6048 results for "canc*"

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• NCTN: Treatment of Atypical Teratoid/Rhabdoid Tumors (AT/RT) of the Central Nervous System with Surgery, Intensive Chemotherapy, and 3-D Conformal Radiation (ACNS0333)

  Study ID: ACNS0333NCT Number: NCT00653068 Children's Oncology Group (COG)Submitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: Treatment of Atypical Teratoid/Rhabdoid Tumors (AT/RT) of the Central Nervous System with Surgery, Intensive Chemotherapy, and 3-D Conformal Radiation (ACNS0333)Trial Description: This phase III trial studies the side effects of combination chemotherapy, 3-dimensional conformal radiation therapy, and an autologous peripheral blood stem cell transplant, and to see how well they work in treating young patients with atypical teratoid/rhabdoid tumor of the central nervous system. Giving high-dose chemotherapy before an autologous peripheral blood stem cell transplant stops the growth of cancer cells by stopping them from dividing or killing them. Giving colony-stimulating factors, such as G-CSF, helps stem cells move from the bone marrow to the blood so they can be collected and stored. Chemotherapy or radiation therapy is then given to prepare the bone marrow for the stem cell transplant. The stem cells are then returned to the patient to replace the blood-forming cells that were destroyed by the chemotherapy or radiation therapy. Clinical data presented in the following publication(s): PMID 32105509 Disease type(s): CNS Neoplasm (Primary Tumor) - Embryonal Tumors of the CNSClinical Dataset(s) included:NCT00653068-D1 (PMID 32105509): There are 3 datasets (-D1 through -D3) for ACNS0333's primary publication, PMID 32105509. This dataset, NCT00653068-D1, provides information on the flow of patients enrolled in ACNS0333 through therapy shown in the CONSORT diagram in Figure 2, baseline characteristics, extent of tumor resection, methylation, ATRT subgroup, SMARCB1 status, induction response, survival, and cause of death data. There is one row for each patient enrolled.NCT00653068-D2 (PMID 32105509): There are 3 datasets (-D1 through -D3) for ACNS0333's primary publication, PMID 32105509. This dataset, NCT00653068-D2, provides specific incidence of grade 4 or higher adverse events that occurred in 5% or more of patients in at least one phase of therapy, as presented in Table A2 (Treatment-Associated Toxicity).NCT00653068-D3 (PMID 32105509): There are 3 datasets (-D1 through -D3) for ACNS0333's primary publication, PMID 32105509. This dataset, NCT00653068-D3, provides event-free survival (EFS) data for the primary analytic comparison: ACNS0333 patients You are encouraged to view the PDF data dictionaries found in the "Documents" tab of the dbGaP study page, which may contain additional information regarding the data or the associated publication(s).

  Study phs004137

• MP2PRT: Genomic and Molecular Characterization of Biomarkers Associated with Tumor Angiogenesis, DNA Repair, and Immunologic Tolerance using Samples from the NRG Oncology Phase 3 Randomized Trial, GOG-0240 (NCT00803062)

  The Molecular Profiling to Predict Response to Treatment (MP2PRT) program is part of the NCI's Cancer Moonshot Initiative. The aim of this program is the retrospective characterization and analysis of biospecimens collected from completed NCI-sponsored trials of the National Clinical Trials Network and the NCI Community Oncology Research Program. This study is one of the selected studies under this program. For this study, genomic characterization (WGS, WXS, Total RNAseq, miRNAseq) has been performed on cervical tumor tissue from patients with advanced disease (persistent, recurrent, and metastatic) and matching germline samples. It is hypothesized that the characterization of these tissues using next generation sequencing will lead to the identification of relevant novel genetic aberrations within the immunologic, DNA repair, and tumor angiogenesis domains that dichotomize the study population into exceptional responders and non-responders to systemic therapy, with a spectrum of response manifesting between the two extremes.

