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312 Sökresultat.

dbGaP phs000573 Genetic Heterogeneity of Diffuse Large B Cell Lymphoma - pht003213.v1.p1

- 2025-01-29 - 5 Formulär, 1 Item-grupp, 2 Dataelement, 1 Språk

Item-grupp: pht003213

Principal Investigator: Sandeep Dave, MD, Duke University, Durham, NC, USA MeSH: Lymphoma, Non-Hodgkin https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000573 We sequenced exomes of 94 DLBCL tumors and cell lines. 34 of the tumors had paired normal tissue. Our work elucidates commonly occurring gene-coding mutations in DLBCL.

Lymphoma, Non-Hodgkin

pht003215.v1.p1

1 Item-grupp 2 Dataelement

pht003216.v1.p1

1 Item-grupp 4 Dataelement

pht003214.v1.p1

1 Item-grupp 3 Dataelement

pht003217.v1.p1

1 Item-grupp 5 Dataelement

dbGaP phs001219 Detection of Genes Predisposing to Hematologic Malignancies - pht007857.v1.p1

- 2023-04-26 - 6 Formulär, 1 Item-grupp, 2 Dataelement, 1 Språk

Item-grupp: pht007857

Principal Investigator: Neil E. Caporaso, MD, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA MeSH: Leukemia, Lymphocytic, Chronic, B-Cell,Hodgkin Disease,Lymphoma, Non-Hodgkin,Waldenstrom Macroglobulinemia,Leukemia, Hairy Cell,Leukemia, Myeloid, Acute,Leukemia, Myelomonocytic, Juvenile https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001219 We have been conducting genetic studies on families at high risk of different hematologic malignancies, in order to define the related tumors in the families, define precursor and other related conditions, and map and identify susceptibility genes. We have focused mainly on four types of lymphoid malignancies: chronic lymphocytic leukemia (CLL), Hodgkin lymphoma (HL), non-Hodgkin lymphoma (NHL), and Waldenström macroglobulinemia (WM). A few families with a rare lymphoma subtype, hairy cell leukemia (HCL) are included. In addition, single large pedigrees with acute myeloid leukemia (AML), and juvenile myelomocytic leukemia (JMML) are included. Families are ascertained for having at least two patients with the same hematologic malignancy and are classified by the type of malignancy that predominates in the family. Multiple types of lymphoid malignancies are often found in the same family. Other data has shown that these conditions aggregate together in families. Verification of cancer diagnoses is obtained through medical records, pathology reports, and flow cytometry. Family members with precursor traits are also included, monoclonal B-cell lymphocytosis (MBL) in CLL families and IgM monoclonal gammopathy of undetermined significance (MGUS) in WM families.

pht007858.v1.p1

1 Item-grupp 6 Dataelement

Eligibility

1 Item-grupp 1 Dataelement

pht007859.v1.p1

1 Item-grupp 3 Dataelement

pht007860.v1.p1

1 Item-grupp 10 Dataelement

pht007861.v1.p1

1 Item-grupp 5 Dataelement

dbGaP phs001282 Genomics of Endemic Burkitt Lymphoma - Eligibility

- 2023-04-02 - 5 Formulär, 1 Item-grupp, 1 Dataelement, 1 Språk

Item-grupp: IG.elig

Principal Investigator: Ann M. Moormann, University of Massachusetts Medical School, Worcester, MA, USA MeSH: Burkitt Lymphoma,Lymphoma, Non-Hodgkin https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001282 This genomic landscape of Burkitt lymphoma represents a multimodal sequencing of tumors and control tissues and individuals to better understand the etiology, and molecular pathogenesis of Burkitt lymphoma including the roles of the associated Plasmodium falciparum malaria and EBV infections. Comprehensive sequencing set includes genomic, transcriptomic, and epigenomic datasets in concert with variable clinical phenotypes and outcome information such as anatomical presentation site, in-hospital survival rates, and EBV genome type. This deposit includes additional small RNA-seq data from endemic BL (eBL) tumors and RNA-sequencing data from sorted NK cell subsets from the peripheral blood of eBL patients. The additional small RNA-seq data are from tumor specimens from 17 eBL cases, of the previously deposited polyA RNA-seq data from 28 eBL cases (phs1282.V1). The additional RNAseq data from Fluorescence-activated cell sorting (FACS) of NK cell subsets, isolated from the peripheral blood of 7 eBL cases. *For initial transcriptome analysis see: Kaymaz et al.* "Comprehensive Transcriptome and Mutational Profiling of Endemic Burkitt Lymphoma Reveals EBV Type-specific Difference." Molecular Cancer Research, 2017. PMID 28465297 *For initial microRNA analysis see: Oduor et al.* "Human and Epstein-Barr Virus miRNA Profiling as Predictive Biomarkers for Endemic Burkitt Lymphoma." Frontiers in Microbiology 8, 2017. PMID 28400759 *For initial NK subsets RNA expression analysis see: Forconi et al.* "A new hope for CD56negCD16pos NK cells as unconventional cytotoxic mediators: an adaptation to chronic diseases." Frontiers in Cellular and Infection Microbiology, Submitted and Under review. *For general overview of cohort study see: Buckle et al.* "Factors influencing survival among Kenyan children diagnosed with endemic Burkitt lymphoma between 2003 and 2011: A historical cohort study." Int J Cancer. 15:1231, 2016, PMID 27136063

