Bayesian Mixture Models for Assessment of Gene Differential Behaviour and Prediction of pCR through the Integration of Copy Number and Gene Expression Data

Filippo Trentini, Yuan Ji, Takayuki Iwamoto, Yuan Qi, Lajos Pusztai, Peter Müller

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

We consider modeling jointly microarray RNA expression and DNA copy number data. We propose Bayesian mixture models that define latent Gaussian probit scores for the DNA and RNA, and integrate between the two platforms via a regression of the RNA probit scores on the DNA probit scores. Such a regression conveniently allows us to include additional sample specific covariates such as biological conditions and clinical outcomes. The two developed methods are aimed respectively to make inference on differential behaviour of genes in patients showing different subtypes of breast cancer and to predict the pathological complete response (pCR) of patients borrowing strength across the genomic platforms. Posterior inference is carried out via MCMC simulations. We demonstrate the proposed methodology using a published data set consisting of 121 breast cancer patients.

Original languageEnglish
Article numbere68071
JournalPLoS One
Volume8
Issue number7
DOIs
Publication statusPublished - Jul 12 2013

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Gene expression
Genes
RNA
Gene Expression
breast neoplasms
gene expression
prediction
DNA
Breast Neoplasms
genes
Microarrays
genomics
methodology
sampling

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Bayesian Mixture Models for Assessment of Gene Differential Behaviour and Prediction of pCR through the Integration of Copy Number and Gene Expression Data. / Trentini, Filippo; Ji, Yuan; Iwamoto, Takayuki; Qi, Yuan; Pusztai, Lajos; Müller, Peter.

In: PLoS One, Vol. 8, No. 7, e68071, 12.07.2013.

Research output: Contribution to journalArticle

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