0 Evaluaciones
ID

45217

Descripción

Principal Investigator: Catherine Wu, Broad Institute, Cambridge, MA, Dana Farber Cancer Institute, Boston MA, USA MeSH: Chronic Lymphocytic Leukemia,Leukemia, Lymphocytic, Chronic, B-Cell https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000435 The somatic genetic basis of chronic lymphocytic leukemia (CLL), a common and clinically heterogenous adult leukemia, remains poorly understood. Massively parallel sequencing technology now provides a method for systematic discovery of genetic alterations that underlie disease, and for uncovering new therapeutic targets and biomarkers. In study version 2 we presented a dataset consisting of DNA sequencing from 169 CLL samples (with matched germline controls). Samples were collected from patients displaying a wide range of characteristics representing the broad clinical spectrum of CLL. Understanding the mutational landscape of CLL provides a starting point for systematic analyses to address fundamental questions in CLL, including how mutated genes alter cellular networks and phenotypes, and thereby contribute to disease heterogeneity. Intratumoral heterogeneity plays a critical role in tumor evolution. To define the contribution of DNA methylation to heterogeneity within tumors, we performed genome-scale bisulfite sequencing of 100 primary chronic lymphocytic leukemias (CLLs; data presented in study version 3). Compared with 26 normal B cell samples, CLLs consistently displayed higher intrasample variability of DNA methylation patterns across the genome, which appears to arise from stochastically disordered methylation in malignant cells. Transcriptome analysis of bulk and single CLL cells revealed that methylationdisorder was linked to low-level expression. Disordered methylation was further associated with adverse clinical outcome. We therefore propose that disordered methylation plays a similar role to that of genetic instability, enhancing the ability of cancer cells to search for superior evolutionary trajectories.

Link

dbGaP study = phs000435

Palabras clave

Versiones (2)
  1. 31/7/22 31/7/22 - Chiara Middel
  2. 12/10/22 12/10/22 - Adrian Schulz
Titular de derechos de autor

Catherine Wu, Broad Institute, Cambridge, MA, Dana Farber Cancer Institute, Boston MA, USA

Subido en

12 de octubre de 2022

DOI

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Licencia

Creative Commons BY 4.0
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    dbGaP phs000435 Whole Exome Sequencing of Chronic Lymphocytic Leukemia

    Inglés

    The dataset contains molecular phenotype data, e.g. status of IGHV (mutated/unmutated), ZAP70, trisomy 12, deletions on chromosomes 11, 13 and 17 (negative/positive), and basic sociodemographic information, i.e. age, gender and ethnicity of n=186 subjects.

    4 formularios  
    pht002523
    Descripción

    pht002523

    Unique Participant Identifier
    Descripción

    SUBJID

    Tipo de datos

    string

    Alias
    UMLS CUI [1,1]
    C2348585
    The main disease(s) for which the participant has been asked to donate a sample for study
    Descripción

    Primary Disease

    Tipo de datos

    string

    Alias
    UMLS CUI [1,1]
    C1542147
    UMLS CUI [1,2]
    C0012634
    Participant's gender as Male or Female
    Descripción

    Gender

    Tipo de datos

    string

    Alias
    UMLS CUI [1,1]
    C0079399
    Participant's age
    Descripción

    Age

    Tipo de datos

    text

    Unidades de medida
    • Years
    Alias
    UMLS CUI [1,1]
    C0001779
    Years
    IGHV is mutation status of the immunoglobulin heavy chain variable region. When the DNA sequence homology of CLL tumor is less than 98% compared to reference, it is designated as "mutated". Homology >98% is considered "unmutated." IGHV mutation status is a CLL prognosis marker; IGHV mutated status is associated with good prognosis.
    Descripción

    IGHV

    Tipo de datos

    text

    Alias
    UMLS CUI [1,1]
    C0449438
    UMLS CUI [1,2]
    C3829560
    UMLS CUI [2,1]
    C2697616
    UMLS CUI [2,2]
    C1265611
    UMLS CUI [2,3]
    C0162326
    UMLS CUI [2,4]
    C0023434
    UMLS CUI [2,5]
    C0026882
    UMLS CUI [3,1]
    C2697616
    UMLS CUI [3,2]
    C1265611
    UMLS CUI [3,3]
    C1298908
    UMLS CUI [3,4]
    C0026882
    UMLS CUI [4,1]
    C3829560
    UMLS CUI [4,2]
    C0023434
    UMLS CUI [4,3]
    C1514475
    UMLS CUI [5,1]
    C1333041
    UMLS CUI [5,2]
    C0278250
    ZAP70 is CLL prognosis marker and positive expression is associated with poor prognosis. ZAP70 expression level is measured by flow cytometry and the cutoff score is 24%.
    Descripción

