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dbGaP phs001145 Exceptional Responders Initiative - pht011921.v1.p1

- 6/14/23 - 2 Formulär, 1 Item-grupp, 2 Dataelement, 1 Språk
Item-grupp: pht011921
Principal Investigator: Barbara Conley, MD, National Institutes of Health, Bethesda, MD, USA MeSH: Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001145 The Exceptional Responders Initiative is a pilot study to investigate the underlying molecular factors driving exceptional treatment responses of cancer patients to drug therapies. Study researchers will examine molecular profiles of tumors from patients either enrolled in a clinical trial for an investigational drug(s) and who achieved an exceptional response relative to other trial participants, or who achieved an exceptional response to a non-investigational chemotherapy. An exceptional response is defined as achievement of either a complete response or a partial response for at least 6 months duration in a trial or treatment where the overall response rate is 10%. The hope is to discover underlying molecular features that can be further investigated and may eventually predict benefit from a given drug or class of drugs for a particular patient. This pilot project will successfully characterize approximately 100 cases of tumor tissue and, when available, case-matched germline DNA. All samples will undergo whole exome sequencing, and cases with sufficient nucleic acids will undergo additional analyses (e.g. whole genome sequencing, mRNA-sequencing, mi RNA sequencing, promoter methylation analysis, SNP etc). Each case will be annotated with demographic and clinical information, along with follow-up information minimally sufficient to correlate molecular profiles with response. Both retrospective and prospective collections will be considered. The project will also accept sequencing data and clinical data from patients who have had sequencing performed outside of this project. All data will be de-identified and placed in a controlled access database so other investigators may use them for additional insights. Clinically annotated tissue specimens meeting the criteria will be provided by groups participating in the Exceptional Cases Initiative to a Biospecimen Core Resource (BCR), which will perform quality control on the tissues, and will use a standard operating procedure to isolate nucleic acids. The nucleic acids will be shipped to a sequencing center to perform whole exome sequencing and analysis. These findings will be made available to the broader cancer research community in a controlled access database.

pht011922.v1.p1

1 Item-grupp 2 Dataelement

dbGaP phs001179 Foundation Medicine Adult Cancer Clinical Dataset (FM-AD) - Eligibility

- 5/29/23 - 3 Formulär, 1 Item-grupp, 1 Dataelement, 1 Språk
Item-grupp: IG.elig
Principal Investigator: Doron Lipson, PhD, Foundation Medicine Inc., Cambridge, MA, USA MeSH: Neoplasms,Thoracic Neoplasms,Digestive System Neoplasms,Breast Neoplasms,Urogenital Neoplasms,Endocrine Gland Neoplasms,Nervous System Neoplasms,Skin Neoplasms,Head and Neck Neoplasms,Abdominal Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001179 The Foundation Medicine adult cancer clinical dataset consists of 18,004 unique solid tumor samples that underwent genomic profiling on a single uniform platform as part of standard clinical care. The dataset is derived from the FoundationOne® genomic profiling assay version 2 that interrogates exonic regions of 287 cancer-related genes and selected introns from 19 genes known to undergo rearrangements in human cancer. Genomic DNA samples were sequenced to over 500x median coverage, and custom computational analyses identified all classes of genomic alterations (base substitutions, insertions and deletions, copy number alterations, and rearrangements). Since matched normal tissue was unavailable for analysis, these data underwent additional filtering to enrich for cancer-related events. The reported data includes genomic alterations that are known and suspected tumor drivers, as well as variants of unknown significance. To preserve patient anonymity, all known or suspected germline variants were removed from the data unless known to be associated with cancer development. The dataset contains genomic alteration profiles generated by FoundationOne version 2 testing for adult cancer patients (over 18 y.o.), and represents a vast diversity of tumor subtypes, including many rare diseases not profiled as part of large-scale profiling efforts. Cases are grouped into 16 broad disease categories containing tumors from 162 unique disease subtypes. Since specimens were profiled as part of clinical care, limited clinical parameters were available, including age, gender, tissue of origin, % of tumor nuclei, and diagnosis. Publication of this dataset is intended to allow the broad scientific community access to this unique cohort for use in scientific research projects of common and rare types of cancer, both for generating leads regarding causal mechanisms as well as cross-testing and confirming existing hypotheses. A pediatric cancer clinical dataset consisting of data from 1,215 patients under 18 y.o. is available separately at: FOUNDATION MEDICINE

pht005673.v1.p1

1 Item-grupp 2 Dataelement

pht005668.v1.p1

1 Item-grupp 2 Dataelement

dbGaP phs001228 Kids First Pediatric Research Program in Susceptibility to Ewing Sarcoma Based on Germline Risk and Familial History of Cancer - Eligibility

