Analysis of case-control association studies with known risk variants

Zaitlen, Noah; Pasaniuc, Bogdan; Patterson, Nick; Pollack, Samuela; Voight, Benjamin; Groop, Leif; Altshuler, David; Henderson, Brian E; Kolonel, Laurence N; Le Marchand, Loic; Waters, Kevin; Haiman, Christopher A; Stranger, Barbara E; Dermitzakis, Emmanouil; Kraft, Peter; Price, Alkes L

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Title		Analysis of case-control association studies with known risk variants
Authors		Zaitlen, Noah Pasaniuc, Bogdan Patterson, Nick Pollack, Samuela Voight, Benjamin Groop, Leif Altshuler, David Henderson, Brian E Kolonel, Laurence N Le Marchand, Loic Waters, Kevin Haiman, Christopher A Stranger, Barbara E Dermitzakis, Emmanouil Kraft, Peter Price, Alkes L show all authors [1 - 16]
Published in		Bioinformatics. 2012, vol. 28, no. 13, p. 1729-37
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
Identifiers		DOI: 10.1093/bioinformatics/bts259 PMID: 22556366
Full text		Article (Published version) (322 Kb) - Free access
Structures		Faculté de médecine / Section de médecine fondamentale / Département de médecine génétique et développement
Research group		Population Genomics and Genetics of Complex Traits (892)
Project		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. 1729-37. https://archive-ouverte.unige.ch/unige:32170