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Gonzalez, J. R., Abellan, C., Abellan, J. J

Bayesian model to detect phenotype-specific genes for copy number data

BMC.Bioinformatics., 2012, 13, 1, , 30, PMID: 22694346

ABSTRACT: BACKGROUND: An important question in genetic studies is to determine those genetic variants, in particular CNVs, that arespecific to different groups of individuals. This could help in elucidating differences in disease predispositionand response to pharmaceutical treatments. We propose a Bayesian model designed to analyze thousands of copynumber variants (CNVs) where only few of them are expected to be associated with a specific phenotype. RESULTS: The model is illustrated by analyzing three major human groups belonging to HapMap data. We also show howthe model can be used to determine specific CNVs related to response to treatment in patients diagnosed withovarian cancer. The model is also extended to address the problem of how to adjust for confounding covariates(e.g., population stratification). Through a simulation study, we show that the proposed model outperforms otherapproaches that are typically used to analyze this data when analyzing common copy-number polymorphisms(CNPs) or complex CNVs. We have developed an R package, called bayesGen, that implements the model andestimating algorithms. CONCLUSIONS: Our proposed model is useful to discover specific genetic variants when different subgroups of individuals areanalyzed. The model can address studies with or without control group. By integrating all data in a unique modelwe can obtain a list of genes that are associated with a given phenotype as well as a different list of genes that areshared among the different subtypes of cases

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