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A TRANSCRIPTOME ANALYSIS BY LASSO PENALIZED COX REGRESSION FOR PANCREATIC CANCER SURVIVAL

TONG TONG WU

Department of Epidemiology and Biostatistics, University of Maryland, College Park, MD 20742, USA

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HAIJUN GONG

Computer Science Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA

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, and

EDMUND M. CLARKE

Computer Science Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA

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https://doi.org/10.1142/S0219720011005744Cited by:22 (Source: Crossref)

Abstract

Pancreatic cancer is the fourth leading cause of cancer deaths in the United States with five-year survival rates less than 5% due to rare detection in early stages. Identification of genes that are directly correlated to pancreatic cancer survival is crucial for pancreatic cancer diagnostics and treatment. However, no existing GWAS or transcriptome studies are available for addressing this problem. We apply lasso penalized Cox regression to a transcriptome study to identify genes that are directly related to pancreatic cancer survival. This method is capable of handling the right censoring effect of survival times and the ultrahigh dimensionality of genetic data. A cyclic coordinate descent algorithm is employed to rapidly select the most relevant genes and eliminate the irrelevant ones. Twelve genes have been identified and verified to be directly correlated to pancreatic cancer survival time and can be used for the prediction of future patient's survival.

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