A comparison of case-only designs for detecting gene × gene interaction in rheumatoid arthritis using genome-wide case-control data in Genetic Analysis Workshop 16Report as inadecuate




A comparison of case-only designs for detecting gene × gene interaction in rheumatoid arthritis using genome-wide case-control data in Genetic Analysis Workshop 16 - Download this document for free, or read online. Document in PDF available to download.

BMC Proceedings

, 3:S73

First Online: 15 December 2009DOI: 10.1186-1753-6561-3-S7-S73

Cite this article as: Clarke, G.M., Pettersson, F.H. & Morris, A.P. BMC Proc 2009 3Suppl 7: S73. doi:10.1186-1753-6561-3-S7-S73

Abstract

We compare and contrast case-only designs for detecting gene × gene G × G interaction in rheumatoid arthritis RA using the genome-wide data provided by Genetic Analysis Workshop 16 Problem 1. Logistic as well as novel multinomial and proportional odds models that do not depend on the specification of additive or dominant models for susceptibility loci were applied to the case-only sample. We identified 519 significant interactions p < 1 × 10 in at least one test. All methods detected unique significant interactions; 169 were common to more than one model and only 21 were common to all models. Results emphasize that categorization of the genetic variables and choice of regression model are critical and hugely influential in the identification of G × G. Porportional odds and multinomial methods provide new tools for identification of G × G interactions.

List of abbreviations usedG × GGene × gene

GAW16Genetic Analysis Workshop 16

LRLikelihood ratio

MAFMinor-allele frequency

RARheumatoid arthritis

SNPSingle-nucleotide polymorphism

Download fulltext PDF



Author: Geraldine M Clarke - Fredrik H Pettersson - Andrew P Morris

Source: https://link.springer.com/



DOWNLOAD PDF




Related documents