6048 results for "canc*"

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• Field Effect-Informed Urine Liquid Biopsy Analysis for Assessment of Adjuvant BCG Response in Non-Muscle Invasive Bladder Cancer

  The goal of this study was to develop a urine tumor DNA-based minimal residual disease liquid biopsy assay for bladder cancer that improves specificity by considering field effect mutations. We performed targeted cell free DNA sequencing on tumor, adjacent normal, and urine cell free DNA (cfDNA) from non-muscle invasive bladder cancer patients and urine cfDNA from healthy controls. We developed a method called RePhyNERX and used it to identify three molecular response classes: complete responders to surgery, responders to adjuvant Bacillus Calmette-Guérin immunotherapy, and non-responders. These molecular classifications correlated with patient outcome. We also performed RNA sequencing on tumor tissues to identify expression differences between the response classes.

  Study phs004110

• The Discovery and Validation of AML Prognostic Biomarkers

  This study includes RNA-Seq and targeted DNA sequencing from a large collection of unsorted mononuclear cells (MNCs) and enriched viable leukemic blasts (VLBs) from bone marrow (BM) and peripheral blood (PBL) specimens collected at diagnosis from adult patients with acute myeloid leukemia (AML). Viable leukemic blasts were isolated using forward by side scatter, DAPI staining and fluorescently-labeled antibodies to CD45, CD34, CD38, and CD117. DNA and RNA were extracted using Qiagen AllPrep DNA/RNA Extraction kits. Transcriptome libraries were generated using KAPA Stranded RNA-Seq Library Preparation Kit after ribosomal RNA depletion with Roche RiboErase. Paired-end 75 bp reads were sequenced on either Illumina HiSeq 2500 (HiSeq) or NovaSeq 6000 (NovaSeq) instruments. RNA-Seq data were analyzed by the Fred Hutch Cancer Center Bioinformatics Shared Resource. STAR 2.7.1, with 2-pass mapping, was used to align reads to human reference genome GRCh37/hg19. Internal tandem duplication in FLT3 (FLT3-ITD) were identified via fragment analyses. DNA was sequenced using Illumina TruSight™ Myeloid Sequencing Panel and supplemented with in-house targeted MiSeq assays for CEBPA and NRAS exon 3 loci inadequately covered by TruSight™ platform on Illumina MiSeq instrument. Paired-end reads were first aligned to the human genome reference assembly (GRCh37/hg19) using Burrows-Wheeler Aligner (BWA, v0.7.12) and then, the resulting alignment data were processed according to the best practice of Genome Analysis Toolkit (GATK, v3.5).

  Study phs002805

• Southern Community Cohort Study - the Gut Microbiome Project

  The Southern Community Cohort Study (SCCS) is an ongoing prospective cohort study, with the aim to investigate risk factors of cancer and other chronic diseases across 12 southeastern U.S. states: Alabama, Arkansas, Florida, Georgia, Kentucky, Louisiana, Mississippi, North Carolina, South Carolina, Tennessee, Virginia, and West Virginia. Approximately 86,000 adults, two-thirds Black people, between 40 and 79 years of age were enrolled from 2002 to 2009. Approximately 86% of the participants were recruited from community health centers (CHCs) and institutions providing basic health care and preventative services in underserved areas, so the cohort encompassed a substantial number of individuals characterized by low income, low education, and lack of insurance. The remaining 14% of cohort participants were recruited through mail-based general population sampling. Sociodemographic characteristics, lifestyle factors including tobacco exposure and alcohol consumption, and personal medical history were collected at cohort enrollment. Data collection methods varied by recruitment source: CHC participants completed standardized computer-assisted personal interviews, while individuals from the general population responded to self-administered mailed questionnaires. The SCCS Biospecimen Repository includes blood samples from ~40,000, mouth cells from 39,000, urines from 24,000, stool specimens from 8,000 participants, and tumor blocks from incident cancer cases. This microbiome study nested within SCCS included 594 Black participants whose stool samples were analyzed using shotgun metagenomic sequencing. We investigated associations between the gut microbiome and several physical activity measures.

  Study phs004716

• Childhood Cancer Data Initiative (CCDI): NCI-COG Pediatric MATCH Precision Medicine Clinical Trial

  The National Cancer Institute-Children's Oncology Group (NCI-COG) Pediatric Molecular Analysis for Therapy Choice (MATCH) trial provides a framework for biomarker-driven early phase trials of targeted therapies in pediatric and young adult cancer patients across the United States. Pediatric MATCH enrolled more than 1,300 patients with treatment-refractory cancers, offering access to molecular screening and investigational targeted therapies. To further advance this, matched diagnostic, refractory tumor, and normal samples from Pediatric MATCH cases were molecularly characterized, creating one of the largest comprehensive data sets available for childhood cancers. This analysis has the potential to provide novel insights into the genetics of refractory pediatric, adolescent, and young adult cancers, as well as inform potential therapeutic strategies. The following molecular characterization assays were performed: Tumor whole exome sequencing (WES) Tumor whole genome sequencing (WGS) Tumor RNA sequencing (RNA-seq) Blood whole exome sequencing (WES) Blood whole genome sequencing (WGS)

