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

Statistics in Medicine
Jichen YangGuanghua Xiao

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 ...Continue Reading

References

Jul 3, 1999·Nature Genetics·S TavazoieG M Church
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Sep 26, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jonathan R PollackPatrick O Brown
Jun 17, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew J AguirreLynda Chin
Oct 12, 2004·Biostatistics·Adam B OlshenMichael Wigler
Nov 9, 2004·Bioinformatics·Ole Christian LingjaerdeAnne-Lise Børresen-Dale
Dec 25, 2004·Biostatistics·Pei WangRobert Tibshirani
Sep 8, 2006·Nature·Janakiraman KrishnamurthyNorman E Sharpless
Feb 10, 2007·Science·Barbara E StrangerEmmanouil T Dermitzakis
May 16, 2008·Biometrics·Wessel N van Wieringen, Mark A van de Wiel
Apr 29, 2009·Biometrics·Stacia M DeSantisRebecca A Betensky
Jul 1, 2009·BMC Bioinformatics·Renée X MenezesJudith M Boer
Aug 4, 2009·Human Molecular Genetics·Luz D OrozcoAldons J Lusis
Feb 23, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hyungwon ChoiDebashis Ghosh
Dec 7, 2010·Cell·Uri David AkaviaDana Pe'er
Nov 23, 2011·Statistics in Medicine·Shuangge MaKuangnan Fang
Feb 14, 2012·Nature Methods·Riku LouhimoSampsa Hautaniemi
Jun 1, 2008·Journal of the American Statistical Association·Subharup GuhaDonna Neuberg
Aug 21, 2012·Cell·Deepak NijhawanWilliam C Hahn
Aug 21, 2012·Trends in Genetics : TIG·Koichiro Inaki, Edison T Liu
Mar 30, 2013·Science·Bert VogelsteinKenneth W Kinzler

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Citations

Nov 2, 2016·Nucleic Acids Research·Joakim Karlsson, Erik Larsson
Apr 1, 2016·Statistical Analysis and Data Mining·Binghui LiuWei Pan

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