Search Results - EGA European Genome-Phenome Archive

HINTS Geo-Coded Data 2017 (HINTS 5 Cycle 1)

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 5 includes four data collection cycles over the course of four years. The first round of data collection for HINTS 5 (Cycle 1) was conducted from January 25 through May 5, 2017 with a goal of obtaining 3,500 completed questionnaires, with a final sample including 3,285 respondents.

Study phs004210

Clonal Hematopoiesis Dynamics and Evolutionary Fitness During Breast Cancer Treatment Impact Clinical Outcomes

We investigated the impact of cancer therapies on clonal hematopoiesis (CH), the age-associated expansion of somatically mutated hematopoietic stem cells, in patients with breast cancer. We examined 392 serial peripheral blood samples collected before and after treatment using chemotherapy, radiation, and/or hormone therapy from a prospective cohort of 171 patients. Ultra-deep targeted DNA exon sequencing was performed across 81 genes (custom Agilent SureSelectXTHS2 panel, median coverage > 5000x) implicated in hematologic malignancies and CH, enabling precise characterization of the mutational spectrum and longitudinal tracking of clonal dynamics. The primary objective was to understand how different cancer treatments (i.e., chemotherapy, radiation, and hormone therapy) alter the effective hematopoietic population and select for or against specific CH clones. Our analysis revealed that cytotoxic therapies induced significant reductions in allelic diversity, creating therapeutic bottlenecks that led to selective clonal expansion. These selective dynamics were associated with worse clinical outcomes, where patients with positively selected CH during treatment experienced significantly shorter progression-free and overall survival. Data generated from this study, including the sequencing data, treatment exposure data, and clinical outcomes will be made available through dbGaP. Mutation calls used for analyses are included in the medRxiv (2025.08.27.25334581) supplement and will be available in the published version of the manuscript.

Study phs004283

NCTN_NCORP: The Men's Eating and Living (MEAL) Study: A Randomized Trial of Diet to Alter Disease Progression in Prostate Cancer Patients on Active Surveillance (CALGB-70807)

Study ID: CALGB-70807NCT Number: NCT01238172 Alliance for Clinical Trials in OncologySubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN_NCORP: The Men's Eating and Living (MEAL) Study: A Randomized Trial of Diet to Alter Disease Progression in Prostate Cancer Patients on Active Surveillance (CALGB-70807)Trial Description:RATIONALE: Eating a diet high in vegetables may slow down disease progression in patients with prostate cancer.PURPOSE: This randomized clinical trial is studying how well diet works in altering disease progression in patients with prostate cancer on active surveillance. Clinical data presented in the following publication(s):PMID 31935026 Disease type(s): Reproductive System Neoplasm, Male - Prostate CancerClinical Dataset(s) included:NCT01238172-D1 (PMID 31935026): Dataset NCT01238172-D1 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains baseline characteristics, including baseline serum PSA values.NCT01238172-D2 (PMID 31935026): Dataset NCT01238172-D2 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains information for the consort diagram (inclusion/exclusion status, treatment arm).NCT01238172-D3 (PMID 31935026): Dataset NCT01238172-D3 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains survival and time to alternative treatment data.NCT01238172-D4 (PMID 31935026): Dataset NCT01238172-D4 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains information for patient off treatment reasons.NCT01238172-D5 (PMID 31935026): Dataset NCT01238172-D5 is one of 5 datasets associated with PubMed ID 31935026. This dataset contains information for the dietary patterns analysis included in Table 2 and the eTable.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 phs004238

Childhood Cancer Data Initiative (CCDI): Frameshift Mutation Profiling of Constitutional Mismatch Repair Deficiency Syndrome Patients

Samples from patients with Constitutional Mismatch Repair Deficiency Syndrome (CMMRD) were sequenced using the Archer NextSeq platform to detect frameshift mutations in cell-free DNA (cfDNA), matched tumor samples, and other tissue types. The goal of the study is to evaluate whether a frameshift mutation biomarker panel can be used for disease monitoring. Limited treatment information is included when available. The listed genes represent those in which recurrent frameshift mutations were identified and evaluated as candidate biomarkers for disease monitoring in CMMRD.

Study phs004017

Childhood Cancer Data Initiative (CCDI): Metastatic Osteosarcoma Spatial Profiling

This study contains spatial transcriptional profiling of metastatic osteosarcoma specimens using the Visium platform. This work was done as part of the Childhood Cancer Data Initiative (CCDI).

Study phs003975

Genomic Landscape and Preclinical Therapeutic Insights Developed from Xenograft, Organoid, and Cell Line Models in the NCI's Patient-Derived Models Repository

Patient-derived xenografts (PDXs), organoids (PDOrgs), and two-dimensional cell cultures (PDCs) are powerful tools for translational cancer research. The National Cancer Institute's Patient-Derived Models Repository (NCI PDMR) features preclinical models from primary and metastatic lesions across a broad array of solid tumors, including rare and pediatric cancers, each annotated with genomic data as well as clinical information about the patient from whom the model originated (https://pdmr.cancer.gov). We used these models to demonstrate stable propagation of genomic aberrations over multiple passages, to evaluate patient-specific tumor heterogeneity, and to examine the relationship of the preclinical activity of a panel of approved and investigational anticancer agents in PDXs and PDOrgs to known levels of therapeutic activity in the clinic.

