Next-Generation Sequencing at High Sequencing Depth as a Tool to Study the Evolution of Metastasis Driven by Genetic Change Events of Lung Squamous Cell Carcinoma

Mansour, Hicham; Ouhajjou, Abdelhak; Bajic, Vladimir B.; Incitti, Roberto

doi:10.3389/fonc.2020.01215

Cited by 9 publications

(6 citation statements)

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“…It claims the highest mortality rate among all cancers in China and is primarily categorized into two major histological subtypes: NSCLC and SCLC. Among these, NSCLC accounts for the majority of cases, including ADC and SCC, among other subtypes [1][2][3][4][5]. In recent years, molecular targeted therapy has gained favor due to its specific targeting, minimal side effects, simplicity, and effectiveness.…”

Section: Discussionmentioning

confidence: 99%

“…From a pathological standpoint, lung cancer can be broadly categorized into two main types: non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). NSCLC, constituting roughly 80% to 85% of all cases, is the most prevalent histological subtype, encompassing adenocarcinoma (ADC), squamous cell carcinoma (SCC), and other histological variants [1][2][3][4][5]. In recent years, molecular targeted therapy has gained increasing favor due to its precision in targeting cancer cells, minimal side effects, straightforward administration, and proven efficacy.…”

Section: Introductionmentioning

confidence: 99%

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Nomogram prediction for epidermal growth factor receptor mutation and subtypes in patients with non-small cell lung cancer

Li,

Lei,

Zhang

et al. 2024

Preprint

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Objective: The aim of this study was to develop a nomogram model for predicting epidermal growth factor receptor (EGFR) mutations and their common subtypes in non-small cell lung cancer (NSCLC) patients. Methods: We conducted this study using data from NSCLC patients at the First Affiliated Hospital of Chongqing Medical University in China, including a total of 557 NSCLC patients. We identified independent risk factors for predicting EGFR mutations and their common subtypes through logistic univariable and multivariable analyses. These factors were then integrated to construct a nomogram, which underwent internal validation. We assessed the nomogram's predictive performance using receiver operating characteristic (ROC) curves and calibration plots. We randomly divided the dataset into training (n = 390) and validation (n = 167) cohorts in a 7:3 ratio. Following univariate and multivariate analyses, the nomogram for predicting EGFR mutations included four independent risk factors: age, pathological pattern (adenocarcinoma, ADC), smoking status, and squamous cell carcinoma antigen (SCC) levels. The nomogram for predicting EGFR exon 19 deletion mutation (19-Del) incorporated four independent risk factors: pathological pattern, smoking status, the presence of cytokeratin 21 fragment (CYFRA21.1), and tumor node metastasis (TNM). The nomogram for predicting EGFR exon 21-L858R mutation (21-L858R) included five independent risk factors: age, tumor location, pathological pattern, smoking status, and TNM. Results: In the nomogram for predicting EGFR mutations, the C-index of the nomogram model was 0.769 in the training cohort and 0.757 in the validation cohort. In the nomogram for predicting EGFR exon 19 deletion mutation, the C-index of the nomogram model was 0.673 in the training cohort and 0.743 in the validation cohort. In the nomogram for predicting EGFR exon 21-L858R mutation (21-L858R), the C-index of 0.745 in the training cohort and 0.641 in the validation cohort. The calibration plot of the nomogram shows a good agreement between the predicted probability and the actual probability. Conclusion: We have successfully developed and validated a novel nomogram for predicting EGFR mutation subtypes in NSCLC patients. This nomogram accurately estimates the EGFR mutation subtype and can help identify patients who may benefit from specific, individualized therapies.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Nomogram prediction for epidermal growth factor receptor mutation and subtypes in patients with non-small cell lung cancer

Li,

Lei,

Zhang

et al. 2024

Preprint

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“…Therefore, the traditional qMSP is often unable to achieve the required precision and sensitivity for methylation detection ( 26 ). The next generation sequencing (NGS) can also detect rare mutations but with a lower technical sensitivity than ddPCR, unless (potentially costly) high sequencing depth is reached ( 27 ). Here, we described a novel and highly sensitive assay for the detection of methylated DNA based on ddPCR.…”

