Serum microRNA panel to differentiate malignant pulmonary nodules from benign pulmonary nodules
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE157074 | GEO | 2023/08/27
REPOSITORIES: GEO
Similar Datasets
Project description:BACKGROUND: Following fine needle aspiration, 15-30% of thyroid nodules are not clearly benign or malignant. These cytologically indeterminate nodules are often referred for diagnostic surgery, though most prove benign. A novel diagnostic test measuring the expression of 167 genes has shown promise in improving pre-operative risk assessment. We evaluated this test in a prospective, multicenter study. METHODS: Over 19 months, we performed a prospective study at 49 clinical sites enrolling 3,789 patients and collecting 4,812 samples from thyroid nodules >1cm requiring evaluation. We obtained 577 cytologically indeterminate aspirates with corresponding histopathology of excised lesions on 413. Central blinded histopathologic review served as the reference (“gold”) standard. After applying inclusion criteria, gene expression classifier results were obtained for 265 indeterminate nodules used in this analysis, and performance was calculated. RESULTS: 85 of 265 indeterminate nodules were malignant. The gene expression classifier correctly identified 78 of 85 as ‘suspicious’ (92% sensitivity, [84%-97%] 95% CI). Specificity was 52%, [44%-59%]. The negative predictive value was 95%, 94%, and 85%, respectively, for aspirates with AUS/FLUS, FN/SFN, or ‘suspicious’ cytology. Analysis of 7 false negative cases revealed 6 with a paucity of thyroid follicular cells, suggesting that insufficient sampling of the nodule had occurred. CONCLUSIONS: Though individualized clinical care is recommended, these data support consideration of a conservative approach for most patients with indeterminate FNA cytology and benign gene expression classifier results.
2012-06-25 | GSE34289 | GEO
Project description:BACKGROUND: Following fine needle aspiration, 15-30% of thyroid nodules are not clearly benign or malignant. These cytologically indeterminate nodules are often referred for diagnostic surgery, though most prove benign. A novel diagnostic test measuring the expression of 167 genes has shown promise in improving pre-operative risk assessment. We evaluated this test in a prospective, multicenter study. METHODS: Over 19 months, we performed a prospective study at 49 clinical sites enrolling 3,789 patients and collecting 4,812 samples from thyroid nodules >1cm requiring evaluation. We obtained 577 cytologically indeterminate aspirates with corresponding histopathology of excised lesions on 413. Central blinded histopathologic review served as the reference (“gold”) standard. After applying inclusion criteria, gene expression classifier results were obtained for 265 indeterminate nodules used in this analysis, and performance was calculated. RESULTS: 85 of 265 indeterminate nodules were malignant. The gene expression classifier correctly identified 78 of 85 as ‘suspicious’ (92% sensitivity, [84%-97%] 95% CI). Specificity was 52%, [44%-59%]. The negative predictive value was 95%, 94%, and 85%, respectively, for aspirates with AUS/FLUS, FN/SFN, or ‘suspicious’ cytology. Analysis of 7 false negative cases revealed 6 with a paucity of thyroid follicular cells, suggesting that insufficient sampling of the nodule had occurred. CONCLUSIONS: Though individualized clinical care is recommended, these data support consideration of a conservative approach for most patients with indeterminate FNA cytology and benign gene expression classifier results. 265 cytologically indetermine samples, 47 cytologically benign and 55 cytologically malignant samples
2012-06-24 | E-GEOD-34289 | biostudies-arrayexpress
Project description:Given the pressing clinical problem of making decision in diagnosis for subjects with pulmonary nodules, we aimed to discover novel plasma protein biomarkers for lung adenocarcinoma (LUAD) and benign pulmonary nodules (BPN), then develop an integrative multianalytical model to guide the clinical management of LUAD and BPN patients. Through label-free quantitative plasma proteomic analysis, twelve differentially expressed proteins (DEPs) in LUAD and BPN were screened. The diagnostic abilities of the DEPs were validated in two independent validation cohorts. The results showed that the level of three candidate proteins (PRDX2, PON1, APOC3) were lower in the plasma of LUAD than BPN. The three candidate proteins were combined with three promising computed tomography (CT) indicators (Spiculation, Vascular Notch Sign, Lobulation) and three traditional markers (CEA, CA125, CYFRA21-1) to construct an integrative multianalytical model, which was effective in distinguishing LUAD from BPN, with AUC of 0.904, sensitivity of 81.44% and specificity of 90.14%. Moreover, the model possessed impressive diagnostic performance between early LUADs and BPNs, with the AUC, sensitivity, specificity and accuracy of 0.868, 65.63%, 90.14% and 82.52%, respectively. This model maybe a useful auxiliary diagnostic tool for LUAD and BPN by achieving a better balance of sensitivity and specificity.