    ZAP70

    Tipo de datos

    text

    Alias
    UMLS CUI [1,1]
    C1421567
    UMLS CUI [1,2]
    C0023434
    UMLS CUI [1,3]
    C1514475
    UMLS CUI [2,1]
    C5444885
    UMLS CUI [2,2]
    C0278252
    UMLS CUI [3,1]
    C3244092
    UMLS CUI [3,2]
    C0242485
    UMLS CUI [3,3]
    C0016263
    Trisomy 12 is measured by FISH cytogenetic analysis. Cutoff score is 2%. Trisomy 12 is a neutral prognosis marker.
    Descripción

    Trisomy 12

    Tipo de datos

    text

    Alias
    UMLS CUI [1,1]
    C0432408
    UMLS CUI [1,2]
    C0242485
    UMLS CUI [1,3]
    C0752095
    UMLS CUI [2,1]
    C0432408
    UMLS CUI [2,2]
    C1514475
    UMLS CUI [2,3]
    C4330821
    Del13qhet is measured by FISH cytogenetic analysis of CLL tumor. Del13qhet is chromosome 13q deletion in one allele. Cutoff score is 7%. Del13q is the most common chromosomal abnormalities in CLL and is associated with better prognosis.
    Descripción

    Del13qhet

    Tipo de datos

    text

    Alias
    UMLS CUI [1,1]
    C0019425
    UMLS CUI [1,2]
    C2930913
    UMLS CUI [1,3]
    C0752095
    UMLS CUI [1,4]
    C0023434
    UMLS CUI [2,1]
    C2930913
    UMLS CUI [2,2]
    C0205214
    UMLS CUI [2,3]
    C0008625
    UMLS CUI [2,4]
    C0023434
    UMLS CUI [3,1]
    C2930913
    UMLS CUI [3,2]
    C0278250
    Del13qhomo is measured by FISH cytogenetic analysis of CLL tumor. Del13qhomo is deletion of the 13q region in two alleles. Cutoff score is 7%. Del13q is the most common chromosomal abnormalities in CLL and is associated with better prognosis.
    Descripción

    Del13qhomo

    Tipo de datos

    text

    Alias
    UMLS CUI [1,1]
    C0019904
    UMLS CUI [1,2]
    C2930913
    UMLS CUI [1,3]
    C0752095
    UMLS CUI [1,4]
    C0023434
    UMLS CUI [2,1]
    C2930913
    UMLS CUI [2,2]
    C0205214
    UMLS CUI [2,3]
    C0008625
    UMLS CUI [2,4]
    C0023434
    UMLS CUI [3,1]
    C2930913
    UMLS CUI [3,2]
    C0278250
    Del11q is measured by FISH cytogenetic analysis of CLL tumor, and is associated with poor prognosis. Cutoff score is 5%.
    Descripción

    Del11q

    Tipo de datos

    text

    Alias
    UMLS CUI [1,1]
    C0008628
    UMLS CUI [1,2]
    C0796366
    UMLS CUI [2,1]
    C0278252
    Del17p is measured by FISH cytogenetic analysis of CLL tumor. The deleted region includes TP53, and is associated with poor prognosis. Cutoff score is 8%.
    Descripción

    Del17p

    Tipo de datos

    text

    Alias
    UMLS CUI [1,1]
    C3683846
    UMLS CUI [1,2]
    C0332257
    UMLS CUI [1,3]
    C4524826
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    Similar models

    The dataset contains molecular phenotype data, e.g. status of IGHV (mutated/unmutated), ZAP70, trisomy 12, deletions on chromosomes 11, 13 and 17 (negative/positive), and basic sociodemographic information, i.e. age, gender and ethnicity of n=186 subjects.

