Comparison of Bisulfite Pyrosequencing and Methylation-Specific qPCR for Methylation Assessment

Different methodological approaches are available to assess DNA methylation biomarkers. In this study, we evaluated two sodium bisulfite conversion-dependent methods, namely pyrosequencing and methylation-specific qPCR (MS-qPCR), with the aim of measuring the closeness of agreement of methylation values between these two methods and its effect when setting a cut-off. Methylation of tumor suppressor gene p16/INK4A was evaluated in 80 lung cancer patients from which cytological lymph node samples were obtained. Cluster analyses were used to establish methylated and unmethylated groups for each method. Agreement and concordance between pyrosequencing and MS-qPCR was evaluated with Pearson's correlation, Bland-Altman, Cohen's kappa index and ROC curve analyses. Based on these analyses, cut-offs were derived for MS-qPCR. An acceptable correlation (Pearson's R2 = 0.738) was found between pyrosequencing (PYRmean) and MS-qPCR (NMP; normalized methylation percentage), providing similar clinical results when categorizing data as binary using cluster analysis. Compared to pyrosequencing, MS-qPCR tended to underestimate methylation for values between 0 and 15%, while for methylation >30% overestimation was observed. The estimated cut-off for MS-qPCR data based on cluster analysis, kappa-index agreement and ROC curve analysis were much lower than that derived from pyrosequencing. In conclusion, our results indicate that independently of the approach used for estimating the cut-off, the methylation percentage obtained through MS-qPCR is lower than that calculated for pyrosequencing. These differences in data and therefore in the cut-off should be examined when using methylation biomarkers in the clinical practice

Proteomic approach to improve the diagnosis of malignant pleural effusions

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Validation of Calprotectin As a Novel Biomarker For The Diagnosis of Pleural Effusion: a Multicentre Trial

Discriminating between malignant pleural effusion (MPE) and benign pleural effusion (BPE) remains difficult. Thus, novel and efficient biomarkers are required for the diagnosis of pleural effusion (PE). The aim of this study was to validate calprotectin as a diagnostic biomarker of PE in clinical settings. A total of 425 patients were recruited, and the pleural fluid samples collected had BPE in 223 cases (53.7%) or MPE in 137 patients (33%). The samples were all analysed following the same previously validated clinical laboratory protocols and methodology. Calprotectin levels ranged from 772.48 to 3,163.8 ng/mL (median: 1,939 ng/mL) in MPE, and 3,216-24,000 ng/mL in BPE (median: 9,209 ng/mL; p < 0.01), with an area under the curve of 0.848 [95% CI: 0.810-0.886]. For a cut-off value of </= 6,233.2 ng/mL, we found 96% sensitivity and 60% specificity, with a negative and positive predictive value, and negative and positive likelihood ratios of 96%, 57%, 0.06, and 2.4, respectively. Multivariate analysis showed that low calprotectin levels was a better discriminator of PE than any other variable [OR 28.76 (p < 0.0001)]. Our results confirm that calprotectin is a new and useful diagnostic biomarker in patients with PE of uncertain aetiology which has potential applications in clinical practice because it may be a good complement to cytological methods

Comparison of Bisulfite Pyrosequencing and Methylation-Specific qPCR for Methylation Assessment

Different methodological approaches are available to assess DNA methylation biomarkers. In this study, we evaluated two sodium bisulfite conversion-dependent methods, namely pyrosequencing and methylation-specific qPCR (MS-qPCR), with the aim of measuring the closeness of agreement of methylation values between these two methods and its effect when setting a cut-off. Methylation of tumor suppressor gene p16/INK4A was evaluated in 80 lung cancer patients from which cytological lymph node samples were obtained. Cluster analyses were used to establish methylated and unmethylated groups for each method. Agreement and concordance between pyrosequencing and MS-qPCR was evaluated with Pearson's correlation, Bland-Altman, Cohen's kappa index and ROC curve analyses. Based on these analyses, cut-offs were derived for MS-qPCR. An acceptable correlation (Pearson's R2 = 0.738) was found between pyrosequencing (PYRmean) and MS-qPCR (NMP; normalized methylation percentage), providing similar clinical results when categorizing data as binary using cluster analysis. Compared to pyrosequencing, MS-qPCR tended to underestimate methylation for values between 0 and 15%, while for methylation >30% overestimation was observed. The estimated cut-off for MS-qPCR data based on cluster analysis, kappa-index agreement and ROC curve analysis were much lower than that derived from pyrosequencing. In conclusion, our results indicate that independently of the approach used for estimating the cut-off, the methylation percentage obtained through MS-qPCR is lower than that calculated for pyrosequencing. These differences in data and therefore in the cut-off should be examined when using methylation biomarkers in the clinical practice.Development and application of statistical models for medical scientific researc

Methylation Assessment for the Prediction of Malignancy in Mediastinal Adenopathies Obtained by Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration in Patients with Lung Cancer

Development and application of statistical models for medical scientific researc

Excessive dynamic airway collapse in a small cohort of chronic obstructive pulmonary disease patients

INTRODUCTION: The prevalence of EDAC (Excessive Dynamic Airway Collapse) has not been studied specifically in patients with chronic obstructive pulmonary disease (COPD). OBJECTIVE: The aim of this study was to investigate the prevalence of EDAC in COPD and to determine whether there are clinical factors or functional variables that could influence the degree of expiratory collapse of central airways. METHODS: Prospective observational study of a group of patients with COPD. The degree of tracheobronchial collapse was evaluated by low-dose dynamic airway computed tomography (CT). We recorded clinical and pulmonary function tests data, quality of life and BODE index. RESULTS: This study included 53 patients with COPD, 46 (87%) males, mean age 65 (SD, 9) years. The percentage of collapse at each anatomic level was as follows: Aortic arch, 16.1% (SD, 13.6%); carina, 19.4% (SD, 15.9%); and bronchus intermedius, 21.7% (SD, 16.1%). At the point of maximal collapse, the percentage of collapse was 26.8% (SD, 16%). EDAC was demonstrated at any of the three anatomical points in five patients, corresponding to 9.4% (95% CI, 3.1% to 20.6%) of the sample and affecting the three anatomical points in only two cases. A statistically significant correlation was only found with the total lung capacity (TLC). CONCLUSIONS: The prevalence of EDAC observed in a sample of patients with different levels of COPD severity is low. The degree of dynamic central airway collapse was not related to the patient′s epidemiological or clinical features, and did not affect lung function, symptoms, capacity for effort, or quality of life

Validation of PEDF as a potential biomarker for NSLC

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Intramural hematoma of the pulmonary artery and hemopneumomediastinum after endobronchial ultrasound-guided transbronchial needle aspiration

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a safe and effective technique for the sampling of mediastinal and hilar adenopathies. We describe the first reported case of pulmonary artery intramural hematoma after EBUS-TBNA puncture of this artery. The complication was visualized by ultrasound and resolved spontaneously