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ID

46002

Description

Principal Investigator: Kelly Frazer, PhD, University of California San Diego, CA, USA MeSH: Heart Diseases,Cardiovascular Diseases,Healthy Volunteers https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000924 The iPSCORE Resource of human induced pluripotent stem cells (hiPSCs) was created as part of the Next-Gen Consortium funded by the NHLBI. The overarching purpose of the iPSCORE Resource is to provide a large collection of hiPSCs for use in studying the impact of genetic variation on molecular and physiological phenotypes. This Resource is being used in a number of ongoing studies for which genomic data will be generated and deposited into public repositories and linked through dbGaP. A total of 273 individuals have participated in the study for which 222 have had hiPSCs generated from fibroblasts (available through WiCell (http://www.wicell.org/)). Of the 273 individuals, 181 are part of 55 families that include 24 monozygotic twin pairs and 5 dizygotic twin pairs, allowing for the incorporation of familial relationships into genetic analyses. Germline DNA has been sequenced from blood or fibroblast samples for all 273 individuals (see phs001325) and other genomic data (RNA-seq, DNA methylation, and genotype arrays) has been generated from the 222 hiPSCs derived from a subset of these individuals (phs000924). Current studies include differentiation of these hiPSCs to other cell types, including cardiomyocytes and retinal pigment epithelium, and the generation of additional genomic data.

Lien

dbGaP study=phs000924

Mots-clés

  1. 28/04/2024 28/04/2024 - Madita Rudolph
Détendeur de droits

Kelly Frazer, PhD, University of California San Diego, CA, USA

Téléchargé le

28 avril 2024

DOI

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Licence

Creative Commons BY 4.0

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    dbGaP phs000924 NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource

    This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, subjects's sex, twin IDs, and indicator for monozygotic and dizygotic twins.

    1. StudyEvent: SEV1
      1. Eligibility Criteria
      2. The subject consent data table contains subject IDs, consent information, and pooled subject IDs.
      3. This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, subjects's sex, twin IDs, and indicator for monozygotic and dizygotic twins.
      4. This data table contains mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
      5. This subject phenotype table includes subject's sex, age at enrollment, race (n=3 variables; self-reported, race/ethnicity grouped by researcher, and genetically similar population groups), heart diagnoses (n=5 variables; primary diagnoses and classification, other diagnoses, comments, and disease ontology), IPSCORE IDs, and indicators if subject was part of a study/paper (n=10 variables; iPSCORE resource, aberrant iPSC methylation in twins, WGS, eQTL, allele-specific NKX2-5 binding in iPSC-CMs, Hi-C in iPSCs and iPSC-CMs, mutational burden of iPSCs, iPSC-derived retinal pigment epithelium, structural variation in IPSCORE, and lncrnas in iPSC-CMs).
      6. This sample attributes table includes sample histological type, tumor status, clone and passage number of cell lines, method used to generate iPSCs, analyte type, sample source, genotyping center, sequencing center, array version, array coordinates (n=2 variables; Illumina and paired germline sample), differentiation protocol, chromatin based assay, and indicators if sample was part of a study/paper (n=11 variables; iPSCORE resource, aberrant iPSC methylation in twins, eQTL, allele-specific NKX2-5 binding in iPSC-CMs, Hi-C in iPSCs and iPSC-CMs, mutational burden of iPSCs, iPSC-derived retinal pigment epithelium, structural variation in iPSCORE, lncrnas in iPSC-CMs, differentiation of iPSCs to iPSC-CMs or cardiovascular precursor cells (CVPC), and co-accessibility between ATAC sites within iPSCs), other IDs (n=4 variables; UCSD source tissue, UCSD iPSC clone, UCSD differentiation, WiCell), and sample group as used in iPSCORE resource paper.
    pht006321
    Description

    pht006321

    Alias
    UMLS CUI [1,1]
    C3846158 (Other Coding)
    LOINC
    LA4728-7
    Family ID
    Description

    FAMILY_ID

    Type de données

    text

    Alias
    UMLS CUI [1,1]
    C3669174 (Family pedigree identifier)
    LOINC
    LP173549-9
    SUBJECT_ID
    Description

    SUBJECT_ID

    Type de données

    string

    Alias
    UMLS CUI [1,1]
    C2348585 (Clinical Trial Subject Unique Identifier)
    Father's SUBJECT_ID
    Description

    FATHER_SUBJECT_ID

    Type de données

    string

    Alias
    UMLS CUI [1,1]
    C3669177 (Father identifier)
    LOINC
    MTHU047348
    UMLS CUI [1,2]
    C0030761 (genetic pedigree)
    Mother's SUBJECT_ID
    Description

    MOTHER_SUBJECT_ID

    Type de données

    string

    Alias
    UMLS CUI [1,1]
    C3669352 (Mother identifier)
    LOINC
    MTHU047347
    UMLS CUI [1,2]
    C0030761 (genetic pedigree)
    Subject sex
    Description

