Robust Gene Expression Signature from Formalin-Fixed Paraffin-Embedded Samples Predicts Prognosis of Non-Small-Cell Lung Cancer Patients

• Activity Number: 558
• Type: Topic Contributed
• Date/Time: Wednesday, August 1, 2012 : 2:00 PM to 3:50 PM
• Sponsor: Biometrics Section
• Author(s): Yang Xie*+ and Andy Xiao
• Companies: The University of Texas Southwestern Medical Center and The University of Texas Southwestern Medical Center
• Keywords: formalin-fixed paraffin-embedded samples ; prognosis signature ; microarrays

Abstract

The requirement of frozen tissues for microarray experiments limits the clinical usage of genome-wide expression profiling using microarray technology. The goal of this study is to develop statistical methods to analyze this types of data and test the feasibility of developing lung cancer prognosis gene signatures using genome-wide expression profiling of formalin-fixed paraffin-embedded (FFPE) samples. We randomly selected 100 Non-Small-Cell lung cancer (NSCLC) FFPE samples with annotated clinical information from the UT-Lung SPORE Tissue Bank, and Affymetrix U133 plus 2.0 arrays were used to attain gene expression data. After strict quality control and a novel statistical analysis procedure, we develop a robust prognosis signature for NSCLC. The robust gene signature is strongly associated with lung cancer clinical outcomes,and it has been validated in several independent published microarray data sets. We conclude that genome-wide profiling of FFPE lung cancer samples can identify a set of genes whose expression level provides prognostic information across different platforms and studies, which will allow its application in clinical settings