Comparison of smoking-induced gene expression on Affymetrix Exon and 3'-based expression arrays.

摘要: Cigarette smoke is the major cause of lung cancer and chronic obstructive pulmonary disease in United States. We have previously defined impact tobacco on intrathoracic airway gene expression among healthy nonsmokers smokers using standard 3'-based U133A arrays [12]. In this report, we compared performance Affymetrix GeneChip Human Exon 1.0 ST array with HG-U133A for detecting smoking-related changes large epithelium obtained at bronchoscopy. RNA from same bronchial epithelial cell samples four current three never was hybridized to both arrays. Out 22,215 probe sets HG-U133A, 14,741 RefSeq transcripts were mapped 17,800 core 2 platforms overlapping transcript set. While reproducibility high, had a slightly stronger correlation technical replicates. A majority genes largest fold tightly correlated between platforms, but there number that detected only Furthermore, while study did not enough power detect any differentially expressed 4 vs. 3 False Discovery Rate (FDR) < 0.05, seventy differential FDR 0.05 set platform. These findings suggest all-Exon more robust platform measuring can serve as an effective tool exploring host response damage cigarette smoke.