2024-01-26 | PXD046731 | Pride
Project description: Not available
| S-EPMC6359787 | biostudies-literature
Project description:The clinical diagnosis and treatment of small pulmonary nodules (suspected to be lung metastases) in advanced colorectal cancer patients remain controversy. Previous studies have shown that tumor-informed circulating tumor DNA (ctDNA) blood testing can sensitively detect residual cancer. Postoperative ctDNA in colorectal cancer patients is a valuable biomarker to identify minimal residual disease (MRD) after radical resection, which is possibly useful in redefining the risk group of patients and guiding postoperative treatment. This study aimed to explore the clinical value of therapeutic strategies based on tumor-informed ctDNA test in advanved colorectal cancer patients with small pulmonary nodules.
| 2744776 | ecrin-mdr-crc
Project description:Background: Fine needle aspiration biopsy (FNAB) is the gold-standard procedure for diagnosing malignant thyroid nodules. Indeterminate cytology is identified in 10-40% of cases and molecular testing may guide management in this setting. Current commercial options are expensive, and are either sensitive or specific. The aim of this study was to utilize next generation sequencing (NGS) technology to identify informative diversities in the microRNA (miRNA) expression profile of benign versus malignant thyroid nodules. Methods: Ex-vivo FNAB samples were obtained from thyroid specimens of patients that underwent thyroidectomy at a referral center. miRNA levels were determined using NGS and multiplexing technologies. Statistical analyses identified differences between normal and malignant samples and miRNA expression profiles that associate with malignancy were established. The accuracy of the miRNA signature in predicting histological malignancy was validated using a group of patient specimens with indeterminate cytology results. Results: 274 samples were obtained from 102 patients undergoing thyroidectomy. Of these samples, 71% were benign and 29% were malignant. Nineteen miRNAs were identified as statistically different between benign and malignant samples and were used to classify 35 additional nodules with indeterminate cytology (validation). The miRNA panel’s sensitivity, specificity, negative and positive predictive values and overall accuracy were 91%, 100%, 87%, 100% and 94%, respectively. Conclusion: Using NGS technology we identified a panel of 19 miRNAs that may be utilized to distinguish benign from malignant thyroid nodules with indeterminate cytology. Impact: Our panel may classify indeterminate thyroid nodules at higher accuracy than commercially available molecular tests.
2018-12-21 | GSE116196 | GEO
Project description:Interventions: Gold Standard:Pathological diagnosis;Index test:chest CT
Primary outcome(s): Pulmonary nodules
Study Design: Sequential
| 42108 | ecrin-mdr-crc
Project description:The proteomics aspect of this project was simply to catalog the protein content in microlith nodule isolated from a Pulmonary alveolar microlithiasis patient or from a mouse model of the disease
2023-03-11 | PXD039280 | Pride
Project description: Not available
| S-EPMC6501004 | biostudies-literature
Project description:Exosomes and exosomal miRNAs from the plasma of volunteers were isolated from thyroid nodules and papillary tyriod cancer patients . Profiling of exosomal miRNA was performed using next-generation sequencing(NGS) to identify miRNA candidates for diagnosis.
2019-05-01 | GSE130512 | GEO