Analysis of case–control association studies with known risk variants

Noah Zaitlen, Bogdan Paşaniuc, Nick Patterson, Samuela Pollack, Benjamin Voight, Leif Groop, David Altshuler, Brian E. Henderson, Laurence N. Kolonel, Loic Le Marchand, Kevin Waters, Christopher A. Haiman (+4 others)
2012 Computer applications in the biosciences : CABIOS  
Motivation: 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 Pvalue 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
more » ... , 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. Results: We show via simulation and application to empirical datasets that our approach outperforms both the no conditioning strategy and the standard conditioning strategy, with a properly controlled false-positive rate. Furthermore, in multiple data sets involving diseases of low prevalence, standard conditioning produces a severe drop in test statistics whereas our approach generally performs as well or better than no conditioning. Our approach may substantially improve disease gene discovery for diseases with many known risk variants. Availability: LTSOFT software is available online
doi:10.1093/bioinformatics/bts259 pmid:22556366 pmcid:PMC3381970 fatcat:5seuhk64lvgbxbf24bpgnnj2la