    4 formularios
    Name
    Tipo
    Description | Question | Decode (Coded Value)
    Tipo de datos
    Alias
    Item Group
    pht002523
    SUBJID
    Item
    Unique Participant Identifier
    string
    C2348585 (UMLS CUI [1,1])
    Item
    The main disease(s) for which the participant has been asked to donate a sample for study
    string
    C1542147 (UMLS CUI [1,1])
    C0012634 (UMLS CUI [1,2])
    Primary Disease
    Code List
    The main disease(s) for which the participant has been asked to donate a sample for study
    CL Item
    Head and Neck Cancer (Head and Neck Cancer)
    C0278996 (UMLS CUI [1,1])
    Item
    Participant's gender as Male or Female
    string
    C0079399 (UMLS CUI [1,1])
    Gender
    Code List
    Participant's gender as Male or Female
    CL Item
    Female (Female)
    C0086287 (UMLS CUI [1,1])
    CL Item
    Male (Male)
    C0086582 (UMLS CUI [1,1])
    CL Item
    Not Reported (Not Reported)
    C0439673 (UMLS CUI [1,1])
    Age
    Item
    Participant's age
    text
    C0001779 (UMLS CUI [1,1])
    Item
    IGHV is mutation status of the immunoglobulin heavy chain variable region. When the DNA sequence homology of CLL tumor is less than 98% compared to reference, it is designated as "mutated". Homology >98% is considered "unmutated." IGHV mutation status is a CLL prognosis marker; IGHV mutated status is associated with good prognosis.
    text
    C0449438 (UMLS CUI [1,1])
    C3829560 (UMLS CUI [1,2])
    C2697616 (UMLS CUI [2,1])
    C1265611 (UMLS CUI [2,2])
    C0162326 (UMLS CUI [2,3])
    C0023434 (UMLS CUI [2,4])
    C0026882 (UMLS CUI [2,5])
    C2697616 (UMLS CUI [3,1])
    C1265611 (UMLS CUI [3,2])
    C1298908 (UMLS CUI [3,3])
    C0026882 (UMLS CUI [3,4])
    C3829560 (UMLS CUI [4,1])
    C0023434 (UMLS CUI [4,2])
    C1514475 (UMLS CUI [4,3])
    C1333041 (UMLS CUI [5,1])
    C0278250 (UMLS CUI [5,2])
    IGHV
    Code List
    IGHV is mutation status of the immunoglobulin heavy chain variable region. When the DNA sequence homology of CLL tumor is less than 98% compared to reference, it is designated as "mutated". Homology >98% is considered "unmutated." IGHV mutation status is a CLL prognosis marker; IGHV mutated status is associated with good prognosis.
    CL Item
    Unmutated (0)
    C1298908 (UMLS CUI [1,1])
    C0026882 (UMLS CUI [1,2])
    CL Item
    Mutated (1)
    C0026882 (UMLS CUI [1,1])
    CL Item
    Not Reported (Not Reported)
    C0439673 (UMLS CUI [1,1])
    Item
    ZAP70 is CLL prognosis marker and positive expression is associated with poor prognosis. ZAP70 expression level is measured by flow cytometry and the cutoff score is 24%.
    text
    C1421567 (UMLS CUI [1,1])
    C0023434 (UMLS CUI [1,2])
    C1514475 (UMLS CUI [1,3])
    C5444885 (UMLS CUI [2,1])
    C0278252 (UMLS CUI [2,2])
    C3244092 (UMLS CUI [3,1])
    C0242485 (UMLS CUI [3,2])
    C0016263 (UMLS CUI [3,3])
    ZAP70
    Code List
    ZAP70 is CLL prognosis marker and positive expression is associated with poor prognosis. ZAP70 expression level is measured by flow cytometry and the cutoff score is 24%.
    CL Item
    Negative (0)
    C0205160 (UMLS CUI [1,1])
    CL Item
    Positive (1)
    C1446409 (UMLS CUI [1,1])
    CL Item
    Not Reported (Not Reported)
    C0439673 (UMLS CUI [1,1])
    Item
    Trisomy 12 is measured by FISH cytogenetic analysis. Cutoff score is 2%. Trisomy 12 is a neutral prognosis marker.
    text