  Study phs002883

• Childhood Cancer Data Initiative (CCDI): CCDI Pediatric In Vivo Testing Program - Leukemia

  The goal of this study is to molecularly characterize a large panel of pediatric acute lymphoblastic leukemia (ALL) patient-derived xenografts (PDXs) previously established in immune-deficient mice. These PDXs are utilized as part of the NCI-funded Pediatric Preclinical In vivo Testing (PIVOT) program to identify novel agents and combinations. Biospecimen data include next-generation sequencing (RNAseq, whole exome sequencing, DNA copy number variation), whole-genome analysis of cytogenetic abnormalities, and DNA fingerprint for quality control.

  Study phs003164

• APOLLO-OV: Applied Proteogenomics of High Grade Serous Ovarian Carcinoma

  APOLLO is a proteogenomic study seeking to describe the major genome, transcriptome, proteome and phosphoproteome alterations, subtypes, and molecular predictors of patient outcomes. This study includes 70 high grade serous ovarian carcinoma tissues from the Gynecologic Cancer Center of Excellence (https://medschool.usuhs.edu/gso/research/gyn-cancer-center-of-excellence). Bulk and laser microdissection enriched tumor tissues were profiled by whole genome sequencing, transcriptome sequencing, MS-based proteomics and reverse phase protein arrays. Clinical and sample data include survival times, patient features, and tumor characteristics.

  Study phs003488

• NCTN: A Randomized Phase III Comparison of Standard-Dose (60 Gy) versus High-Dose (74 Gy) Conformal Radiotherapy with Concurrent and Consolidation Carboplatin/Paclitaxel +/- Cetuximab in Patients with Stage IIIA/IIIB Non-Small Cell Lung Cancer (RTOG-0617)

  Study ID: RTOG-0617 NCT Number: NCT00533949 NRG Oncology Submitted in collaboration with the NCTN/NCORP Data Archive Trial Title: NCTN: A Randomized Phase III Comparison of Standard-Dose (60 Gy) versus High-Dose (74 Gy) Conformal Radiotherapy with Concurrent and Consolidation Carboplatin/Paclitaxel +/- Cetuximab in Patients with Stage IIIA/IIIB Non-Small Cell Lung Cancer (RTOG-0617) Trial Description: RATIONALE: Radiation therapy uses high-energy x-rays to kill tumor cells. Drugs used in chemotherapy, such as paclitaxel, carboplatin work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Monoclonal antibodies, such as cetuximab can block tumor growth in different ways. Some block the ability of tumor cells to grow and spread. Others find tumor cells and help kill them or carry tumor-killing substances to them. It is not yet known whether high-dose radiation therapy is more effective than standard-dose radiation therapy when given together with combination chemotherapy with or without cetuximab in treating patients with non-small cell lung cancer. PURPOSE: This randomized phase III trial is studying high-dose or standard-dose radiation therapy given together with chemotherapy with or without cetuximab to see how well they work in treating patients with newly diagnosed stage III non-small cell lung cancer that cannot be removed by surgery. Clinical data presented in the following publication(s): • PMID 25601342 Disease type(s): Lung, Mediastinal and Pleural Neoplasm - Non-Small Cell Lung Cancer Clinical Dataset(s) included: • NCT00533949-D1 (PMID 25601342): There are three datasets for RTOG-0617's primary publication 25601342 (-D1 through -D3). This dataset, NCT00533949-D1, contains treatment arm, baseline characteristics, radiotherapy technique used, EGFR H-score, radiation treatment details, select toxicity data, and survival data. • NCT00533949-D2 (PMID 25601342): There are three datasets for RTOG-0617's primary publication 25601342 (-D1 through -D3). This dataset, NCT00533949-D2, contains adverse events reported in Appendix 10. • NCT00533949-D3 (PMID 25601342): There are three datasets for RTOG-0617's primary publication 25601342 (-D1 through -D3). This dataset, NCT00533949-D3, contains the most frequently reported adverse events reported in Tables 3 and 4. 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 phs004191

• Reduction of Lethal Prostate Cancer Disparities in Underserved Hispanic/Latino Populations

  This pilot study investigated the genomic underpinnings of prostate cancer in Puerto Rican Hispanic/Latino men, a group disproportionately affected by this disease, in terms of incidence, mortality and aggressiveness. By examining tumors from 35 patients for specific genetic mutations and gene expression patterns using cutting-edge genomic sequencing, we aimed to identify distinct genetic profiles that could influence the course of the disease and its treatment. Our initial findings suggest the presence of unique genomic characteristics in this population, offering a promising avenue for developing personalized treatments that could reduce the health disparities observed in these men. This study underscores the importance of including diverse ethnic groups in genomic studies to ensure that the published data required for personalized cancer care are available.