  Study phs002293

• SMARCB1 Missense Mutants Destabilize SWI/SNF Complex Stability and Remodeling Activity

  Study Design and Aims: This study utilizes a comprehensive deep mutational scanning (DMS) approach to systematically assess the functional consequences of 8,418 amino acid substitutions in the SMARCB1 gene, a core subunit of the SWI/SNF chromatin remodeling complex. The primary aim is to evaluate how missense mutations affect SMARCB1's tumor suppressor function and its role in the assembly and activity of distinct SWI/SNF subcomplexes (cBAF, PBAF, and GBAF). By addressing functional impacts across the entire coding sequence of SMARCB1, the study seeks to elucidate the molecular mechanisms underlying chromatin remodeling deficiencies caused by SMARCB1 missense mutations and their implications for cancer biology and diagnostics.Population Information: The study focuses on functional variants of SMARCB1, specifically addressing the mutational landscape relevant to cancers such as malignant rhabdoid tumor (MRTK), atypical teratoid rhabdoid tumor (ATRT), and renal medullary carcinoma (RMC). Variants are modeled using in vitro systems to characterize their functional consequences.Molecular Technologies: This study first uses DMS for the systematic identification of functionally disruptive mutations in SMARCB1. Top hits identified through DMS were validated using complementary molecular technologies. These included RNA sequencing (RNA-Seq) to evaluate transcriptional changes associated with specific mutations, ATAC-sequencing (ATAC-seq) to assess chromatin accessibility and remodeling activity, and mass spectrometry to analyze SWI/SNF complex composition in the presence of specific mutations. Principal Findings: The study identifies a subset of missense mutations within the RPT2 domain of SMARCB1 that impair SWI/SNF complex stability and chromatin remodeling, despite retaining detectable protein expression. Notably, these findings challenge current diagnostic methods that rely solely on immunohistochemistry to assess protein presence, as some functionally disruptive mutations retain detectable expression.Data Available through dbGaP: The dataset includes RNA-Seq and ATAC-seq data detailing transcriptional and chromatin accessibility changes associated with validated mutations, mass spectrometry data documenting SWI/SNF complex composition and stability in the context of specific mutations, and functional assay results for all SMARCB1 variants assessed via DMS. This dataset provides a valuable resource for understanding SMARCB1's role in chromatin biology and for improving the classification of variants of uncertain significance (VUS) in clinical diagnostics.

  Study phs003896

• Transcriptome-Wide Association Study (TWAS) to Identify Susceptibility Genes for Colorectal Cancer

  This study included genotype data from 420 study participants of East Asian descent, along with RNA-seq (n=300) and small RNA seq data (n=400) generated from their colorectal tissue samples. We used the transcriptome data and genotype data from these individuals to build a prediction model for each coding gene and long non-coding RNA, and perform a Transcriptome-Wide Association Study (TWAS) of colorectal cancer in East Asian populations.

  Study phs002813

• Transcriptional Profiling of a Dana-Farber Cancer Institute Early-Onset Colorectal Cancer Cohort

  We generated bulk RNA-seq data from 83 early-onset colorectal cancer primary tumors. Tumor samples were obtained from patients seen at the Dana-Farber Cancer Institute's Gastrointestinal Cancer Center with an age of diagnosis less than 50 years.

  Study phs004807

• GWA Study of Oral Cavity, Pharynx and Larynx Cancers in European, and North and South American Populations - CIDR

  There is striking geographical variation in head and neck cancer (HNC) incidence globally. Some of the highest incidence rates have been observed in Southern and Eastern Europe and South America. The goal of this project is to assess susceptibility loci across and within ancestral backgrounds, using the All of Us array. Ten studies have come together in this initiative.

  Study phs002503

• Proteogenomic Characterization of Human Uterine Cervical Cancer

  We report a proteogenomic analysis of human cervical cancer. Mutation-phosphorylation correlations revealed associations of proliferation and invasion-related signaling pathways with somatic mutations in significantly mutated genes. mRNA-protein abundance correlations identified molecules with tumor promoting or suppressing functions correlating with patient survival. Integrated clustering of mRNA, protein, and phosphorylation data provided six subtypes (Sub1-6) of cervical cancer. Compared with the previous subtypes identified from transcriptome data, protein data further identified subgroups of squamous carcinoma and adenocarcinoma based on stromal and immune characteristics. In the squamous subgroups, Sub4 showed higher T-cell immunity than Sub5, and myeloid-derived suppressive immune cells that inhibit T-cell proliferation were enriched in Sub5. In the adeno subtypes, Sub3 had higher myofibroblasts that modulate anti-tumor immunity than Sub6. These stromal and immune features were consistent with the survival patterns of patients in the subtypes. Our proteogenomic analysis provides patient stratification and therapeutic targets in cervical cancer and improves our understanding of cancer biology.

