scholarly journals Digital PCR for the Analysis of MYC Copy Number Variation in Lung Cancer

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Alexander Brik ◽  
Daniel G. Weber ◽  
Swaantje Casjens ◽  
Peter Rozynek ◽  
Swetlana Meier ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cancer Patients ◽  
Copy Number ◽  
Digital Pcr ◽  
Copy Number Variations ◽  
Clinical Diagnostics ◽  
Gene Copy ◽  
Clinicopathological Parameters ◽  
Lung Cancer Patients

Background. MYC (v-myc avian myelocytomatosis viral oncogene homolog) is one of the most frequently amplified genes in lung tumors. For the analysis of gene copy number variations, dPCR (digital PCR) is an appropriate tool. The aim of our study was the assessment of dPCR for the detection of MYC copy number variations (CNV) in lung tissue considering clinicopathological parameters. Material and Methods. MYC status was analyzed with dPCR as well as qPCR (quantitative PCR) using gDNA (genomic DNA) from tumor and adjacent nontumor tissue samples of lung cancer patients. The performance of MYC was estimated based on the AUC (area under curve). Results. The results of the MYC amplification correlated significantly between dPCR and qPCR (rS=0.81, P<0.0001). The MYC copy number revealed by dPCR showed statistically significant differences between tumor and adjacent nontumor tissues. For discrimination, a sensitivity of 43% and a specificity of 99% were calculated, representing 55 true-positive and one false-positive tests. No statistically significant differences could be observed for age, sex, and smoking status or the clinicopathological parameters (histological subtype, grade, and stage). Conclusion. The results of the study show that dPCR is an accurate and reliable method for the determination of MYC copy numbers. The application is characterized by high specificity and moderate sensitivity. MYC amplification is a common event in lung cancer patients, and it is indicated that the determination of the MYC status might be useful in clinical diagnostics.

scholarly journals Digital PCR for determination of cytochrome P450 2D6 and sulfotransferase 1A1 gene copy number variations

2017 ◽  
Vol 11 (6) ◽  
pp. 336-341 ◽  
Author(s):  
Yutaro Motoi ◽  
Kazufumi Watanabe ◽  
Hiroyuki Honma ◽  
Yousuke Tadano ◽  
Hiroshi Hashimoto ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Copy Number ◽  
Gene Copy Number ◽  
Digital Pcr ◽  
Copy Number Variations ◽  
Gene Copy ◽  
Cytochrome P450 2D6 ◽  
Sulfotransferase 1A1 ◽  
P450 2D6

scholarly journals Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Filippo Martignano ◽  
Uday Munagala ◽  
Stefania Crucitta ◽  
Alessandra Mingrino ◽  
Roberto Semeraro ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cancer Patients ◽  
Liquid Biopsy ◽  
Copy Number ◽  
Dna Analysis ◽  
Copy Number Variations ◽  
Nanopore Sequencing ◽  
Cell Free Dna ◽  
Lung Cancer Patients ◽  
Free Dna

AbstractIn the “precision oncology” era the characterization of tumor genetic features is a pivotal step in cancer patients’ management. Liquid biopsy approaches, such as analysis of cell-free DNA from plasma, represent a powerful and noninvasive strategy to obtain information about the genomic status of the tumor. Sequencing-based analyses of cell-free DNA, currently performed with second generation sequencers, are extremely powerful but poorly scalable and not always accessible also due to instrumentation costs. Third generation sequencing platforms, such as Nanopore sequencers, aim at overcoming these obstacles but, unfortunately, are not designed for cell-free DNA analysis.Here we present a customized workflow to exploit low-coverage Nanopore sequencing for the detection of copy number variations from plasma of cancer patients. Whole genome molecular karyotypes of 6 lung cancer patients and 4 healthy subjects were successfully produced with as few as 2 million reads, and common lung-related copy number alterations were readily detected.This is the first successful use of Nanopore sequencing for copy number profiling from plasma DNA. In this context, Nanopore represents a reliable alternative to Illumina sequencing, with the advantages of minute instrumentation costs and extremely short analysis time.The availability of protocols for Nanopore-based cell-free DNA analysis will make this analysis finally accessible, exploiting the full potential of liquid biopsy both for research and clinical purposes.