    SEX

    Type de données

    text

    Alias
    UMLS CUI [1,1]
    C0079399 (Gender)
    SNOMED
    263495000
    LOINC
    LP61312-2
    Number indicating pair of monozygotic twins
    Description

    TWIN_ID

    Type de données

    text

    Alias
    UMLS CUI [1,1]
    C0041432 (Monozygotic twins)
    SNOMED
    2256007
    UMLS CUI [1,2]
    C0600091 (Identifier)
    SNOMED
    118522005
    LOINC
    LP31795-5
    An indicator when an individual is a monozygotic or dizygotic twin.
    Description

    MZorDZ

    Type de données

    text

    Alias
    UMLS CUI [1,1]
    C0041427 (Twin sibling (person))
    SNOMED
    11286003
    UMLS CUI [1,2]
    C2348585 (Clinical Trial Subject Unique Identifier)
    UMLS CUI [1,3]
    C0030761 (genetic pedigree)

    Similar models

    This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, subjects's sex, twin IDs, and indicator for monozygotic and dizygotic twins.

    1. StudyEvent: SEV1
      1. Eligibility Criteria
      2. The subject consent data table contains subject IDs, consent information, and pooled subject IDs.
      3. This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, subjects's sex, twin IDs, and indicator for monozygotic and dizygotic twins.
      4. This data table contains mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
      5. This subject phenotype table includes subject's sex, age at enrollment, race (n=3 variables; self-reported, race/ethnicity grouped by researcher, and genetically similar population groups), heart diagnoses (n=5 variables; primary diagnoses and classification, other diagnoses, comments, and disease ontology), IPSCORE IDs, and indicators if subject was part of a study/paper (n=10 variables; iPSCORE resource, aberrant iPSC methylation in twins, WGS, eQTL, allele-specific NKX2-5 binding in iPSC-CMs, Hi-C in iPSCs and iPSC-CMs, mutational burden of iPSCs, iPSC-derived retinal pigment epithelium, structural variation in IPSCORE, and lncrnas in iPSC-CMs).
      6. This sample attributes table includes sample histological type, tumor status, clone and passage number of cell lines, method used to generate iPSCs, analyte type, sample source, genotyping center, sequencing center, array version, array coordinates (n=2 variables; Illumina and paired germline sample), differentiation protocol, chromatin based assay, and indicators if sample was part of a study/paper (n=11 variables; iPSCORE resource, aberrant iPSC methylation in twins, eQTL, allele-specific NKX2-5 binding in iPSC-CMs, Hi-C in iPSCs and iPSC-CMs, mutational burden of iPSCs, iPSC-derived retinal pigment epithelium, structural variation in iPSCORE, lncrnas in iPSC-CMs, differentiation of iPSCs to iPSC-CMs or cardiovascular precursor cells (CVPC), and co-accessibility between ATAC sites within iPSCs), other IDs (n=4 variables; UCSD source tissue, UCSD iPSC clone, UCSD differentiation, WiCell), and sample group as used in iPSCORE resource paper.
    Name
    Type
    Description | Question | Decode (Coded Value)
    Type de données
    Alias
    Item Group
    pht006321
    C3846158 (UMLS CUI [1,1])
    FAMILY_ID
    Item
    Family ID
    text
    C3669174 (UMLS CUI [1,1])
    SUBJECT_ID
    Item
    SUBJECT_ID
    string
    C2348585 (UMLS CUI [1,1])
    FATHER_SUBJECT_ID
    Item
    Father's SUBJECT_ID
    string
    C3669177 (UMLS CUI [1,1])
    C0030761 (UMLS CUI [1,2])
    MOTHER_SUBJECT_ID
    Item
    Mother's SUBJECT_ID
    string
    C3669352 (UMLS CUI [1,1])
    C0030761 (UMLS CUI [1,2])
    Item
    Subject sex
    text
    C0079399 (UMLS CUI [1,1])
    Code List
    Subject sex
    CL Item
    Female (F)
    C0086287 (UMLS CUI [1,1])
    CL Item
    Male (M)
    C0086582 (UMLS CUI [1,1])
    TWIN_ID
    Item
    Number indicating pair of monozygotic twins
    text
    C0041432 (UMLS CUI [1,1])
    C0600091 (UMLS CUI [1,2])
    Item
    An indicator when an individual is a monozygotic or dizygotic twin.
    text
    C0041427 (UMLS CUI [1,1])
    C2348585 (UMLS CUI [1,2])
    C0030761 (UMLS CUI [1,3])
    Code List
    An indicator when an individual is a monozygotic or dizygotic twin.
    CL Item
    not a twin (0)
    CL Item
    dizygotic (DZ)
    CL Item
    monozygotic (MZ)

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