Section: Discussionmentioning

confidence: 99%

The Application Value of Syndecan-2 Gene Methylation for Colorectal Cancer Diagnosis: A Clinical Study and Meta-Analyses

et al. 2022

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ObjectiveSyndecan-2 (SDC2) methylation has been previously reported as a sensitive biomarker for the early detection of colorectal cancer (CRC). Droplet digital PCR (ddPCR) is the latest development of PCR technology. It can accurately detect and quantify the target sequence of nucleic acid. ddPCR is widely used in research and clinical diagnosis. In the present study, we aimed to develop a ddPCR method to detect SDC2 gene methylation and evaluate the diagnostic value of SDC2 gene methylation.MethodsFirst, a ddPCR method was developed to measure SDC2 methylation in stool samples collected from 51 cases of normal, 23 cases of adenoma, and 86 cases of CRC. Subsequently, a meta-analysis of existing studies was conducted to judge the diagnostic value of SDC2 gene methylation in CRC. PUBMED, EMBASE, Web of Science, and Scopus databases were searched for relative studies. Meta-analysis was performed using Meta Disc 1.4 and STATA 15.0 software.ResultsThe ddPCR showed that the linearity, sensitivity, and specificity for the detection of SDC2 gene methylation could be down to 0.1% methylation level and 5 ng of methylated DNA input. In 109 cases of CRC, 107 cases could be detected, and the sensitivity was 98.17%. The median value of the percentage of methylated reference (PMR) in colorectal adenoma and CRC patients was significantly higher compared with the normal individuals (p < 0.001). In addition, we found that the PMR value was associated with the clinical staging of CRC. The difference of PMR in stage II and stage IIIA was statistically significant (p < 0.05). Moreover, the meta-analysis showed that 11 out of 87 studies were identified to report the feasibility of SDC2 gene methylation as a method to diagnose early CRC. The pooled sensitivity and specificity of SDC2 gene methylation test for CRC were 0.80 [95% CI (0.68–0.88)] and 0.93 [95% CI (0.91–0.94)], respectively. The pooled diagnostic odds ratio (DOR) and area under curve (AUC) were 52.46 [95% CI (30.43–90.45)] and 0.94 [95% CI (0.92, 0.96)], respectively.ConclusionsThe ddPCR method was more sensitive and convenient to detect SDC2 gene methylation, and the pooled analysis showed that methylated SDC2 was a valuable biomarker for the non-invasive detection of CRC.

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“…The dPCR can identify rare frequent alleles with high accuracy (Cheung et al, 2018). The NGS can also detect rare mutations but with a lower technical sensitivity than dPCR, unless (potentially costly) high sequencing depth is reached (Cheung et al, 2018;Mansour et al, 2020). In contrast to dPCR, massively parallel sequencing approaches can be designed to detect somatic mutations in either known or unknown driver genes.…”

Section: Molecular Biology Approaches In Liquid Biopsymentioning

confidence: 99%

Updates on Clinical Use of Liquid Biopsy in Colorectal Cancer Screening, Diagnosis, Follow-Up, and Treatment Guidance

Mazouji

Ouhajjou²,

Incitti

et al. 2021

Front. Cell Dev. Biol.

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Colorectal cancer (CRC) is one of the most common cancers worldwide, being the third most diagnosed in the world and the second deadliest. Solid biopsy provides an essential guide for the clinical management of patients with colorectal cancer; however, this method presents several limitations, in particular invasiveness, and cannot be used repeatedly. Recently, clinical research directed toward the use of liquid biopsy, as an alternative tool to solid biopsy, showed significant promise in several CRC clinical applications, as (1) detect CRC patients at early stage, (2) make treatment decision, (3) monitor treatment response, (4) predict relapses and metastases, (5) unravel tumor heterogeneity, and (6) detect minimal residual disease. The purpose of this short review is to describe the concept, the characteristics, the genetic components, and the technologies used in liquid biopsy in the context of the management of colorectal cancer, and finally we reviewed gene alterations, recently described in the literature, as promising potential biomarkers that may be specifically used in liquid biopsy tests.

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Next-Generation Sequencing at High Sequencing Depth as a Tool to Study the Evolution of Metastasis Driven by Genetic Change Events of Lung Squamous Cell Carcinoma

Cited by 9 publications

References 58 publications

Nomogram prediction for epidermal growth factor receptor mutation and subtypes in patients with non-small cell lung cancer

Nomogram prediction for epidermal growth factor receptor mutation and subtypes in patients with non-small cell lung cancer

The Application Value of Syndecan-2 Gene Methylation for Colorectal Cancer Diagnosis: A Clinical Study and Meta-Analyses

Updates on Clinical Use of Liquid Biopsy in Colorectal Cancer Screening, Diagnosis, Follow-Up, and Treatment Guidance

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