6048 results for "canc*"

in 29.69 milliseconds.

• Center for Cancer Genomics (CCG) Cancers of Unknown Primary Project (CUPP)

  The Cancers of Unknown Primary Project (CUPP) aims to characterize difficult tumor types with the goal of determining future best treatment practices. NCI will utilize whole exome sequencing, copy-number variation, DNA methylation in conjunction with transcriptome sequencing to provide a comprehensive genomic landscape of Cancers of Unknown Primary (CUP). The samples will be processed and submitted for genomic characterization using pipelines and procedures established within the Center for Cancer Genomics (CCG).

  Study phs001801

• Derivation of Doxorubicin Mutational Signatures in Cancer

  Study design and aims: This study utilizes doxorubicin exposed cell lines to derive doxorubicin mutational signatures. To validate the methodology used (bulk whole-genome sequencing of cells exposed to drug with a pulsed dose-escalation approach), cisplatin mutational signatures are first derived and compared to previously published data (single constant dose of drug and whole-genome sequencing of single-cell clones). The primary aim of the study was to characterize the impact of doxorubicin mutagenesis on the genome. Furthermore, to assess the presence of derived doxorubicin signatures in patient samples treated with a doxorubicin-containing regimen. Population information: The study utilizes atypical teratoid rhabdoid tumor (ATRT) (n=2) and renal medullary carcinoma (RMC) (n=2) cell lines. To acquire cisplatin and doxorubicin exposed cells, parental cells were treated with escalating doses of cisplatin and doxorubicin in a pulsed manner for between 2-12 months. This study also contains 2 cell lines derived from one patient with metastatic disease, treated with a doxorubicin-containing regimen. Molecular technologies: Whole-genome sequencing of the bulk cell population.Principal findings: Cisplatin mutational signatures were consistent with previously published data. This study identified two related single-base substitution (SBS) doxorubicin mutational signatures. While the two resulting signatures had some similarities, they differed in their frequencies of C > A (SBS-Doxorubicin-1) and T > C (SBS-Doxorubicin-2) substitutions. A double-base substitution (DBS) signature was also observed in association with SBS-Doxorubicin-2. This DBS signature harbored peaks at TG > CA, TG > GT, and TT > CC substitutions. Next, two INDEL signatures were derived. The first consisted of 1bp insertions and deletions at T homopolymers, >=2bp insertions at repetitive DNA, and microhomology deletions. The second consisted of >=2bp insertions at non-repetitive regions. Finally, both SBS-Doxorubicin signatures were found to be significantly present in patient samples exposed to a doxorubicin-containing regimen. Data Available through dbGaP: This dataset contains paired-end whole genome sequencing of parental (n=4), cisplatin exposed (n=2), and doxorubicin exposed (n=4) SMARCB1-deficient cell lines, as well as cell lines derived from one patient with metastatic disease (n=2), where the patient was treated with a doxorubicin-containing regimen.

  Study phs004740

• NCTN: A Phase III Randomized Study of Nivolumab Plus Ipilimumab versus Nivolumab for Previously Treated Patients with Stage IV Squamous Cell Lung Cancer and No Matching Biomarker (Lung-Map Sub-Study) (S1400I)

  Study ID: S1400INCT Number: NCT02785952SWOG Cancer Research NetworkSubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Phase III Randomized Study of Nivolumab plus Ipilimumab versus Nivolumab for Previously Treated Patients with Stage IV Squamous Cell Lung Cancer and No Matching Biomarker (Lung-Map Sub-Study) (S1400I)Trial Description: This randomized phase III trial compares nivolumab with ipilimumab and nivolumab alone in treating patients with stage IV squamous cell lung cancer that has come back after previous treatment. This is a "non-match" sub-study that includes all screened patients not eligible for a biomarker-driven sub-study. Monoclonal antibodies, such as nivolumab and ipilimumab, may be able to shrink tumors. It is not yet known whether nivolumab works better with or without ipilimumab in treating patients with squamous cell lung cancer. Clinical data presented in the following publication(s):PMID 34264316 Disease type(s): Lung, Mediastinal and Pleural Neoplasm - Non-Small Cell Lung CancerClinical Dataset(s) included:NCT02785952-D1 (PMID 34264316): There are three datasets (-D1 through -D3) for PMID 34264316, a primary publication for S1400I. This clinical dataset, NCT02785952-D1, contains patient-level data (one row per patient), including baseline, demographic, metastatic sites, and treatment information. It also contains assessment, survival, reasons for going off treatment, tumor mutational burden, PDL1 expression, and patient-reported outcome data.NCT02785952-D2 (PMID 34264316): There are three datasets (-D1 through -D3) for PMID 34264316, a primary publication for S1400I. This toxicity dataset, NCT02785952-D2, contains event-level data (one row per patient per adverse event experienced on trial).NCT02785952-D3 (PMID 34264316): There are three datasets (-D1 through -D3) for PMID 34264316, a primary publication for S1400I. This dataset, NCT02785952-D3, contains biomarker data (one row per patient per gene alteration).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 phs004242

