Detection of candidate tumor driver genes using a fully integrated Bayesian approach

Jichen Yang, Xinlei Wang, Minsoo Kim, Yang Xie, Guanghua Xiao

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

DNA copy number alterations (CNAs), including amplifications and deletions, can result in significant changes in gene expression and are closely related to the development and progression of many diseases, especially cancer. For example, CNA-associated expression changes in certain genes (called candidate tumor driver genes) can alter the expression levels of many downstream genes through transcription regulation and cause cancer. Identification of such candidate tumor driver genes leads to discovery of novel therapeutic targets for personalized treatment of cancers. Several approaches have been developed for this purpose by using both copy number and gene expression data. In this study, we propose a Bayesian approach to identify candidate tumor driver genes, in which the copy number and gene expression data are modeled together, and the dependency between the two data types is modeled through conditional probabilities. The proposed joint modeling approach can identify CNA and differentially expressed genes simultaneously, leading to improved detection of candidate tumor driver genes and comprehensive understanding of underlying biological processes. We evaluated the proposed method in simulation studies, and then applied to a head and neck squamous cell carcinoma data set. Both simulation studies and data application show that the joint modeling approach can significantly improve the performance in identifying candidate tumor driver genes, when compared with other existing approaches.

Original languageEnglish (US)
Pages (from-to)1784-1800
Number of pages17
JournalStatistics in Medicine
Volume33
Issue number10
DOIs
StatePublished - May 10 2014

Fingerprint

Bayes Theorem
Bayesian Approach
Driver
Tumor
Gene
Genes
Neoplasms
Joint Modeling
Cancer
Gene Expression Data
Gene Expression
Joints
Simulation Study
Biological Phenomena
Conditional probability
Progression
Amplification
Transcription
Deletion
Disease Progression

Keywords

  • Bayesian joint modeling
  • Hidden Markov model
  • Integrative analysis

ASJC Scopus subject areas

  • Epidemiology
  • Statistics and Probability
  • Medicine(all)

Cite this

Detection of candidate tumor driver genes using a fully integrated Bayesian approach. / Yang, Jichen; Wang, Xinlei; Kim, Minsoo; Xie, Yang; Xiao, Guanghua.

In: Statistics in Medicine, Vol. 33, No. 10, 10.05.2014, p. 1784-1800.

Research output: Contribution to journalArticle

Yang, Jichen ; Wang, Xinlei ; Kim, Minsoo ; Xie, Yang ; Xiao, Guanghua. / Detection of candidate tumor driver genes using a fully integrated Bayesian approach. In: Statistics in Medicine. 2014 ; Vol. 33, No. 10. pp. 1784-1800.
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