scholarly journals MET increased gene copy number and primary resistance to gefitinib therapy in non-small-cell lung cancer patients

2009 ◽  
Vol 20 (2) ◽  
pp. 298-304 ◽  
Author(s):  
F. Cappuzzo ◽  
P.A. Jänne ◽  
M. Skokan ◽  
G. Finocchiaro ◽  
E. Rossi ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cancer Patients ◽  
Copy Number ◽  
Gene Copy Number ◽  
Small Cell ◽  
Gene Copy ◽  
Small Cell Lung ◽  
Primary Resistance ◽  
Lung Cancer Patients

PD-L1 gene copy number and promoter polymorphisms regulate PD-L1 expression in tumor cells of non-small cell lung cancer patients

2019 ◽  
Vol 237 ◽  
pp. 10-18
Author(s):  
Paweł Krawczyk ◽  
Anna Grenda ◽  
Kamila Wojas-Krawczyk ◽  
Marcin Nicoś ◽  
Tomasz Kucharczyk ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cancer Patients ◽  
Tumor Cells ◽  
Copy Number ◽  
Gene Copy Number ◽  
Small Cell ◽  
Gene Copy ◽  
Small Cell Lung ◽  
Promoter Polymorphisms ◽  
Lung Cancer Patients

scholarly journals Quantification of Plasma miRNAs by Digital PCR for Cancer Diagnosis

2013 ◽  
Vol 8 ◽  
pp. BMI.S13154 ◽  
Author(s):  
Jie Ma ◽  
Ning Li ◽  
Maria Guarnera ◽  
Feng Jiang
Keyword(s):  
Lung Cancer ◽  
Cancer Patients ◽  
Cancer Diagnosis ◽  
Copy Number ◽  
Dynamic Range ◽  
Quantitative Polymerase Chain Reaction ◽  
Digital Pcr ◽  
Lung Cancer Patients ◽  
Plasma Microrna ◽  
Plasma Mirnas

Analysis of plasma microRNAs (miRNAs) by quantitative polymerase chain reaction (qPCR) provides a potential approach for cancer diagnosis. However, absolutely quantifying low abundant plasma miRNAs is challenging with qPCR. Digital PCR offers a unique means for assessment of nucleic acids presenting at low levels in plasma. This study aimed to evaluate the efficacy of digital PCR for quantification of plasma miRNAs and the potential utility of this technique for cancer diagnosis. We used digital PCR to quantify the copy number of plasma microRNA-21-5p (miR-21–5p) and microRNA-335–3p (miR-335–3p) in 36 lung cancer patients and 38 controls. Digital PCR showed a high degree of linearity and quantitative correlation with miRNAs in a dynamic range from 1 to 10,000 copies/μL of input, with high reproducibility. qPCR exhibited a dynamic range from 100 to 1X107 copies/μL of input. Digital PCR had a higher sensitivity to detect copy number of the miRNAs compared with qPCR. In plasma, digital PCR could detect copy number of both miR-21–5p and miR-335–3p, whereas qPCR was only able to assess miR-21–5p. Quantification of the plasma miRNAs by digital PCR provided 71.8% sensitivity and 80.6% specificity in distinguishing lung cancer patients from cancer-free subjects.

scholarly journals Expression signature, prognosis value and immune characteristics of cathepsin F in non-small cell lung cancer identified by bioinformatics assessment

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Liyuan Song ◽  
Xianhui Wang ◽  
Wang Cheng ◽  
Yi Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Molecular Markers ◽  
Cancer Patients ◽  
Targeted Therapies ◽  
Poor Prognosis ◽  
Immune Cell ◽  
Clinicopathological Parameters ◽  
Cancer Specific Survival ◽  
Lung Cancer Patients ◽  
Favorable Prognosis