pht006096.v2.p1

1 Item-grupp 3 Dataelement

pht006098.v2.p1

1 Item-grupp 5 Dataelement

pht006099.v2.p1

1 Item-grupp 12 Dataelement

pht006097.v2.p1

1 Item-grupp 3 Dataelement

dbGaP phs001378 scRNA-Seq Reveals Lymphoma B Cell Diversity and T Cell Immune Checkpoint Co-Expression - pht006689.v1.p1

- 2023-02-19 - 5 Formulär, 1 Item-grupp, 4 Dataelement, 1 Språk

Item-grupp: pht006689

Principal Investigator: Hanlee Ji, MD, Stanford University School of Medicine, Palo Alto, USA MeSH: Lymphoma, Follicular,Lymphoma, Non-Hodgkin https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001378 Follicular lymphoma (FL) is a generally incurable B-cell malignancy which has the potential to transform into highly aggressive lymphomas. Genomic studies indicate it is often a small subpopulation rather than the dominant population in the FL that gives rise to the more aggressive subtype. To resolve the underlying transcriptional networks of follicular B-cell lymphomas at single molecule and cell resolution, we leveraged droplet-based barcoding technology for highly parallel single cell RNA-Seq. We analyzed the transcriptomes from tens of thousands of cells derived from five primary FL tumors. Simultaneously, we conducted multi-dimensional flow cell sorting to validate our characterizing of cellular lineages and critical expressed proteins. For each tumor, we identified multiple cellular subpopulations, matching known hematopoietic lineages. Comparison of gene expression by matched malignant and normal B cells from the same patient revealed tumor-specific features. Malignant B cells exhibited restricted immunoglobulin light chain expression (either Ig Kappa or Ig Lambda), as well the expected upregulation of the BCL2 gene, but also down-regulation of the FCER2, CD52 and MHC class II genes. By leveraging the single-cell resolution on large numbers of cells per patient, we were able to examine tumor-resident T cells. We identified pairs of immune checkpoint molecules that were co-expressed, providing a potentially useful strategy for selection of patient-tailored combination immunotherapies. In summary, massively parallel measurement of single-cell expression in thousands of tumor cells and tumor-resident lymphocytes can be used to obtain a systems-level view of the tumor microenvironment and identify new avenues for therapeutic development.

Eligibility

1 Item-grupp 8 Dataelement

pht006690.v1.p1

1 Item-grupp 4 Dataelement

pht006691.v1.p1

1 Item-grupp 5 Dataelement

pht006692.v1.p1

1 Item-grupp 9 Dataelement

dbGaP phs000689 Genomic Analysis of Peripheral T-Cell Lymphomas - Eligibility

- 2023-01-13 - 4 Formulär, 1 Item-grupp, 2 Dataelement, 1 Språk

Item-grupp: IG.elig

Principal Investigator: Adolfo Ferrando, Institute for Cancer Genetics, Columbia University, New York, NY, USA MeSH: Lymphoma, T-Cell, Peripheral,Lymphoma, Non-Hodgkin https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000689 Peripheral T-cell lymphomas (PTCLs) are a heterogeneous and poorly understood group of non Hodgkin lymphomas. We aim to identify new genetic alterations in PTCL transformation by using a combination of whole exome sequencing of tumor-normal DNA pairs, RNAseq analysis and targeted deep sequencing of candidate genes. Our data identified highly recurrent mutations in epigenetic factors such as TET2, DNMT3A and IDH2 as well as a new highly prevalent mutation in RHOA, the G17V allele that is present in almost 70% of angioimmunoblastic T-cell lymphomas (AITL) and almost 20% of not otherwise specified PTCL (PTCL NOS) samples. In addition, we describe new and recurrent genetic defects including mutations in FYN, ATM, B2M and CD58 implicating SRC signaling, impaired DNA damage response and escape from immune surveillance processes as key players in the pathogenesis of PTCL.

