Application of Next Generation Sequencing in Pleural Effusion Molecular Profiling Using Oncomine™ Lung Cell-Free Total Nucleic Acid Research Assay

Date 24 November 2018
Event ESMO Asia 2018 Congress
Session Poster display - Cocktail
Topics Thoracic Malignancies
Translational Research
Presenter Chan Xiang
Citation Annals of Oncology (2018) 29 (suppl_9): ix143-ix149. 10.1093/annonc/mdy446
Authors C. Xiang, R. Zhao, S. Ma, L. Guo, Y. Han
  • Department Of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, 200030 - Shanghai/CN



Pleural effusion is commonly observed in patients with advanced lung cancer and its molecular profiling has not been fully investigated. Cell-free (cf) DNA or RNA isolated from cancer patient’s plasma has allowed noninvasive tumor genome analysis, however, there are few study of detection and characterization of cfDNA or cfRNA in pleural effusions and its application in cancer patient treatment. Here we reported the utilization of cell free total nucleic acid (cfTNA) isolated from pleural fluid of late stage lung cancer patient with Next-generation sequencing (NGS) liquid biopsy assay-Oncomine™ Lung cfTNA Assay. The assay simultaneously query about 168 hotspots across ALK, BRAF, EGFR, ERBB2, KRAS, MAP2K1, MET, NRAS, PIK3CA, ROS1, and TP53, CNV (MET), gene fusions (ALK, RET, ROS1) as well as MET exon 14 skipping which have been frequently identified in NSCLC. A comprehensive study of these mutations provides information for therapy decision, disease monitor as well as new drug development.


Ten paired cfTNA were isolated from plural fluid of Non-Small Cell Lung Cancer (NSCLC) subjects, and their matched tumor TNA were extracted from formalin-fixed paraffin-embedded (FFPE) cell pellet collected from same plural fluid. Libraries were prepared using Oncomine Lung Cell-Free Total Nucleic Acid Research Assay and sequenced with Ion S5 Sequencing instrument. Data were analyzed using Ion Reporter 5.6.


All cfTNA have been isolated from twenty patient pleural fluid (yield range is 41-1227 ng from 4ml fluid). Bioanalyzer profile of these cfTNA verified the fragmentation pattern, which is similar to cfTNA isolated from plasma. 20ng of cfTNA were tested with Oncomine™ cfDNA Lung assay test, matched somatic variants were detected at a frequency between 6.4% to 54.3% in cfDNA and between 1.2% to 67.6% in corresponding DNA isolated from FFPE.


Oncomine™ Lung cfTNA research assay provided an easy, quick and reliable solution in detecting molecular profile using cfTNA isolated from pleural fluid. Molecular analysis of pleural fluid can be used in clinical practice for treatment of late stage cancer patients with pleural fluid.

Editorial acknowledgement

Clinical trial identification

Legal entity responsible for the study

Shanghai Chest Hospital.


Has not received any funding.


All authors have declared no conflicts of interest.