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Scientific article
Open access
English

Analysis of case-control association studies with known risk variants

Published inBioinformatics, vol. 28, no. 13, p. 1729-1737
Publication date2012
Abstract

The question of how to best use information from known associated variants when conducting disease association studies has yet to be answered. Some studies compute a marginal P-value for each Several Nucleotide Polymorphisms independently, ignoring previously discovered variants. Other studies include known variants as covariates in logistic regression, but a weakness of this standard conditioning strategy is that it does not account for disease prevalence and non-random ascertainment, which can induce a correlation structure between candidate variants and known associated variants even if the variants lie on different chromosomes. Here, we propose a new conditioning approach, which is based in part on the classical technique of liability threshold modeling. Roughly, this method estimates model parameters for each known variant while accounting for the published disease prevalence from the epidemiological literature.

Keywords
  • Case-Control Studies
  • Genetic Association Studies
  • Genome-Wide Association Study
  • Humans
  • Logistic Models
  • Models, Statistical
  • Polymorphism, Single Nucleotide
  • Prevalence
  • Risk
  • Software
Funding
  • Autre - Jeantet
Citation (ISO format)
ZAITLEN, Noah et al. Analysis of case-control association studies with known risk variants. In: Bioinformatics, 2012, vol. 28, n° 13, p. 1729–1737. doi: 10.1093/bioinformatics/bts259
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Article (Published version)
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Identifiers
ISSN of the journal1367-4803
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