pht003679.v1.p1

1 Item-grupp 5 Dataelement

pht003680.v1.p1

1 Item-grupp 5 Dataelement

pht003681.v1.p1

1 Item-grupp 8 Dataelement

dbGaP phs000729 Follicular Lymphoma 2013 - Malek - Eligibility

- 2022-12-13 - 5 Formulär, 1 Item-grupp, 1 Dataelement, 1 Språk

Item-grupp: IG.elig

Principal Investigator: Sami N. Malek, MD, University of Michigan Department of Internal Medicine, Division of Hematology-Oncology, Ann Arbor, MI, USA MeSH: Lymphoma, Follicular,Lymphoma, Non-Hodgkin https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000729 A cohort of follicular lymphoma cases had tumor cells purified from tissue samples after informed consent using flow cytometry. DNA was extracted from the cells, and samples were subjected to solution-based exome capture using the Illumina TruSeq Exome Enrichment Kit and the Illumina HiSeq 2000 platform.

pht003773.v1.p1

1 Item-grupp 3 Dataelement

pht003774.v1.p1

1 Item-grupp 3 Dataelement

pht003775.v1.p1

1 Item-grupp 4 Dataelement

pht003776.v1.p1

1 Item-grupp 6 Dataelement

dbGaP phs000502 Genome-Wide Analysis of Splenic Marginal Zone Lymphoma - pht002815.v1.p1

- 2022-12-13 - 4 Formulär, 1 Item-grupp, 5 Dataelement, 1 Språk

Item-grupp: pht002815

Principal Investigator: Laura Pasqualucci, MD, Institute for Cancer Genetics, Columbia University, New York, NY, USA MeSH: Lymphoma, Non-Hodgkin,Lymphoma, B-Cell https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000502 Splenic Marginal Zone Lymphoma (SMZL) is a B-cell malignancy of unknown pathogenesis and thus orphan of targeted therapies. By integrating whole-exome sequencing and copy-number analysis of 8 paired tumor-normal DNAs from patients with SMZL, we show that the typical SMZL exome carries ~30 genetic alterations. Targeted resequencing of selected candidates in an extended panel of 40-117 samples revealed activating mutations of NOTCH2, a gene required for marginal-zone (MZ) development, as the most frequent and SMZL-specific lesion, accounting for approximately 20% of cases. Additional altered genes suggest that deregulation of signaling pathways normally involved in MZ development (NOTCH, NF-kappa B, and B-cell receptor) represents a critical event in SMZL pathogenesis. These findings have direct implications for the treatment of SMZL patients since drugs are available which can target NOTCH as well as other pathways deregulated in this disease.

Eligibility

1 Item-grupp 2 Dataelement

pht002814.v1.p1

1 Item-grupp 3 Dataelement

pht002813.v1.p1

1 Item-grupp 2 Dataelement

dbGaP phs000559 PAGE: Epidemiologic Architecture for Genes Linked to Environment (EAGLE) - BioVU Cancer Project - Eligibility