• DNA Methylation in Prostate Tumor and Paired Benign Tissue for African and European Ancestry Men

  We recruited prostate cancer (PCa) patients undergoing robotic-assisted laparoscopic radical prostatectomy at the University of Chicago Medical Center Urology Clinic between 2011 and 2017. Our study includes 76 African American (AA) and 75 European American (EA) men with PCa of Gleason Score (GS) ≥7, recruited by the Epidemiology Research Recruitment Core at the University of Chicago. All patients consented to the collection of questionnaire data, prostate tissue, and medical records. The study was approved by the Institutional Review Board of the University of Chicago. Following prostatectomy, prostate tissue was sent to the Human Tissue Research Center (HTRC) at the University of Chicago. Each sample underwent histological examination and Gleason scoring by University of Chicago genitourinary pathologists. The presence of adenocarcinoma was confirmed by overexpression of alpha-methylacyl-coenzyme-A racemase (AMACR) and areas for DNA extraction were marked. Tissue samples used for DNA extraction were obtained using with either a 1mm biopunch or laser microdissection of a 100 µm2 area of tissue. Genome-wide DNA methylation profiles were generated using Illumina's Infinium MethylationEPIC BeadChip array kit. Genome-wide SNP data was generated (from benign tissue DNA) using the Illumina Infinium Multi-Ethnic Global-8 v1.0 array at the University of Chicago Genomics Core Facility. We performed imputation using the Haplotype Reference Consortium (HRC, Version r1.1 2016) panel, which includes all samples from the 1,000 Genomes Project (Phase 3), using the Michigan Imputation Server. The imputed SNP data for mQTL analysis was imputed based on genotype SNP data which was all from benign tissue DNA and the methylation data was identified in both tumor and benign tissue, both AA and EA men, and identified QTLs co-occuring with prostate cancer susceptibility loci.Data including SNP genotypes, DNA methylation, tissue type, and participant characteristics will be available in dbGaP.

  Study phs003516

• NCTN: Dexamethasone Compared with Prednisone During Induction Therapy and Methotrexate with or without Leucovorin During Maintenance Therapy in Treating Patients with Newly Diagnosed High-Risk Acute Lymphoblastic Leukemia (AALL0232)

  Study ID: AALL0232NCT Number: NCT00075725 Children's Oncology Group (COG)Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: Dexamethasone Compared with Prednisone during Induction Therapy and Methotrexate with or without Leucovorin during Maintenance Therapy in Treating Patients with Newly Diagnosed High-Risk Acute Lymphoblastic Leukemia (AALL0232)Trial Description: This randomized phase III trial is studying dexamethasone to see how well it works compared to prednisone during induction therapy. This trial is also studying methotrexate and leucovorin calcium to see how well they work compared to methotrexate alone during maintenance therapy in treating patients with newly diagnosed acute lymphoblastic leukemia (ALL). Drugs used in chemotherapy, such as dexamethasone, prednisone, methotrexate, and leucovorin calcium, work in different ways to stop cancer cells from dividing so they stop growing or die. Giving more than one drug may kill more cancer cells. It is not yet known which combination chemotherapy regimen is more effective in treating acute lymphoblastic leukemia. Clinical data presented in the following publication(s):PMID 27114587Disease type(s): Hematopoietic Neoplasm/Leukemia - Acute Lymphoblastic LeukemiaClinical Dataset(s) included:NCT00075725-D1 (PMID 27114587): There are three datasets associated with this publication (NCT00075725-D1, NCT00075725-D2, and NCT00075725-D3): NCT00075725-D1 includes all patients enrolled on the study. This dataset contains baseline characteristics, BCR-ABL fusion status, MLL rearrangement, bone marrow status at end of induction, and survival data.NCT00075725-D2 (PMID 27114587): There are 3 datasets associated with this publication (NCT00075725-D1, NCT00075725-D2, and NCT00075725-D3). NCT00075725-D2 is the subset of patients included in the randomized comparison between Capizzi and High-dose Methotrexate. The dataset includes baseline characteristics, BCR-ABL fusion status, MLL rearrangement, bone marrow status at end of induction, and survival data. Outcomes (EFS time, EFS indicator) in this dataset are different from the outcomes in NCT00075725-D1. The outcome of those assigned to Capizzi who subsequently received High-dose Methotrexate was censored at time of therapy crossover, since in AALL0232, therapy changes were recommended to provide HD-MTX to all participants who had not yet completed maintenance course 1 or received cranial irradiation.NCT00075725-D3 (PMID 27114587): There are three datasets associated with this publication (NCT00075725-D1, NCT00075725-D2, and NCT00075725-D3). NCT00075725-D3 is the toxicity data observed in the randomized cohorts (steroid and methotrexate).Additional whole genome genotyping data for this trial is available under phs001350.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 phs004039

• Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial (ALLHAT-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. ObjectivesHypertension Study: To determine whether treatment with a calcium channel blocker or an angiotensin-converting enzyme inhibitor lowers the incidence of coronary heart disease (CHD) or other cardiovascular disease (CVD) events vs treatment with a diuretic.Lipid Study: To determine whether pravastatin compared with usual care reduces all-cause mortality in older, moderately hypercholesterolemic, hypertensive participants with at least an additional CHD risk factor. BackgroundHypertension Study: Antihypertensive therapy is well established to reduce hypertension-related morbidity and mortality, but the optimal first-step therapy is unknown.Lipid Study: Studies have demonstrated that statins administered to individuals with risk factors for coronary heart disease (CHD) reduce CHD events. However, many of these studies were too small to assess all-cause mortality or outcomes in important subgroups.ParticipantsHypertension Study: A total of 33,357 participants. Lipid Study: A total of 10,355 participants. Baseline mean total cholesterol was 224 mg/dL; LDL-C, 146 mg/dL; high-density lipoprotein cholesterol, 48 mg/dL; and triglycerides, 152 mg/dL. Mean age was 66 years; 49% were women, 38% black and 23% Hispanic, 14% had a history of CHD, and 35% had type 2 diabetes. DesignHypertension Study: A randomized, double-blind, active-controlled clinical trial conducted from February 1994 through March 2002. Participants were randomly assigned to receive chlorthalidone, 12.5 to 25 mg/d (n = 15,255); amlodipine, 2.5 to 10 mg/d (n = 9048); or lisinopril, 10 to 40 mg/d (n = 9054) for planned follow-up of approximately 4 to 8 years. The primary outcome was combined fatal CHD or nonfatal myocardial infarction, analyzed by intent-to-treat. Secondary outcomes were all-cause mortality, stroke, combined CHD (primary outcome, coronary revascularization, or angina with hospitalization), and combined CVD (combined CHD, stroke, treated angina without hospitalization, heart failure (HF), and peripheral arterial disease).Lipid Study: Multicenter (513 primarily community-based North American clinical centers), randomized, non-blinded trial conducted from 1994 through March 2002 in a subset of participants from the Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial (ALLHAT). The interventions in the trial were pravastatin, 40 mg/d, vs usual care. The primary outcome was all-cause mortality, with follow-up for up to 8 years. Secondary outcomes included non-fatal myocardial infarction or fatal CHD (CHD events) combined, cause-specific mortality, and cancer.ConclusionsHypertension Study: Thiazide-type diuretics are superior in preventing one or more major forms of CVD and are less expensive. They should be preferred for first-step antihypertensive therapy.Lipid Study: Pravastatin did not reduce either all-cause mortality or CHD significantly when compared with usual care in older participants with well-controlled hypertension and moderately elevated LDL-C. The results may be due to the modest differential in total cholesterol (9.6%) and LDL-C (16.7%) between pravastatin and usual care compared with prior statin trials supporting cardiovascular disease prevention.

  Study phs004021

• Pre-Existing Skin-Resident CD8 and γδ T Cell Circuits Mediate Immune Response in Merkel Cell Carcinoma and Predict Immunotherapy Efficacy

  Merkel cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer with a ~50% response rate to immunotherapy. Here, we attempted to identify novel predictive biomarkers of response through extensive and deep multi-omics interrogation of 186 samples from 116 patients. We collectively integrated bulk RNAseq, single-cell RNAseq, multiplex immunofluorescence, and spatial transcriptomics. Importantly, we were also able to study 14 matched pairs of tissue samples from pre- and post-immunotherapy. In non-responders, tumors show evidence of increased tumor cell cycling, expression of neuronal stem cell markers, and IL-1α/β. Responders have evidence of increased type I/II interferon signatures and evidence of pre-existing tissue resident (Trm) CD8 or Vδ1 γδ T cells that functionally converge with overlapping antigen-specific transcriptional programs and clonal expansion of multiple T cell receptors. Spatial transcriptomics demonstrated higher co-localization of T cells with B and dendritic cells in responders, with evidence of expression of chemokines important for co-stimulation. Finally, immunotherapy increased clonal expansion or recruitment of Trm and Vδ1 cells in tumors in responders, further underscoring their therapeutic importance. These data identify potential novel actionable biomarkers and therapeutic targets for MCC.