Abstract Background In recent years, immunotherapies and targeted therapies contribute to population-level improvement in NSCLC cancer-specific survival, however, the two novel therapeutic options have mainly benefit patients containing mutated driven genes. Thus, to explore other potential genes related with immunity or targeted therapies may provide novel options to improve survival of lung cancer patients without mutated driven genes. CTSF is unique in human cysteine proteinases. Presently, CTSF has been detected in several cell lines of lung cancer, but its role in progression and prognosis of lung cancer remains unclear. Methods CTSF expression and clinical datasets of lung cancer patients were obtained from GTEx, TIMER, CCLE, THPA, and TCGA, respectively. Association of CTSF expression with clinicopathological parameters and prognosis of lung cancer patients was analyzed using UALCAN and Kaplan–Meier Plotter, respectively. LinkedOmics were used to analyze correlation between CTSF and CTSF co-expressed genes. Protein–protein interaction and gene–gene interaction were analyzed using STRING and GeneMANIA, respectively. Association of CTSF with molecular markers of immune cells and immunomodulators was analyzed with Immunedeconv and TISIDB, respectively. Results CTSF expression was currently only available for patients with NSCLC. Compared to normal tissues, CTSF was downregulated in NSCLC samples and high expressed CTSF was correlated with favorable prognosis of NSCLC. Additionally, CTSF expression was correlated with that of immune cell molecular markers and immunomodulators both in LUAD and LUSC. Noticeably, high expression of CTSF-related CTLA-4 was found to be associated with better OS of LUAD patients. Increased expression of CTSF-related LAG-3 was related with poor prognosis of LUAD patients while there was no association between CTSF-related PD-1/PD-L1 and prognosis of LUAD patients. Moreover, increased expression of CTSF-related CD27 was related with poor prognosis of LUAD patients while favorable prognosis of LUSC patients. Conclusions CTSF might play an anti-tumor effect via regulating immune response of NSCLC.

Diagnostic and prognostic values of circular RNAs for lung cancer: a meta-analysis

2020 ◽  
pp. postgradmedj-2019-137178
Author(s):  
Qian Yang ◽  
Lizhen Chen ◽  
Li Yang ◽  
Yuanshuai Huang
Keyword(s):  
Lung Cancer ◽  
Cancer Patients ◽  
Meta Analysis ◽  
Area Under The Curve ◽  
High Sensitivity ◽  
Cochrane Library ◽  
Clinicopathological Parameters ◽  
Circular Rnas ◽  
Lung Cancer Patients ◽  
Diagnostic Values

Circular RNAs (circRNAs) may serve as potential biomarkers for patients with lung cancer. The aim of this meta-analysis was to analyse the diagnostic, prognostic and clinicopathological values of circRNAs in lung cancer patients. A systematic search of PubMed, Embase, Web of Science, Scopus and the Cochrane Library databases was performed for relevant articles from inception to 29 January 2020. Pooled parameters including sensitivity, specificity and area under the curve (AUC) were used to assess the diagnostic performance, HRs and 95% CIs were used to evaluate overall survival (OS) and ORs were used to estimate clinicopathological parameters. 52 studies from 45 articles were enrolled in this study, including 17 on diagnosis and 35 on prognosis. For diagnostic values, circRNAs could discriminate lung cancer patients from the controls, with AUC of 0.83 (95% CI: 0.79 to 0.86), a relatively high sensitivity of 0.77 (95% CI: 0.73 to 0.81) and specificity of 0.75 (95% CI: 0.71 to 0.79). For prognostic significances, overexpression of 23 upregulated circRNAs was relevant to a poor prognosis (OS: HR=2.21, 95% CI: 1.96 to 2.49, p<0.001), and overexpression of 9 downregulated circRNAs was correlated with a favourable prognosis (OS: HR=0.62, 95% CI: 0.53 to 0.73, p<0.001). As for clinicopathological parameters, high expression of 23 upregulated circRNAs was associated with unfavourable clinicopathological features while 9 downregulated circRNAs proved the contrary. In conclusion, this study confirmed that circRNAs might serve as important biomarkers for diagnostic and prognostic values of lung cancer.

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