- 2022-12-12 - 5 Formulär, 1 Item-grupp, 20 Dataelement, 1 Språk

Item-grupp: IG.elig

Principal Investigator: Dana Crawford, PhD, Vanderbilt University, Nashville, TN, USA MeSH: Neoplasms,Breast Neoplasms,Colorectal Neoplasms,Endometrial Neoplasms,Lung Neoplasms,Lymphoma, Non-Hodgkin,Ovarian Neoplasms,Melanoma,Prostatic Neoplasms https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000559 As part of Population Architecture using Genomics and Epidemiology PAGE study (Phase I), the Epidemiologic Architecture using Genomics and Epidemiology (EAGLE I) project accessed both epidemiologic- and clinic-based collections. The epidemiologic-based collection of EAGLE I included the National Health and Nutritional Examination Surveys (NHANES), ascertained between 1991-1994 (NHANES III), 1999-2002, and 2007-2008. NHANES is a population-based cross-sectional survey now conducted every year in the United States to assess the health status of Americans at the time of ascertainment and to assess trends over the years of survey. Genetic NHANES consists of 19,613 DNA samples linked to thousands of variables including demographics, health and lifestyle variables, physical examination variables, laboratory variables, and exposures. NHANES is diverse with almost one-half of the samples (46.4%) coming from self-reported Mexican Americans and non-Hispanic blacks. In contrast to NHANES, BioVU is a clinic-based collection of 150,000 DNA samples from Vanderbilt University Medical Center linked to de-identified electronic medical records (EMRs). Approximately 12% of BioVU's overall DNA sample collection is from African American, Hispanic, and Asian patients. The overall goals of PAGE I and EAGLE I were broad and several-fold:- Replicate genome-wide association study (GWAS)- identified variants in European Americans; - Identify population-specific and trans-population genotype-phenotype associations; - Identify genetic and environmental modifiers of these associations. NHANES is an excellent resource for the study of quantitative traits associated with common human diseases. However, given that the age range of NHANES spans childhood to late adulthood and not all diseases are surveyed, NHANES is less useful for the study of adult-onset diseases such as major cancers. Therefore, under American Recovery and Reinvestment Act (ARRA) funding, EAGLE as part of PAGE I defined eight major cancers sites for genetic analysis in BioVU, Vanderbilt's biorepository linked to de-identified EMRs. The eight major cancers defined for this study included melanoma, breast, ovarian, prostate, colorectal, lung, endometrial, and Non-Hodgkin's lymphoma (NHL). Cancer cases were defined using a combination of ICD-9 codes and tumor registry entries. Controls include BioVU participants without cancer and encompassing the age and gender distributions of cancer cases. Targeted genotyping of GWAS-identified variants for these diseases (124 SNPs) and ancestry informative markers (128 AIMs) was performed by the Center for Human Genetics Research Vanderbilt DNA Resources Core. After quality control, a total of 116 cancer-associated SNPs and 122 AIMs were available for downstream analyses.

pht003614.v1.p1

1 Item-grupp 2 Dataelement

pht003615.v1.p1

1 Item-grupp 3 Dataelement

pht003616.v1.p1

1 Item-grupp 58 Dataelement

pht003617.v1.p1

1 Item-grupp 5 Dataelement

dbGaP phs000562 The Genetic Landscape of Mutations in Burkitt Lymphoma - pht003104.v1.p1

- 2022-11-04 - 4 Formulär, 1 Item-grupp, 2 Dataelement, 1 Språk

Item-grupp: pht003104

Principal Investigator: Sandeep Dave, MD, MS, Duke University, Durham, NC, USA MeSH: Burkitt Lymphoma,Lymphoma, Non-Hodgkin https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000562 Burkitt lymphoma (BL) is characterized by deregulation of *MYC*, but the contribution of other genetic mutations to the disease is largely unknown. We sequenced exomes of 59 BL tumors, 14 of which had paired normal tissue. Our work elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates *ID3* as a novel tumor suppressor gene.

pht003105.v1.p1

1 Item-grupp 3 Dataelement

pht003107.v1.p1

1 Item-grupp 5 Dataelement

pht003106.v1.p1

1 Item-grupp 4 Dataelement

dbGaP phs000328 Genome-Wide Analysis of Diffuse Large B-Cell Lymphoma (De Novo and Derived from the High Grade Transformation of Follicular Lymphoma) - Eligibility

