 3
  • Debashis Ghosh
    • 1
    • 2
  1. 1.Department of StatisticsPennsylvania State UniversityUniversity ParkUSA
  2. 2.Department of Public Health SciencesPennsylvania State UniversityUniversity ParkUSA
  3. 3.Department of Human GeneticsEmory UniversityAtlantaUSA

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