title: A novel kernel for correcting size bias in the logistic kernel machine test with an application to rheumatoid arthritis.
abstract: OBJECTIVE
  The logistic kernel machine test (LKMT) is a testing procedure tailored towards high-dimensional genetic data. Its use in pathway analyses of case-control genome-wide association studies results from its computational efficiency and flexibility in incorporating additional information via the kernel. The kernel can be any positive definite function; unfortunately, its form strongly influences the test's power and bias. Most authors have recommended the use of a simple linear kernel. We demonstrate via a simulation that the probability of rejecting the null hypothesis of no association just by chance increases with the number of SNPs or genes in the pathway when applying a simple linear kernel.
  
  
  METHODS
  We propose a novel kernel that includes an appropriate standardization in order to protect against any inflation of false positive results. Moreover, our novel kernel contains information on gene membership of SNPs in the pathway.
  
  
  RESULTS
  When applying the novel kernel to data from the North American Rheumatoid Arthritis Consortium, we find that even this basic genomic structure can improve the ability of the LKMT to identify meaningful associations. We also demonstrate that the standardization effectively eliminates problems of size bias.
  
  
  CONCLUSIONS
  We recommend the use of our standardized kernel and urge caution when using non-adjusted kernels in the LKMT to conduct pathway analyses.
authors: Department of Genetic Epidemiology, Medical School, Georg-August University Göttingen, Göttingen, Germany. saskia.freytag@med.uni-goettingen.de
authors: Saskia
authors: S
authors: Freytag
authors: Heike
authors: H
authors: Bickeböller
authors: Christopher I
authors: CI
authors: Amos
authors: Thomas
authors: T
authors: Kneib
authors: Martin
authors: M
authors: Schlather
mesh_terms: D001172:Arthritis, Rheumatoid / Q000453:epidemiology / Q000235:genetics*; D015982:Bias; D003198:Computer Simulation; D005796:Genes; D055106:Genome-Wide Association Study; D006801:Humans; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D018401:Sample Size