- 2022-10-12 - 4 Formulär, 1 Item-grupp, 8 Dataelement, 1 Språk

Item-grupp: IG.elig

Principal Investigator: Riccardo Dalla-Favera, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA MeSH: Lymphoma, Follicular,Lymphoma, Non-Hodgkin https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000328 *Version 1.* Diffuse Large B-cell Lymphoma (DLBCL) represents the most common form of B-cell non-Hodgkin Lymphoma (B-NHL), accounting for ~30% of the *de novo* diagnoses and also arising as a frequent clinical evolution of Follicular Lymphoma (FL). The molecular pathogenesis of DLBCL is associated with multiple genetic lesions that in part distinctly segregate with individual phenotypic subtypes, suggesting the involvement of distinct oncogenic pathways. However, the lesions identified so far likely represent only a fraction of those necessary for malignant transformation. In order to characterize the entire set of structural alterations present in the DLBCL genome, we have integrated next generation whole exome sequencing analysis of 6 DLBCL cases and genome-wide high-density SNP array analysis of 72 DLBCL cases. We report here that FL and DLBCL harbor frequent structural alterations inactivating *CREBBP* and, more rarely, *EP300*, two highly related histone and non-histone acetyltransferases (HATs) that act as transcriptional co-activators in multiple signaling pathways. Overall, ~37% of DLBCL and 36% of FL cases display genomic deletions and/or somatic point mutations that remove or inactivate the HAT coding domain of these two genes. These lesions commonly affect a single allele, suggesting that reduction in HAT dosage is important for lymphomagenesis. We demonstrate specific defects in the acetylation-mediated inactivation of the BCL6 oncoprotein and activation of the p53 tumor suppressor. These results identify *CREBBP/EP300* mutations as a major pathogenic mechanism shared by common forms of B-NHL, and have direct implications for the use of drugs targeting acetylation/deacetylation mechanisms. *Version 2.* Follicular lymphoma (FL) is an indolent, but incurable disease that, in 30-40% of cases, undergoes transformation to an aggressive diffuse large B cell lymphoma (DLBCL). The history of clonal evolution and the mechanisms that underlie transformation to DLBCL (tFL) remain largely unknown. Using whole exome sequencing and copy number analysis of 39 tFL patients, including 12 with paired sequential FL/tFL biopsies, we show that, in most cases, FL and tFL arise by divergent evolution from a common mutated precursor cell through the acquisition of distinct genetic lesions. Mutations in epigenetic modifiers (e.g., *MLL2, CREBBP, EZH2, ARID1A*) and anti-apoptotic genes (*BCL2, FAS*) were observed in 93% (36/39) and 78% (30/39) of cases, respectively, and were invariably shared between the two disease phases, suggesting an early acquisition in the common mutated precursor. Conversely, the development of tFL is associated with deregulation of genes involved in the control of cell proliferation, cell cycle progression and DNA damage responses (*CDKN2A/2B, MYC, TP53*), as well as with an aberrant activity of the somatic hypermutation mechanism. Finally, we show that the genomic profile of tFL shares significant similarities with that of germinal center B-cell type *de novo* DLBCL, but also displays unique combinations of altered genes that may explain the dismal clinical course of tFL. *Version 3. *This version includes thirty-five additional de novo DLBCL samples, newly diagnosed, and their paired normal DNA from previously untreated patients, which were analyzed by whole exome sequencing (n=27T and 25N), whole genome sequencing (8T and 10N), and/or targeted HLA-next generation sequencing (n=26T/N pairs) in order to identify genetic alterations associated with loss of surface MHC-II expression.

pht002132.v3.p1

1 Item-grupp 3 Dataelement

pht002133.v3.p1

1 Item-grupp 2 Dataelement

pht002134.v3.p1

1 Item-grupp 7 Dataelement

Multicenter Pivotal Phase III Study of Iodine-131 Anti-B1 Antibody (Murine) Radioimmunotherapy - Laboratory Results Baseline, Infusion Record Therapy Dose - Day 0 and Day 7

- 2022-04-06 - 1 Formulär, 12 Item-grupper, 66 Dataelement, 1 Språk

Item-grupper: Administration, Laboratory Tests-Hematology, Laboratory Tests-Blood Chemistry, Pregnancy Test, Beta-2 Microglobulin (Serum), Infusion Record Dosimetric Dose - Day 0 and Day 7, Baseline HAMA (human antimurine antibody), Dosimetric Dose, Anti-B1 Dose, Infusion Rate, Vital Signs, Adverse Experiences

https://clinicaltrials.gov/show/NCT00989664 Eligibility check Study ID: 104504 Clinical Study ID: BEX104504 Study Title: Multicenter, Pivotal Phase III Study of Iodine-131 Anti-B1 Antibody (Murine) Radioimmunotherapy for Chemotherapy Refractory Low Grade B Cell Lymphomas and Low Grade Lymphomas that have Transformed to Higher Grade Histologies Patient Level Data: Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier: NCT00989664 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: Phase 2 Study Recruitment Status: Completed Generic Name: tositumomab Trade Name: Bexxar Study Indication: Lymphoma, Non-Hodgkin

Iodine-131 Anti-B1 Antibody for Non Hodgkin’s Lymphomas NCT00996593 - Physical Examination, Laboratory Results Hematology/ Chemistry Week 13 (Visit 8)

- 2022-04-01 - 1 Formulär, 6 Item-grupper, 37 Dataelement, 1 Språk

Item-grupper: Date of physical examination, B- Symptoms, Physical Examination, Organ/ System, Hematology, Chemistry

Study ID: 104507 Clinical Study ID: BEX104507 Study Title: Phase II Study of Iodine-131 Anti-B1 Antibody for Non Hodgkin’s Lymphoma Patients who have Previously Received Rituximab Patient Level Data: Study Listed on ClinicalStudyDataRequest.com Clinicaltrials.gov Identifier: NCT00996593 Sponsor: GlaxoSmithKline Collaborators: N/A Phase: Phase 2 Study Recruitment Status: Completed Generic Name: tositumomab Trade Name: Bexxar Study Indication: Lymphoma, Non-Hodgkin

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