- 5/16/23 - 3 Formulär, 1 Item-grupp, 1 Dataelement, 1 Språk
Item-grupp: IG.elig
Principal Investigator: Joshua D. Schiffman, MD, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA MeSH: Sarcoma, Ewing,Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001228 The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans-NIH effort initiated in response to the 2014 Gabriella Miller Kids First Research Act and supported by the NIH Common Fund. This program focuses on gene discovery in pediatric cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). Ewing sarcoma (EWS) is a deadly bone cancer that occurs in children and adolescents. Mounting evidence suggests that a genetic predisposition exists for this pediatric cancer, although the specific genetic contribution has yet to be identified. EWS has never been linked to a specific cancer predisposition syndrome, although several case reports have been published that describe siblings and cousins with EWS. Furthermore, neuroectodermal tumors appear to occur more commonly in families with EWS. The two consistent epidemiology findings in EWS include a very strong Caucasian predilection and increased rates of hernia in EWS patients and their family members. Finally, the role of genetic microsatellite repeats in EWS tumorigenesis has been recently described, and these GGAA microsatellites are polymorphic in repeat size and location across the genome. The study goals of this Kids First project include (1) To identify cancer predisposition genes in EWS trios increasing disease risk, (2) To identify genome-wide GGAA microsatellite repeats in EWS trios increasing disease risk, and (3) To identity de novo mutation and structural variant rates in EWS trios reflecting underlying DNA repair defects that increase disease risk. As part of the Kids First Common Fund initiative, this study proposal will further elucidate the genetic contribution to pediatric cancer development. Around 375 of these trios were selected for whole genome sequencing as part of the Gabriella Miller Kids First fund. The EWS trios have been collected as part of the Children's Oncology Group's AEPI10N5 Study ("Genetic Epidemiology of Ewing Sarcoma"), and each trio has associated phenotypic data including a detailed family history. We will interrogate the sequence data using our genomic analysis pipeline at the University of Utah and the Utah Science Technology and Research initiative's (USTAR) Center for Genetic Discovery. We will look for the genetic contribution to ES and the sequence data with be shared in a repository designated by the Kids First Common Fund. All of the WGS and phenotype data from this study is accessible through kidsfirstdrc.org, where other Kids First datasets can also be accessed. The WGS of these ~375 EWS trios will help us to understand the genetic origins of a deadly childhood cancer and may lead to novel strategies for prevention and treatment.

pht008133.v1.p1

1 Item-grupp 2 Dataelement

pht008134.v1.p1

1 Item-grupp 2 Dataelement

dbGaP phs001286 The Prostate, Lung, Colon, Ovary Screening Trial (PLCO) - Eligibility

- 3/20/23 - 5 Formulär, 1 Item-grupp, 6 Dataelement, 1 Språk
Item-grupp: IG.elig
Principal Investigator: Neal Freedman, PhD, MPH, National Cancer Institute, Rockville, MD, USA MeSH: Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001286 The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial is a large population-based randomized trial designed and sponsored by the National Cancer Institute (NCI) to determine the effects of screening on cancer-related mortality and secondary endpoints in over 150,000 men and women aged 55 to 74. The screening component of the trial was completed in 2006. However, participants have been under follow-up for cancer incidence and mortality since that time. In addition, PLCO included a large biological sample biorepository which has served as a unique resource for cancer research, particularly for etiologic and early-marker studies. As part of these efforts, PLCO has been used for a large number of genome-wide association and exome sequencing studies for different types of cancer.

