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

Link

dbGaP study = phs001282

Keywords

Versions (1)
  1. 4/2/23 4/2/23 - Simon Heim
Copyright Holder

Ann M. Moormann, University of Massachusetts Medical School, Worcester, MA, USA

Uploaded on

April 2, 2023

DOI

To request one please log in.

License

Creative Commons BY 4.0
Model comments :

You can comment on the data model here. Via the speech bubbles at the itemgroups and items you can add comments to those specificially.

Back to model comments
Itemgroup comments for :

Item comments for :

  • Newest
  • Oldest
  • Popular
  • Newest
    • Newest
    • Oldest
    • Popular

No comments

In order to download data models you must be logged in. Please log in or register for free.

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
Back to the top of the page

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])
Back to the top of the page 

Help

Do you need help on how to use the search function? Please watch the corresponding tutorial video for more details and learn how to use the search function most efficiently.

Watch Tutorial