Comparison of PNA Clamping-assisted Fluorescence Melting Curve Analysis and PNA Clamping in Detecting EGFR Mutations in Matched Tumor Tissue, Cell Block, Pleural Effusion and Blood of Lung Cancer Patients With Malignant Pleural Effusion

Background and Objective. Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Pseudomonas aeruginosa, and Mycobacterium tuberculosis are primary respiratory bacterial pathogens contributing to morbidity and mortality in developing countries. This study evaluated the diagnostic performance of multiplex real-time PCR with fluorescence melting curve analysis (MCA) assay, which was used to detect eight respiratory bacterial pathogens simultaneously. Methods. A total of 157 sputum specimens were examined by multiplex real-time with fluorescence MCA, and the results were compared with the conventional culture method. Results. Multiplex real-time PCR with fluorescence MCA specifically detected and differentiated eight respiratory bacterial pathogens by different melting curve peaks for each amplification product within 2 hours and exhibited high repeatability. The limit of detection ranged from 64 to 102 CFU/mL in the multiplex PCR system. Multiplex real-time PCR with fluorescence MCA showed a sensitivity greater than 80% and a 100% specificity for each pathogen. The kappa correlation of eight bacteria ranged from 0.89 to 1.00, and the coefficient of variation ranged from 0.05% to 0.80%. Conclusions. Multiplex real-time PCR with fluorescence MCA assay is a sensitive, specific, high-throughput, and cost-effective method to detect multiple bacterial pathogens simultaneously.

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Comparison of fusions detection by next generation sequencing between malignant pleural effusion and tumor tissue in lung cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.e21059 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. e21059-e21059

Author(s):

Yurong Xu ◽

Yingxue Qi ◽

Ningning Luo ◽

Qin Zhang ◽

Yaqing Wu ◽

...

Keyword(s):

Lung Cancer ◽

Pleural Effusion ◽

Gene Fusion ◽

Malignant Pleural Effusion ◽

Tumor Tissue ◽

Fisher Exact Test ◽

Gene Fusions ◽

Exact Test ◽

Lung Cancer Patients ◽

Generation Sequencing

e21059 Background: Anaplastic lymphoma kinase ( ALK), c-ros oncogene 1 receptor tyrosine kinase ( ROS1), ret proto-oncogene ( RET) and neurotrophic receptor kinase ( NTRK) are important driver genes in lung cancer. Each of these four genes fusions as therapeutic targets have been recommended by the national comprehensive cancer network (NCCN) guidelines for non-small cell lung cancer (NSCLC). Malignant pleural effusion (MPE) is observed in multy types of malignancies, especially in lung cancer. Studies have indicated that next generation sequencing (NGS) detection of somatic mutations by MPE is reliable. Nevertheless, the distribution and comparison of fusions in lung cancer between malignant pleural effusion and tumor tissue specimen have not been well characterized yet. Methods: In this study, 9-gene, 69-gene and 539-gene panel NGS profiling were performed by MPE and tumor tissue in 640 and 10013 patients with lung cancer respectively. The variation analysis between patients with or without gene fusion in different sample groups were calculated by fisher exact test via SPSS v26.0. Results: In lung cancer patients using MPE detection, 59 of 640 (9.22%) were found harboring at least one of the four gene fusions, and the ratio of ALK, ROS1, RET and NTRK fusion was 6.25% (40/640), 1.41% (9/640), 0.63% (4/640) and 0.47% (3/640) respectively. Meanwhile, we found gene fusions in 6.25% (626/10013) lung cancer patients using tumor tissue detection, including 3.66% (366/10013) ALK fusion, 1.07% (107/10013) ROS1 fusion, 1.09% (108/10013) RET fusion and 0.22% (626/10013) NTRK fusion. Significant differences of gene fusion frequency between different sample groups were found via fisher exact test ( p = 0.005), especially ALK fusion ( p = 0.001). Conclusions: The frequency of fusion in MPE was significantly higher than in tumor tissue, especially ALK fusion. However, as a retrospective study, the conclusions and the specific mechanisms are needed to be verified.

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