pht007887.v2.p2

1 Item-grupp 3 Dataelement

pht007888.v2.p2

1 Item-grupp 2 Dataelement

pht007889.v2.p2

1 Item-grupp 2 Dataelement

pht007890.v2.p2

1 Item-grupp 6 Dataelement

dbGaP phs001287 CPTAC 3 Study - Eligibility

- 3/13/23 - 3 Formulär, 1 Item-grupp, 9 Dataelement, 1 Språk
Item-grupp: IG.elig
Principal Investigator: MeSH: Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001287 Recently, significant progress has been made in characterizing and sequencing the genomic alterations in statistically robust numbers of samples from several types of cancer. For example, The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and other similar efforts are identifying genomic alterations associated with specific cancers (e.g., copy number aberrations, rearrangements, point mutations, epigenomic changes, etc.) The availability of these multi-dimensional data to the scientific community sets the stage for the development of new molecularly targeted cancer interventions. Understanding the comprehensive functional changes in cancer proteomes arising from genomic alterations and other factors is the next logical step in the development of high-value candidate protein biomarkers. Hence, proteomics can greatly advance the understanding of molecular mechanisms of disease pathology via the analysis of changes in protein expression, their modifications and variations, as well as protein=protein interaction, signaling pathways and networks responsible for cellular functions such as apoptosis and oncogenesis. Realizing this great potential, the NCI launched the third phase of the CPTC initiative in September 2016. As the Clinical Proteomic Tumor Analysis Consortium, CPTAC continues to define cancer proteomes on genomically-characterized biospecimens. The purpose of this integrative approach was to provide the broad scientific community with knowledge that links genotype to proteotype and ultimately phenotype. In this third phase of CPTAC, the program aims to expand on CPTAC II and genomically and proteomically characterize over 2000 samples from 10 cancer types (Lung Adenocarcinoma, Pancreatic Ductal Adenocarcinoma, Glioblastoma Multiforme, Acute Myeloid Leukemia, Clear cell renal Carcinoma, Head and Neck Squamous Cell Carcinoma, Cutaneous Melanoma, Sarcoma, Lung Squamous Cell Carcinoma, Uterine Corpus Endometrial Carcinoma) .Germline DNA is obtained from blood and Normal control samples for proteomics varied by organ site. All cancer samples were derived from primary and untreated tumor.

pht006104.v9.p5

1 Item-grupp 3 Dataelement

pht006105.v9.p5

1 Item-grupp 3 Dataelement

dbGaP phs001337 AACR Project GENIE - pht009620.v1.p1

- 3/9/23 - 3 Formulär, 1 Item-grupp, 3 Dataelement, 1 Språk
Item-grupp: pht009620
Principal Investigator: MeSH: Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001337 AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) is an international pancancer registry of real-world data assembled through data sharing between 19 leading international cancer centers with the goal of improving clinical decision-making. The registry leverages ongoing clinical sequencing efforts (CLIA/ISO-certified) at participating cancer centers by pooling their data to create a novel, open-access registry to serve as an evidence base for the entire cancer community. Genomic and baseline clinical data from more than 70,000 tumors is accessible through the efforts of our strategic and technical partners, Sage Bionetworks and cBioPortal. The consortium and its activities are driven by openness, transparency, and inclusion to ensure that the project output remains accessible to the global cancer research community and ultimately benefits patients.

pht009621.v1.p1

1 Item-grupp 3 Dataelement

Eligibility

1 Item-grupp 1 Dataelement

UFK HD: Gynäkologische Tumore - Anamnesis

- 2/13/23 - 1 Formulär, 3 Item-grupper, 45 Dataelement, 2 Språk
Item-grupper: anamnesis_general, anamnesis_specific, WHO-5
Dieses Projekte soll an der UFK HD im Bereich der gynäkologischen Tumore (1) die strukturierte Datenerfassung gemäß CDISC Standard ermöglich und (2) die klinische Arbeit entlang des Patientinnenweges digitalisieren und zur Arbeitserleichterung für die beteiligten Mitarbeiter:innen führen. Affiliation: Department of Obstetrics and Gynecology, Heidelberg University Hospital

dbGaP phs001374 VA APOLLO Project - Research for Precision Oncology (RePOP) - pht008335.v2.p1

- 2/7/23 - 3 Formulär, 1 Item-grupp, 2 Dataelement, 1 Språk
Item-grupp: pht008335
Principal Investigator: Louis Fiore, MD, VA Boston Healthcare System, Boston, MA, USA MeSH: Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001374 The Research for Precision Oncology Program (RePOP) is a research activity that establishes a cohort of Veterans diagnosed with cancer and who have had genomic analyses performed on their tumor tissue as part of standard of care. All data relevant to a patient's cancer and cancer care will be collected under RePOP, including patient demographics, co-morbidities, genomic analysis, treatments, medications, lab values, imaging studies, and outcomes. All RePOP participants will have signed/verbal informed consent and signed HIPAA authorization to have their data stored and shared from RePOP's Precision Oncology Program Data Repository (PODR). The Applied Proteogenomics OrganizationaL Learning and Outcomes (APOLLO) network is a collaboration between NCI, the Department of Defense (DoD), and the Department of Veterans Affairs (VA) to incorporate proteogenomics into patient care as a way of looking beyond the genome, to the activity and expression of the proteins that the genome encodes. The emerging field of proteogenomics aims to better predict how patients will respond to therapy by screening their tumors for both genetic abnormalities and protein information, an approach that has been made possible in recent years due to advances in proteomic technology.

