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Bioinformatics Advance Access originally published online on July 20, 2007
Bioinformatics 2007 23(18):2470-2476; doi:10.1093/bioinformatics/btm364
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Analysis of array CGH data for cancer studies using fused quantile regression

Youjuan Li and Ji Zhu *

Department of Statistics, University of Michigan, Michigan, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: The identification of DNA copy number changes provides insights that may advance our understanding of initiation and progression of cancer. Array-based comparative genomic hybridization (array-CGH) has emerged as a technique allowing high-throughput genome-wide scanning for chromosomal aberrations. A number of statistical methods have been proposed for the analysis of array-CGH data. In this article, we consider a fused quantile regression model based on three motivations: (1) quantile regression may provide a more comprehensive picture for the ratio profile of copy numbers than the standard mean regression approach; (2) for simplicity, most available methods assume uniform spacing between neighboring clones, while incorporating the information of physical locations of clones may be helpful and (3) most current methods have a set of tuning parameters that must be carefully tuned, which introduces complexity to the implementation.

Results: We formulate the detection of regions of gains and losses in a fused regularized quantile regression framework, incorporating physical locations of clones. We derive an efficient algorithm that computes the entire solution path for the resulting optimization problem, and we propose a simple estimate for the complexity of the fitted model, which leads to convenient selection of the tuning parameter. Three published array-CGH datasets are used to demonstrate our approach.

Availability: R code are available at http://www.stat.lsa.umich.edu/~jizhu/code/cgh/

Contact: jizhu{at}umich.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Jonathan Wren

Received on March 25, 2007; revised on June 12, 2007; accepted on July 8, 2007

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