    C0432408 (UMLS CUI [1,1])
    C0242485 (UMLS CUI [1,2])
    C0752095 (UMLS CUI [1,3])
    C0432408 (UMLS CUI [2,1])
    C1514475 (UMLS CUI [2,2])
    C4330821 (UMLS CUI [2,3])
    Trisomy 12
    Code List
    Trisomy 12 is measured by FISH cytogenetic analysis. Cutoff score is 2%. Trisomy 12 is a neutral prognosis marker.
    CL Item
    Negative (0)
    C0205160 (UMLS CUI [1,1])
    CL Item
    Positive (1)
    C1446409 (UMLS CUI [1,1])
    Item
    Del13qhet is measured by FISH cytogenetic analysis of CLL tumor. Del13qhet is chromosome 13q deletion in one allele. Cutoff score is 7%. Del13q is the most common chromosomal abnormalities in CLL and is associated with better prognosis.
    text
    C0019425 (UMLS CUI [1,1])
    C2930913 (UMLS CUI [1,2])
    C0752095 (UMLS CUI [1,3])
    C0023434 (UMLS CUI [1,4])
    C2930913 (UMLS CUI [2,1])
    C0205214 (UMLS CUI [2,2])
    C0008625 (UMLS CUI [2,3])
    C0023434 (UMLS CUI [2,4])
    C2930913 (UMLS CUI [3,1])
    C0278250 (UMLS CUI [3,2])
    Del13qhet
    Code List
    Del13qhet is measured by FISH cytogenetic analysis of CLL tumor. Del13qhet is chromosome 13q deletion in one allele. Cutoff score is 7%. Del13q is the most common chromosomal abnormalities in CLL and is associated with better prognosis.
    CL Item
    Negative (0)
    CL Item
    Positive (1)
    Item
    Del13qhomo is measured by FISH cytogenetic analysis of CLL tumor. Del13qhomo is deletion of the 13q region in two alleles. Cutoff score is 7%. Del13q is the most common chromosomal abnormalities in CLL and is associated with better prognosis.
    text
    C0019904 (UMLS CUI [1,1])
    C2930913 (UMLS CUI [1,2])
    C0752095 (UMLS CUI [1,3])
    C0023434 (UMLS CUI [1,4])
    C2930913 (UMLS CUI [2,1])
    C0205214 (UMLS CUI [2,2])
    C0008625 (UMLS CUI [2,3])
    C0023434 (UMLS CUI [2,4])
    C2930913 (UMLS CUI [3,1])
    C0278250 (UMLS CUI [3,2])
    Del13qhomo
    Code List
    Del13qhomo is measured by FISH cytogenetic analysis of CLL tumor. Del13qhomo is deletion of the 13q region in two alleles. Cutoff score is 7%. Del13q is the most common chromosomal abnormalities in CLL and is associated with better prognosis.
    CL Item
    Negative (0)
    C0205160 (UMLS CUI [1,1])
    CL Item
    Positive (1)
    C1446409 (UMLS CUI [1,1])
    Item
    Del11q is measured by FISH cytogenetic analysis of CLL tumor, and is associated with poor prognosis. Cutoff score is 5%.
    text
    C0008628 (UMLS CUI [1,1])
    C0796366 (UMLS CUI [1,2])
    C0278252 (UMLS CUI [2,1])
    Del11q
    Code List
    Del11q is measured by FISH cytogenetic analysis of CLL tumor, and is associated with poor prognosis. Cutoff score is 5%.
    CL Item
    Negative (0)
    C0205160 (UMLS CUI [1,1])
    CL Item
    Positive (1)
    C1446409 (UMLS CUI [1,1])
    Item
    Del17p is measured by FISH cytogenetic analysis of CLL tumor. The deleted region includes TP53, and is associated with poor prognosis. Cutoff score is 8%.
    text
    C3683846 (UMLS CUI [1,1])
    C0332257 (UMLS CUI [1,2])
    C4524826 (UMLS CUI [1,3])
    Del17p
    Code List
    Del17p is measured by FISH cytogenetic analysis of CLL tumor. The deleted region includes TP53, and is associated with poor prognosis. Cutoff score is 8%.
    CL Item
    Negative (0)
    C0205160 (UMLS CUI [1,1])
    CL Item
    Positive (1)
    C1446409 (UMLS CUI [1,1])
    Volver a la parte superior de la página 

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