Study phs003984

NCTN: Sargramostim, Vaccine Therapy, or Sargramostim and Vaccine Therapy in Preventing Disease Recurrence in Patients with Melanoma That Has Been Removed by Surgery (E4697)

Study ID: E4697NCT Number: NCT01989572 ECOG-ACRIN Cancer Research Group Submitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: Sargramostim, Vaccine Therapy, or Sargramostim and Vaccine Therapy in Preventing Disease Recurrence in Patients With Melanoma That Has Been Removed By Surgery (E4697)Trial Description: This randomized phase III trial studies sargramostim or vaccine therapy alone to see how well they work compared to sargramostim and vaccine therapy together in preventing disease recurrence in patients with melanoma that has been removed by surgery. Sargramostim may stimulate the immune system in different ways and stop tumor cells from growing. Vaccines made from peptides may help the body build an effective immune response to kill tumor cells. It is not yet known whether yeast derived sargramostim and vaccine therapy are more effective alone or together in preventing recurrence of melanoma.Clinical data presented in the following publication(s):PMID 26351350Disease type(s): Skin Neoplasm - Melanoma Clinical Dataset(s) included:NCT01989572-D1 (PMID 26351350): There are two datasets for E4697's primary publication 26351350 (-D1 and -D2). This dataset contains data for baseline characteristics, stratification factors, prior and on-study treatment, and disease-free and overall survival. Unless otherwise specified, blank values indicate missing data. Due to data cleaning efforts, data may contain slight discrepancies from that reported in Table 1, Table 3, and Figure 1 in the publication.NCT01989572-D2 (PMID 26351350): There are two datasets for E4697's primary publication 26351350 (-D1 and -D2). This dataset contains data for adverse event analyses. Unless otherwise specified, blank values indicate missing data.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 phs004396

MP2PRT: Genomic and Molecular Characterization of Biomarkers Associated With Self-Reported Race/Ethnicity in High-Risk Endometrial Cancers From NRG Oncology/GOG Protocol 210, Molecular Staging of Endometrial Cancer (NCT00340808)

The Molecular Profiling to Predict Response to Treatment (MP2PRT) program is part of the NCI 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, titled “Genomic and molecular characterization of biomarkers associated with self-reported race/ethnicity in high-risk endometrial cancers from NRG Oncology/GOG Protocol 210, Molecular Staging of Endometrial Cancer (NCT00340808)”, is one of the selected studies under this program. For this study, genomic characterization (i.e., Whole Genome Sequencing (WGS), Total RNA-Seq, Ancestry Genotyping) was performed on endometrial tumor tissue and matching normal tissue previously collected from patients with high-risk endometrial cancer. It is hypothesized that there are distinct molecular markers that high-risk endometrial cancers possess that can be used to predict the risk of recurrence and death for those women and by reported standard of care therapies. It is also hypothesized that there will be differences in molecular finding between self-reported black and white women that may account for some of the differences in outcomes.

Study phs002965

Dendritic Cell Redundancy Enables Priming of Anti-Tumor CD4 T Cells in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is resistant to current immunotherapies. Using mouse models, we achieved durable remissions and immunological memory after administration of anti-CTLA-4 and anti-PD-1. The mechanism of action involves activation of cDC2 cells and CD4 T cells. To validate these findings in humans, we collected tumor samples from patients with pancreatic cancer. We performed single-cell RNA-seq analyses to assess the abundance of cDC2 cells before and after treatment. This dataset consists of Illumina NovaSeq sequencing output (FASTQ files) from blood and tumor libraries prepared using the 10x Genomics Single Cell 5′ Immune Profiling kit. FASTQ files are provided for gene expression (GEX), TCR, and, for multiplexed samples, HTO libraries.

Study phs004508

NCTN: A Randomized Phase III Trial of Endocrine Therapy plus Entinostat/Placebo in Patients with Hormone Receptor-Positive Advanced Breast Cancer (E2112)

Study ID: E2112NCT Number: NCT02115282 ECOG-ACRIN Cancer Research GroupSubmitted in collaboration with the NCTN/NCORP Data ArchiveTrial Title: NCTN: A Randomized Phase III Trial of Endocrine Therapy plus Entinostat/Placebo in Patients with Hormone Receptor-Positive Advanced Breast Cancer (E2112)Trial Description: This randomized phase III trial studies exemestane and entinostat to see how well they work compared to exemestane alone in treating patients with hormone receptor-positive breast cancer that has spread to nearby tissue or lymph nodes (locally advanced) or another place in the body (metastatic). Estrogen can cause the growth of breast cancer cells. Endocrine therapy using exemestane may fight breast cancer by lowering the amount of estrogen the body makes. Entinostat may stop the growth of tumor cells by blocking some of the enzymes needed for cell growth. It is not yet known whether exemestane is more effective with or without entinostat in treating breast cancer. Clinical data presented in the following publication(s):PMID 34357781 Disease type(s): Breast Neoplasm - Breast Cancer - InvasiveBreast Neoplasm - Breast Neoplasm, MiscellaneousClinical dataset(s) included:NCT02115282-D1 (PMID 34357781): There are two datasets for PMID 34357781. This dataset, NCT02115282-D1, contains baseline characteristics, stratification factors, ER and PgR status, treatment, lysine acetylation, grade 5 toxicity, and efficacy data. NCT02115282-D2 (PMID 34357781): There are two datasets for PMID 34357781. This dataset, NCT02115282-D2, contains toxicity data. 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 phs004252

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