A Hierarchical Bayesian Model for Inference of Copy Number Variants and Their Association To Gene Expression

Alberto Cassese*, Michele Guindani, Mahlet G Tadesse, Francesco Falciani, Marina Vannucci

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

A number of statistical models have been successfully developed for the analysis of high-throughput data from a single source, but few methods are available for integrating data from different sources. Here we focus on integrating gene expression levels with comparative genomic hybridization (CGH) array measurements collected on the same subjects. We specify a measurement error model that relates the gene expression levels to latent copy number states which, in turn, are related to the observed surrogate CGH measurements via a hidden Markov model. We employ selection priors that exploit the dependencies across adjacent copy number states and investigate MCMC stochastic search techniques for posterior inference. Our approach results in a unified modeling framework for simultaneously inferring copy number variants (CNV) and identifying their significant associations with mRNA transcripts abundance. We show performance on simulated data and illustrate an application to data from a genomic study on human cancer cell lines.
Original languageEnglish
Pages (from-to)148-175
Number of pages28
JournalAnnals of Applied Statistics
Volume8
Issue number1
DOIs
Publication statusPublished - 21 Sep 2014
Externally publishedYes

Keywords

  • Bayesian hierarchical models, comparative genomic
  • comparative genomic

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