  Study phs004487

• Blood and Marrow Clinical Trials Network - Allogeneic Hematopoietic Cell Transplant for Hematological Cancers and Myelodysplastic Syndromes in HIV-Infected Individuals (BMT CTN-0903-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.Objectives: To evaluate the safety and effectiveness of allogeneic hematopoietic cell transplantation for patients with hematologic malignancies or myelodysplastic syndromes and coincident-HIV infection.Background: Allogeneic hematopoietic cell transplantation (alloHCT) has been a safe and curative option for many patients with hematologic malignancies but was not well studied in the HIV+ population despite the interest in the HIV research community of the curative potential of alloHCT. Hematologic malignancies in people with HIV infection (HIV+) have been associated with poor outcomes due to opportunistic infections, but the development of antiretroviral therapy (ART) has increased the possibility of these patients achieving clinical outcomes comparable to those of the general population following stem cell transplant. The BMT CTN 0903 trial was designed to evaluate the safety and effectiveness of alloHCT for patients with HIV infection and hematologic malignancies.Participants: Patients had documented HIV infection, were a minimum of 15 years of age and had acute myeloid leukemia (AML) or acute lymphocytic leukemia (ALL) in first or second complete remission (CR); Int-2 or high-risk myelodysplastic syndromes (MDS) with CCR5delta32. AlloHCT using cord blood units or T-cell depletion was not allowed. Patients with history of prior alloHCT were excluded. Patients had to meet adequate organ function. Karnofsky/Lansky performance status ≥ 70% and could not have active central nervous system disease, HIV infection resistant to all antiretroviral therapy, or opportunistic infection unresponsive to treatment.There were seventeen HIV-infected patients with acute leukemia, myelodysplasia (MDS), NHL or classical HL who were enrolled in the trial.Design: Patients with HIV infection and hematological malignancies or myelodysplastic syndromes (MDS) were treated with either reduced-intensity conditioning (RIC) or myeloablative conditioning (MAC) followed by alloHCT. RIC or MAC was at the discretion of investigator. Where feasible, an attempt was made to identify hematopoietic cell donors who were homozygotes for the CCR5delta32 polymorphism. Graft-versus-host disease (GVHD) was treated per institutional standards.Four regimens were permitted for conditioning. RIC regimens were: fludarabine and busulfan (Flu/Bu), and fludarabine and melphalan (Flu/Mel). MAC regimens were busulfan and fludarabine (Bu/Flu), or cyclophosphamide and total body irradiation (Cy/TBI). GVHD prophylaxis regimens included tacrolimus/methotrexate, tacrolimus/sirolimus, and post-transplant cyclophosphamide with tacrolimus/mycophenolate. Patients receiving busulfan-containing preparative regimens were not eligible to receive tacrolimus/sirolimus. A committee reviewed individual patient's HIV treatment history and ART options before initiation of the transplant conditioning regimen and advised changes to minimize potential drug interactions. It was recommended that ART be continued except ritonavir-containing regimens during MAC.The goal of the study was to assess the 100-day non-relapse mortality. Secondary endpoints included 100-day disease status, percentage donor chimerism, hematologic function, infections, six-month overall survival (OS), incidence of acute and chronic GVHD, immunologic reconstitution, and impact of alloHCT upon measures of HIV persistence in blood including peripheral blood mononuclear (PBMC)-associated HIV DNA and infectious virus from resting CD4+T-cells using a quantitative virus outgrowth assay.Follow-up visits occurred weekly through 8 weeks post-transplant, at 100 days, 6 months, 1 year, and 2 years.Conclusions: There was no non-relapse mortality (NRM) at 100 days, or at 6 months, and therefore no evidence to suggest that NRM is prohibitive or more than that seen in non-HIV-infected patients. The cumulative incidence of grades II-IV acute GVHD was 41%. After year one, overall survival was 59%. In patients who achieved complete chimerism, cell-associated HIV DNA and inducible infectious virus in the blood were not detectable.

  Study phs004697

• Niraparib in Pancreatic Cancer

  Pancreatic cancer patients with pathogenic variants in DNA repair genes may benefit from PARP inhibitor therapy, but efficacy beyond germline BRCA1/2 mutations remains uncertain. This multicenter phase II trial (NCT03601923) enrolled 32 patients with advanced pancreatic cancer harboring germline or somatic pathogenic variants in BRCA1, BRCA2, PALB2, ATM, or CHEK2 who had not progressed on prior platinum-based chemotherapy. Patients received niraparib 200-300 mg daily. Here we deposit the whole exome samples of six patients from the study (N=13 total samples). Patients P02, P03, P06, and P21 have matched tumor-normal blood pairs; patient P22 has a single tumor sample; and patient P30 has four tumor samples collected at different timepoints for longitudinal analysis.

  Study phs004405