Eligibility

1 Item-grupp 5 Dataelement

pht008334.v2.p1

1 Item-grupp 2 Dataelement

dbGaP phs000673 University of Michigan Clinical Sequencing Exploratory Research (CSER) - Eligibility

- 1/25/23 - 5 Formulär, 1 Item-grupp, 16 Dataelement, 1 Språk
Item-grupp: IG.elig
Principal Investigator: Arul Chinnaiyan, MD PhD, Michigan Center for Translational Pathology, University of Michigan, MI, USA MeSH: Neoplasms,Breast Neoplasms,Sarcoma,Prostatic Neoplasms,Aromatase Inhibitors,Hematologic Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000673 Overview. The personalization of therapy for cancer will require molecular characterization of unique and shared genetic aberrations. In particular, patients who have a sarcoma or other rare cancers and are candidates for clinical trials could potentially benefit by identifying eligibility for "targeted" drugs based on the "actionable" genes in their specific tumor. Growing technological advances in genomic sequencing has now made it possible to consider the use of sequence data in a clinical setting. For instance, comprehensive testing that includes whole exome and transcriptome sequencing may identify biomarkers for predictive or prognostic purposes and thereby inform treatment choices and prevention strategies. Thus, the translation of high throughput next generation sequencing would support a "personalized" strategy for cancer. However, the translation of clinical sequencing bears unique challenges including identifying patients who could benefit, developing informed consent and human subjects protections, outlining measurable outcomes, interpreting what results should be reported and validated, and how results should be reported. In addition, we know very little about how patients and clinicians will respond to the potentially confusing and overwhelming amount of information generated by genomic sequencing, and we lack model processes for clinically evaluating and presenting these data. For the promise of our innovative biotechnologies to be realized, "translational genomics" research that evaluates genomic applications within real-world clinical settings will be required. This proposal brings together expertise at the University of Michigan including clinical oncology, cancer genetics, genomic science/bioinformatics, clinical pathology, social and behavioral sciences, and bioethics in order to implement this clinical cancer sequencing project. Three integrated Projects have the following themes: Project 1) "Clinical Genomic Study" will identify patients with a rare cancer (i.e., 15 out of 100,000 individuals per year) who are eligible for clinical trials, consent them to the study, obtain biospecimens (tumor tissue, germline tissue), store clinical data, and assemble a multi-disciplinary Sequencing Tumor Board to deliberate on return of actionable or incidental genomic results; Project 2) "Sequencing & Analysis" will process biospecimens and perform comprehensive sequencing and analysis of tumors to identify point mutations, copy number changes, rearrangements/gene fusions, and aberrant gene expression; Project 3) "Ethics & Psychosocial Analysis" will observe the expert review process for evaluating sequence results and will examine the clinician and patient response to the informed consent process, delivery of genomic sequence results, and use of genomic results.

pht003661.v4.p1

1 Item-grupp 5 Dataelement

pht003662.v4.p1

1 Item-grupp 4 Dataelement

pht003663.v4.p1

1 Item-grupp 9 Dataelement

pht003660.v4.p1

1 Item-grupp 5 Dataelement

dbGaP phs000661 Germline Sequencing for Aggressive Prostate Carcinoma - pht003538.v1.p1

- 1/23/23 - 4 Formulär, 1 Item-grupp, 3 Dataelement, 1 Språk
Item-grupp: pht003538
Principal Investigator: Elaine Mardis, PhD, The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA MeSH: Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000661 This study aims to elucidate the genetic determinants of susceptibility to aggressive prostate carcinoma. To this end, germ line whole exome sequence has been generated from patients with aggressive prostate cancer. Whole genome sequence for a representative subset of tumors from patients whose cancer was resistant to primary therapy is included as well. This deep genomic interrogation will allow the identification of rare, functionally disruptive variants that may play a role in disease progession and response to treatment.

