Exon Level Expression Profiling analysis of early stage NSCLC suffering rapidly relapse

Postoperative recurrence is the main cause of poor prognosis in early stage lung adenocarcinoma (LUAD). Factors that can predict recurrence risk are critically needed.we designed a screening procedure based on gene profile data.The differentially expressed genes (DEGs) between patients with recurrence-free survival (RFS)<1 year and RFS>3 years were found.Cox proportional hazards model, IHC and Kaplan-Meier survival analysis were preformed to validate these biomarkers in TCGA and Daping validation sets. To identify DEGs between the RFS<1 year (n=7)and >3year(n=7) subgroups in the Daping discovery set, transcriptome analysis was performed. Tissue cores with >70% tumor content was obtained from formalin-fixed and paraffin-embedded (FFPE) tissue. RNA was extracted from deparaffinized and proteinase K–treated FFPE tissue (20–40 mg) using the RNA prep Pure FFPE Kit (QIAGEN, Valencia, CA) according to the manufacturer’s instructions. RNA concentration and quality were assessed by absorbance spectrometry on a NanoDrop (Thermo Fisher Scientific, Wilmington, DE). We performed gene expression profiling of the 14 FFPE-derived LUAD tissues using a GeneChip® Human Transcriptome Array 2.0 (Affymetrix, Santa Clara, CA). The total RNA input was 500 pg–10 µg. Data were processed by Affymetrix® Transcriptome Analysis Console software 3.0.