  Study phs002916

• Cancer Associated Fibroblasts Drive Epithelial to Mesenchymal Transition and Classical to Basal Change in Pancreatic Cancer Cells with Loss of IL-8 Expression

  We examined the transcriptional changes induced by cancer associated fibroblasts in pancreatic ductal adenocarcinoma patient-derived tumor organoids. We hypothesized that cancer associated fibroblasts (CAFs) impacted tumor cell transcriptional phenotypes to promote more tumorigenic behavior. Using patient-matched cells from 8 patients, we compared the transcriptional profiles of patient-derived organoids in monoculture to patient-derived organoids co-cultured with autologous CAFs. Similarly, we looked at the transcriptional changes in matched patient-derived CAFs grown in monoculture or co-cultured with patient-derived organoids. With a focus on intercellular crosstalk, we identified crosstalk between CAFs and patient-derived organoids through changes in tumor cell classification (classical vs basal) and a phenotype of more prominent epithelial to mesenchymal transition. We also identified IL8 as a regulator for maintaining a classical tumor cell phenotype. This was identified by bulk RNA sequencing and examined dynamically in organoid-CAF co-culture. This dbGaP deposit is the bulk RNA sequencing data for these 8 patients. The deposit for 3 additional patients from this cohort who did not receive neoadjuvant chemotherapy can be found at: phs003563.

  Study phs004499

• Multiomic Landscape of Multiple Myeloma Precursor and Relapsed Disease

  Multiple myeloma (MM) is a treatable, though incurable, plasma cell malignancy. The molecular mechanisms driving disease onset and the emergence of drug resistance remain elusive. To better characterize the mutational, transcriptional, and epigenetic alterations that accompany MM disease evolution, we accessed molecular data from MM patients treated at Moffitt Cancer Center, with bone marrow biopsies collected between 2011 and 2023.We performed scMultiome (single-cell, paired RNA/ATAC-Seq, 10x Genomics) on 18 CD138+-selected bone marrow aspirate samples, including: 2 healthy donors, 3 patients with monoclonal gammopathy of undetermined significance (MGUS), 4 with smoldering myeloma (SMM), 3 with newly diagnosed MM (NDMM), 1 with early relapse MM (ERMM, 1 to 3 lines of therapy), and 5 with late relapse MM (LRMM, 4 or more lines of therapy). Our dataset includes a sequential sample: a patient with a premalignant condition ("scMultiome_SMM_4") that progressed to active myeloma ("scMultiome_NDMM_3"). These data allow for the assessment of transcriptional and epigenetic dysregulation at the cellular level. Our findings illustrate the dynamic epigenetic and transcriptional landscapes that accompany MM disease progression.We also conducted CUT&Tag analysis on 4 NDMM and 4 LRMM samples to map histone modifications, specifically H3K27ac, to investigate their role in transcriptional reprogramming observed in advanced stages of MM. This analysis revealed sample heterogeneity in terms of super-enhancer-regulated genes associated with active transcription.This cohort also includes samples from the clinical trial NCT04151667, “Daratumumab-Based Response-Adaptive Therapy for Older Adults With Newly Diagnosed Multiple Myeloma.” We performed scRNAseq (single-cell RNA sequencing, 10x Genomics) on 30 CD138+-selected bone marrow aspirate samples and 31 pre-sort samples featuring bone marrow mononuclear cells of various cell types from 5 healthy donors and 11 patients with newly diagnosed MM (NDMM). Our dataset includes sequential samples for all 11 NDMM patients, both prior to induction therapy (denoted by ‘a') with Daratumumab and Dexamethasone, and at cycle 2 day 22 (C2D22, i.e., 60 days after induction therapy start, denoted by ‘b'). For three NDMM patients, we also have samples at relapse (denoted by ‘c'). These data allow for the assessment of transcriptional dysregulation at the single-cell level in both the tumor and immune-tumor microenvironment, associated with Daratumumab treatment in NDMM patients.In addition to the molecular data, demographic, and phenotypic information for all samples is provided.

  Study phs003892

• Whole-Exome Sequencing of Acute Myeloid Leukemia

  The Fanconi anemia (FA) pathway is a tumor-suppressive network comprised of at least 22 genes. We demonstrate that the FA pathway disruption sensitizes Acute Myeloid Leukemia (AML) cells to PLK1 inhibition (iPLK1). We obtained cryopreserved mononuclear cells (MNCs) derived from the bone marrow of 16 adult AML patients from the Indiana University Simon Comprehensive Cancer Center (IUSCCC) Biospecimen Collection and Banking Core as a panel for comparative volasertib (iPLK1) sensitivity assessment. Through whole-exome sequencing (WES), we identified multiple pathogenic mutations in FA pathway and FA pathway-associated genes. We found that higher FA pathway mutation burden correlated with sensitivity to volasertib.

  Study phs003966