  Study phs003629

• Analyzing Somatic Mutagenesis in Systemic Sclerosis

  The study was undertaken with the aim of estimating differences in the mutational burden in lung tissues from healthy vs systemic sclerosis (SSc) patients. SSc is an auto-immune disease, with patients often developing cancer. However, the etiology of this phenomenon is poorly understood. As such we sought to uncover potential molecular mechanisms prevalent within SSc tissues that might be potentiating cancer. Samples were randomly collected from individuals from two broad ethnic groups, European (EA) and African American (AA). In total, samples were obtained from 7 individuals belonging to the EA group and 4 individuals from the AA group. For this study, ethnicity was not included as a confounding variable, given that the data set has roughly comparable number of individuals from both ethnicities for the healthy and SSc cohorts. Study participants ranged in age from 37-63 years old. Median age (52 years old) of healthy individuals was comparable to the SSc cohort (~48 years old). Participants were self-described as current/former smokers or non-smokers. Lung tissues were obtained under a protocol approved by the University of Pittsburgh Institutional Review Board. Written informed consent statements were provided to the University of Pittsburgh IRB by the study participants/patients. Sample sizes were determined by the ability of bulk lung fibroblast tissues to stably propagate in culture until single cell clones could be obtained. Samples for which sufficient cell density could not be achieved for downstream high-depth sequencing analysis were excluded from the study and are not reported. Five or greater than 5 samples are collected from each cohort including healthy and SSc patients. Subjects were allocated to two basic cohorts based on diagnosis at the time of explant. Participants with no reported lung anomalies were allocated to the "healthy" cohort, whereas individuals with reported lung abnormalities, primarily SSc with pulmonary fibrosis and/or hypertension were allocated to the "SSc" cohort. All tissue samples were cultured, propagated and processed in identical fashion without requiring individual-specific protocols. Additionally, equivalent amounts of DNA were used for preparing sequencing libraries from both cohorts, and all samples were sequenced using Illumina whole genome sequencing (WGS) and analyzed using identical computational pipelines. Our study primarily discovered that there is a significantly higher burden of somatic mutations in SSc samples, compared to healthy samples. We observed an overall increase in a range of mutations in genomes of SSc patients, including single base substitutions, indels, structural variants and copy number alterations. Additionally, we uncovered a novel mutation signature associated with SSc samples, hinting at the activity of POLH in these samples, and highlighting the potential nexus between inflammation, DNA damage, and cancer.

  Study phs003700

• CSER: Exome Sequencing in Diverse Populations in Colorado and Oregon/CHARM Cancer Health Assessments Reaching Many

  The CHARM (Cancer Health Assessment Reaching Many) study, part of the Clinical Sequencing Evidence-Generating Research (CS.ER2) effort, aimed to assess the utility of clinical exome sequencing and how it affects care in diverse populations. The study population included adults at risk for hereditary cancer syndromes. The primary objective was the implementation of a hereditary cancer risk assessment program in healthy 18-49 year-olds in primary care settings within a vertically integrated health delivery system (Kaiser Permanente) and a federal qualified health center (Denver Health). The investigators aimed to assess clinical exome sequencing implementation and interpretation, as well as tailored interactions for low health literacy including a contextualized consent process, and a modified approach to results disclosure and genetic counseling. The investigators were also assessing the clinical utility (healthcare utilization and adherence to recommended care) and personal utility of primary and additional results from clinical exome sequencing, and evaluate the ethical and policy implications of considering personal utility of genomic information decisions for health care coverage.Sequencing and analysis for CHARM was conducted at the Northwest Clinical Genomics Laboratory, University of Washington, Seattle (https://nwgc.gs.washington.edu/).

  Study phs002111

• HINTS Geo-Coded Data 2014 (HINTS 4 Cycle 4)

  The Health Information National Trends Survey (HINTS) is a nationally representative survey which has been administered every few years by the National Cancer Institute since 2003. HINTS 4 includes four mail-mode data collection cycles over the course of three years. Cycle 4 was conducted from August 19 through November 17, 2014. Cycle 4 was conducted by mail using a protocol similar to that used in Cycles 1, 2, and 3 with a goal of obtaining 3,500 completed questionnaires, with a final respondent sample of 3,677.

  Study phs004209