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ID

45667

Description

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

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dbGaP study = phs001282

Keywords

Versions (1)
  1. 4/2/23 4/2/23 - Simon Heim
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Ann M. Moormann, University of Massachusetts Medical School, Worcester, MA, USA

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April 2, 2023

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Creative Commons BY 4.0
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    dbGaP phs001282 Genomics of Endemic Burkitt Lymphoma

    English

    Eligibility Criteria

    5 forms  
    Inclusion and exclusion criteria
    Description

    Inclusion and exclusion criteria

    Alias
    UMLS CUI [1,1]
    C1512693
    UMLS CUI [1,2]
    C0680251
    Fine needle aspirates and venous blood were prospectively obtained between 2009 and 2012 at time of diagnosis and prior to commencing chemotherapy at Jaramogi Oginga Odinga Teaching and Referral Hospital (JOOTRH), a regional referral hospital for pediatric cancer in western Kenya. Tumor aspirates were smeared and stained with Giemsa/May-Grunwald for morphologic diagnosis by microscopy. Morphology was assessed by two independent pathologists to verify the diagnosis. Peripheral Blood Mononuclear Cells (PBMCs) were isolated from the blood immediately after collection and PBMCs were cryopreserved for future studies. Written informed consent was obtained from a parent or legal guardian of the child before enrollment. Ethical approval was obtained from the Institutional Review Board at the University of Massachusetts Medical School and the Scientific and Ethics Review Unit at the Kenya Medical Research Institute. Approval for this study was also granted by the JOOTRH, Kenya Ministry of Health Ethical Review Committee.
    Description

    Fine needle aspirates and venous blood were prospectively obtained between 2009 and 2012 at time of diagnosis and prior to commencing chemotherapy at Jaramogi Oginga Odinga Teaching and Referral Hospital (JOOTRH), a regional referral hospital for pediatric cancer in western Kenya. Tumor aspirates were smeared and stained with Giemsa/May-Grunwald for morphologic diagnosis by microscopy. Morphology was assessed by two independent pathologists to verify the diagnosis. Peripheral Blood Mononuclear Cells (PBMCs) were isolated from the blood immediately after collection and PBMCs were cryopreserved for future studies. Written informed consent was obtained from a parent or legal guardian of the child before enrollment. Ethical approval was obtained from the Institutional Review Board at the University of Massachusetts Medical School and the Scientific and Ethics Review Unit at the Kenya Medical Research Institute. Approval for this study was also granted by the JOOTRH, Kenya Ministry of Health Ethical Review Committee.

    Data type

    boolean

    Alias
    UMLS CUI [1,1]
    C1280568
    UMLS CUI [1,2]
    C0444255
    UMLS CUI [1,3]
    C0807981
    UMLS CUI [1,4]
    C5203987
    UMLS CUI [1,5]
    C0332152
    UMLS CUI [1,6]
    C3665472
    UMLS CUI [1,7]
    C0019982
    UMLS CUI [1,8]
    C0278704
    UMLS CUI [1,9]
    C0022558
    UMLS CUI [2,1]
    C0370199
    UMLS CUI [2,2]
    C1293976
    UMLS CUI [2,3]
    C3839409
    UMLS CUI [2,4]
    C1261322
    UMLS CUI [2,5]
    C0334901
    UMLS CUI [2,6]
    C1711411
    UMLS CUI [2,7]
    C0011900
    UMLS CUI [3,1]
    C1321301
    UMLS CUI [3,2]
    C0204727
    UMLS CUI [3,3]
    C0010405
    UMLS CUI [4,1]
    C0514044
    UMLS CUI [4,2]
    C4296904
    UMLS CUI [4,3]
    C4554082
    UMLS CUI [4,4]
    C2346845
    UMLS CUI [4,5]
    C0036378
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    Similar models

    Eligibility Criteria

    5 forms
    Name
    Type
    Description | Question | Decode (Coded Value)
    Data type
    Alias
    Item Group
    Inclusion and exclusion criteria
    C1512693 (UMLS CUI [1,1])
    C0680251 (UMLS CUI [1,2])
    Fine needle aspirates and venous blood were prospectively obtained between 2009 and 2012 at time of diagnosis and prior to commencing chemotherapy at Jaramogi Oginga Odinga Teaching and Referral Hospital (JOOTRH), a regional referral hospital for pediatric cancer in western Kenya. Tumor aspirates were smeared and stained with Giemsa/May-Grunwald for morphologic diagnosis by microscopy. Morphology was assessed by two independent pathologists to verify the diagnosis. Peripheral Blood Mononuclear Cells (PBMCs) were isolated from the blood immediately after collection and PBMCs were cryopreserved for future studies. Written informed consent was obtained from a parent or legal guardian of the child before enrollment. Ethical approval was obtained from the Institutional Review Board at the University of Massachusetts Medical School and the Scientific and Ethics Review Unit at the Kenya Medical Research Institute. Approval for this study was also granted by the JOOTRH, Kenya Ministry of Health Ethical Review Committee.
    Item
    Fine needle aspirates and venous blood were prospectively obtained between 2009 and 2012 at time of diagnosis and prior to commencing chemotherapy at Jaramogi Oginga Odinga Teaching and Referral Hospital (JOOTRH), a regional referral hospital for pediatric cancer in western Kenya. Tumor aspirates were smeared and stained with Giemsa/May-Grunwald for morphologic diagnosis by microscopy. Morphology was assessed by two independent pathologists to verify the diagnosis. Peripheral Blood Mononuclear Cells (PBMCs) were isolated from the blood immediately after collection and PBMCs were cryopreserved for future studies. Written informed consent was obtained from a parent or legal guardian of the child before enrollment. Ethical approval was obtained from the Institutional Review Board at the University of Massachusetts Medical School and the Scientific and Ethics Review Unit at the Kenya Medical Research Institute. Approval for this study was also granted by the JOOTRH, Kenya Ministry of Health Ethical Review Committee.
    boolean
    C1280568 (UMLS CUI [1,1])
    C0444255 (UMLS CUI [1,2])
    C0807981 (UMLS CUI [1,3])
    C5203987 (UMLS CUI [1,4])
    C0332152 (UMLS CUI [1,5])
    C3665472 (UMLS CUI [1,6])
    C0019982 (UMLS CUI [1,7])
    C0278704 (UMLS CUI [1,8])
    C0022558 (UMLS CUI [1,9])
    C0370199 (UMLS CUI [2,1])
    C1293976 (UMLS CUI [2,2])
    C3839409 (UMLS CUI [2,3])
    C1261322 (UMLS CUI [2,4])
    C0334901 (UMLS CUI [2,5])
    C1711411 (UMLS CUI [2,6])
    C0011900 (UMLS CUI [2,7])
    C1321301 (UMLS CUI [3,1])
    C0204727 (UMLS CUI [3,2])
    C0010405 (UMLS CUI [3,3])
    C0514044 (UMLS CUI [4,1])
    C4296904 (UMLS CUI [4,2])
    C4554082 (UMLS CUI [4,3])
    C2346845 (UMLS CUI [4,4])
    C0036378 (UMLS CUI [4,5])
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