pht003540.v1.p1

1 Item-grupp 2 Dataelement

pht003541.v1.p1

1 Item-grupp 5 Dataelement

pht003539.v1.p1

1 Item-grupp 3 Dataelement

dbGaP phs000725 Rare Cancer Tumors Project - pht003882.v2.p1

- 1/6/23 - 9 Formulär, 1 Item-grupp, 5 Dataelement, 1 Språk
Item-grupp: pht003882
Principal Investigator: David A. Wheeler, PhD, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA MeSH: Neoplasms,Brain Neoplasms,Germinoma,Neoplasms, Germ Cell and Embryonal,Endodermal Sinus Tumor,Teratoma,Carcinoma, Embryonal,Choriocarcinoma,Polycythemia Vera,Craniopharyngioma https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000725 A large proportion of common cancers affecting patients around the world have been selected for comprehensive cancer genome studies. Further efforts will be needed to tackle the remaining tumor types, including the rare forms of cancers. Although rare, these cancers tend to be more aggressive and fast growing with an early recurrence following initial chemotherapy and poor prognosis. Besides, patients diagnosed with rare cancers may have difficulty finding a physician knowledgeable in treating their type of cancer. While sample collection is a major challenge, the integrated genomic analyses would identify novel causative genes in these rare cancers, shed new light on the biology of the rare cancers, as well as guide novel targeted cancer therapies. Through efficient collaboration, the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine (BCM) has collected/is expected to collect 20 different types of rare cancers, 15-30 cases each. Whole-exome sequencing and high-resolution SNP array analysis were/will be performed for all cases and whole-genome sequencing was designed for a selected subset of the cases. *The Rare Cancer Tumors Cohort is utilized in the following dbGaP sub-studies.* To view genotypes, other molecular data, and derived variables collected in this sub-study, please click on the following sub-study below or in the "Sub-studies" section of this top-level study page phs000725 Rare Cancer Tumors Cohort.- phs000754 Intracranial Germ Cell Tumors - phs000861 Craniopharyngioma Tumors - phs000859 Sezary Syndrome Genomic Analysis

pht003885.v2.p1

1 Item-grupp 3 Dataelement

pht003886.v2.p1

1 Item-grupp 5 Dataelement

pht004475.v2.p1

1 Item-grupp 4 Dataelement

pht004476.v2.p1

1 Item-grupp 6 Dataelement

pht004585.v2.p1

1 Item-grupp 5 Dataelement

Eligibility

1 Item-grupp 1 Dataelement

dbGaP phs000677 An APOBEC Cytidine Deaminase Mutagenesis in Human Cancers - pht003581.v1.p1

- 12/29/22 - 3 Formulär, 1 Item-grupp, 5 Dataelement, 1 Språk
Item-grupp: pht003581
Principal Investigator: Dmitry A. Gordenin, PhD, National Institute of Environmental Health Sciences (NIEH, DHHS), Research Triangle Park, NC, USA MeSH: Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000677 *Reprinted from Roberts et al. "An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers", Nature Genetics, 45:970-976, 2013, with permission of Nature Publishing Group:* Recent studies indicate that a subclass of APOBEC cytidine deaminases, which convert cytosine to uracil during RNA editing and retrovirus or retrotransposon restriction, may induce mutation clusters in human tumors. We show here that throughout cancer genomes APOBEC-mediated mutagenesis is pervasive and correlates with APOBEC mRNA levels. Mutation clusters in whole-genome and exome data sets conformed to the stringent criteria indicative of an APOBEC mutation pattern. Applying these criteria to 954,247 mutations in 2,680 exomes from 14 cancer types, mostly from The Cancer Genome Atlas (TCGA), showed a significant presence of the APOBEC mutation pattern in bladder, cervical, breast, head and neck, and lung cancers, reaching 68% of all mutations in some samples. Within breast cancer, the HER2-enriched subtype was clearly enriched for tumors with the APOBEC mutation pattern, suggesting that this type of mutagenesis is functionally linked with cancer development. The APOBEC mutation pattern also extended to cancer-associated genes, implying that ubiquitous APOBEC-mediated mutagenesis is carcinogenic.

pht003582.v1.p1

1 Item-grupp 3 Dataelement

pht003583.v1.p1

1 Item-grupp 4 Dataelement

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