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Association of Molecular Subtypes with Pathologic Response, PFS and OS in a Phase II Study of Coexpression Extrapolation (COXEN) with Neoadjuvant Chemotherapy (NAC) for Localized, Muscle-Invasive Bladder Cancer (SWOG S1314 NCT02177695)

ABSTRACT: Association of Molecular Subtypes with Pathologic Response, PFS and OS in a Phase II Study of Coexpression Extrapolation (COXEN) with Neoadjuvant Chemotherapy (NAC) for Localized, Muscle-Invasive Bladder Cancer (SWOG S1314 NCT02177695)

PROVIDER: PRJNA1022039 | ENA |

REPOSITORIES: ENA

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Association of Molecular Subtypes with Pathologic Response, PFS and OS in a Phase II Study of Coexpression Extrapolation (COXEN) with Neoadjuvant Chemotherapy (NAC) for Localized, Muscle-Invasive Bladder Cancer (SWOG S1314; NCT02177695)

Project description:Investigation of RNA-based molecular subtypes as additional predictive biomarkers for neoadjuvant chemotherapy response, progression-free survival and survival in patients treated in S1314.

2023-11-28 | GSE244266 | GEO

Burkholderia pseudomallei OS strain:OS

Project description:Burkholderia pseudomallei OS strain:OS Genome sequencing and assembly

| PRJNA188496 | ENA

Validation of the DNA Damage Immune Response (DDIR) Signature in Triple-Negative Breast Cancer (TNBC) Patients from the SWOG 9313c Trial

Project description:Purpose: The purpose of this study was to independently validate two biomarkers, a 44-gene DNA Damage Immune Response (DDIR) signature and stromal tumor-infiltrating lymphocytes (sTILs), as prognostic markers in TNBC patients treated with adjuvant doxorubicin (A) and cyclophosphamide (C) in SWOG 9313. Materials & Methods: 425 centrally determined TNBC cases from S9313 were identified. DDIR signature was performed on RNA isolated from FFPE tumor tissue (n=381), and samples were classified as DDIR-negative or positive using predefined cutoffs. Evaluation of sTILs was performed as previously described. Markers were tested for prognostic value for disease-free and overall survival (DFS, OS) using Cox regression models adjusted for treatment assignment nodal status and tumor size. Results: Among 425 TNBC patients, median age was 45 years, and 33% were node-positive. DDIR was successfully tested in 90% (381/425) of cases, of which 62% were DDIR signature-positive. DDIR signature positivity was associated with improved DFS (HR=0.67; 95% CI 0.48–0.92, P=0.014) and OS (HR=0.61; 95% CI 0.43–0.89, P=0.009). sTILs density assessment was available in 99% of patients and was associated with improved DFS (HR=0.70; 95% CI 0.51–0.96, P=0.028 for sTILs density ≥20% vs. <20%) and OS (HR=0.59; 95% CI 0.41–0.85, P=0.004 for sTILs density ≥20% vs. <20%). The DDIR signature score and sTILs density were moderately correlated (r=0.62) which precluded statistical significance for DFS in a joint model (P=0.08 for DDIR and P=0.25 for sTILs). Conclusion: The prognostic role of sTILs and DDIR in early-stage TNBC was confirmed. DDIR signature conferred improved prognosis in two-thirds of TNBC patients treated with adjuvant AC. DDIR signature has potential to stratify outcome and identify patients with less projected benefit following AC chemotherapy. Clinical trial number: Int0137 (The trial pre-dates Clinicaltrial.Gov website establishment)

2019-09-13 | GSE137356 | GEO

Oniticellus cinctus strain:OS

Project description:Oniticellus cinctus strain:OS Metagenomic assembly

| PRJNA321463 | ENA

CALGB/SWOG 80405 ct DNA Biomarker Evaluation

Project description:CALGB/SWOG 80405 ct DNA Biomarker Evaluation

| PRJNA846484 | ENA

CALGB/SWOG 80405 ct DNA Biomarker Evaluation

Project description:CALGB/SWOG 80405 ct DNA Biomarker Evaluation

| PRJNA846485 | ENA

mRNA Expression data from human osteosarcoma (OS)

Project description:To explore possible oncogenic factors in OS, we used a microarray-based approach to profile changes in the expression of mRNAs in five OS cell lines and human mesenchymal stem cells (hMSCs). We used a microarray-based approach to profile the mRNA expression of OS

2015-07-01 | GSE70414 | GEO

miRNA Expression data from human osteosarcoma (OS)

Project description:To explore possible oncogenic factors in OS, we used a microarray-based approach to profile changes in the expression of miRNAs in five OS cell lines and human mesenchymal stem cells (hMSCs). We used a microarray-based approach to profile in the miRNA expression of OS

2015-07-01 | GSE70367 | GEO

Heterogenous radiomics patterns are associated with poor survivals and dysregulated pathways in medulloblastoma

Project description:Background. To develop a radiomics signature for predicting overall survival (OS) and progression-free survival (PFS) in patients with medulloblastoma (MB), and to investigate the incremental prognostic value and underlying biological pathways of the radiomics signature.Methods. A radiomics signature was constructed based on five magnetic resonance (MR) sequences (T1, T1c, T2, FLAIR and ADC) from a training cohort (n = 83) using LASSO-Cox model. Association between the signature and survival was evaluated on a testing cohort (n = 83). Incremental prognostic value of the signature beyond clinicomolecular factors was assessed with respect to calibration, discrimination, reclassification and clinical usefulness by a radiomics-clinicomolecular nomogram. Key pathways associated with the signature were identified. Prognostic value of pathway genes was assessed in a public TCGA cohort.Results. The radiomics signature was significantly associated with OS/PFS, independent from clinicomolecular factors. The radiomics-clinicomolecular nomogram predicted OS (C-index 0.762) and PFS (C-index 0.697) better than either the radiomics signature (C-index: OS: 0.649; PFS: 0.593) or the clinicomolecular nomogram (C-index: OS: 0.725; PFS: 0.691) only, with a better calibration and classification accuracy (net reclassification improvement: OS: 0.298, P = 0.022; PFS: 0.252, P = 0.026). Nine pathways were significantly correlated with the radiomics signature. Average expression value of pathway genes achieved significant risk stratification in public cohort (log-rank P = 0.016). Conclusion. This study demonstrated radiomics signature was an independent prognostic marker and offered incremental value over clinicomolecular factors in OS/PFS predictions for MB patients. The signature was associated with dysregulated pathways affecting patient prognosis in MB.

2020-06-01 | GSE151519 | GEO

Gene expression profile at single cell level of cells from OS tissue of OS lung metastatic patient

Project description:The tumor microenvironment remains unclear in OS lung metastatic patient. We used single cell RNA-seq to analyze the non-immune and immune landscape of the tumor microenvironment in OS patients.

2024-01-17 | GSE234187 | GEO

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