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ID

45640

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=phs001325 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 (this study) 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.

Link

dbGaP-study=phs001325

Keywords

Versions (1)
  1. 3/12/23 3/12/23 - Chiara Middel
Copyright Holder

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

Uploaded on

March 12, 2023

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License

Creative Commons BY 4.0
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    dbGaP phs001325 NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource - Whole Genome Sequence

    English

    This sample attributes table includes sample histological type, tumor status, analyte type, sample source, other IDs (UCSD source tissue, UCSD iPSC clone, WiCell), sequencing center, clone and passage.

    6 forms  
    1. StudyEvent: SEV1
      1. Eligibility Criteria
      2. The subject consent data table contains subject IDs and consent information.
      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, analyte type, sample source, other IDs (UCSD source tissue, UCSD iPSC clone, WiCell), sequencing center, clone and passage.
    pht006353
    Description

    pht006353

    Alias
    UMLS CUI [1,1]
    C3846158
    De-identified unique Sample ID
    Description

    SAMPLE_ID

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C2348585
    UMLS CUI [1,2]
    C4684638
    Cell or tissue type or subtype of sample
    Description

    HISTOLOGICAL_TYPE

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C2347026
    UMLS CUI [1,2]
    C0007634
    UMLS CUI [1,3]
    C0332307
    UMLS CUI [2,1]
    C2347026
    UMLS CUI [2,2]
    C0007634
    UMLS CUI [2,3]
    C0449560
    UMLS CUI [3,1]
    C1292533
    UMLS CUI [3,2]
    C0332307
    UMLS CUI [4,1]
    C1292533
    UMLS CUI [4,2]
    C0449560
    Tumor status
    Description

    IS_TUMOR

    Data type

    text

    Alias
    UMLS CUI [1,1]
    C0475752
    Original clone number from which cell line was expanded
    Description

    CLONE

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C0205313
    UMLS CUI [1,2]
    C1522642
    UMLS CUI [1,3]
    C0007600
    Passage number of cell line which was analysed
    Description

    PASSAGE

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C5236382
    UMLS CUI [1,2]
    C0007600
    UMLS CUI [1,3]
    C0936012
    UUID Identifier for tissue sample of fibroblast, blood or iPSC
    Description

    UCSD_SOURCE_TISSUE_ID

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C1710569
    UMLS CUI [1,2]
    C0016030
    UMLS CUI [2,1]
    C1710569
    UMLS CUI [2,2]
    C0178913
    UMLS CUI [3,1]
    C1710569
    UMLS CUI [3,2]
    C2717959
    UUID Identifier for iPSC clone. If the cell is an iPSC-derived cell type, this indicates the source clone.
    Description

    UCSD_IPSC_CLONE_ID

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C1710569
    UMLS CUI [1,2]
    C2717959
    UMLS CUI [1,3]
    C1522642
    UMLS CUI [2,1]
    C2717959
    UMLS CUI [2,2]
    C0449475
    UMLS CUI [2,3]
    C0449416
    UMLS CUI [2,4]
    C1522642
    WiCell identifier assigned to iPSC line archived at WiCell Research Institute, Wisconsin, USA
    Description

    WICELL_ID

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C3846158
    UMLS CUI [1,2]
    C0600091
    UMLS CUI [1,3]
    C2717959
    UMLS CUI [1,4]
    C1301943
    Analyte Type
    Description

    ANALYTE_TYPE

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C4744818
    Organisation providing original sample
    Description

    SAMPLE_SOURCE

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C1549759
    UMLS CUI [1,2]
    C1138603
    UMLS CUI [1,3]
    C0205313
    UMLS CUI [1,4]
    C2347026
    Name of the center which conducted sequencing
    Description

    SEQUENCING_CENTER

    Data type

    text

    Alias
    UMLS CUI [1,1]
    C1301943
    UMLS CUI [1,2]
    C0565990
    UMLS CUI [1,3]
    C1561491
    Back to the top of the page

    Similar models

    This sample attributes table includes sample histological type, tumor status, analyte type, sample source, other IDs (UCSD source tissue, UCSD iPSC clone, WiCell), sequencing center, clone and passage.

    6 forms
    1. StudyEvent: SEV1
      1. Eligibility Criteria
      2. The subject consent data table contains subject IDs and consent information.
      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, analyte type, sample source, other IDs (UCSD source tissue, UCSD iPSC clone, WiCell), sequencing center, clone and passage.
    Name
    Type
    Description | Question | Decode (Coded Value)
    Data type
    Alias
    Item Group
    pht006353
    C3846158 (UMLS CUI [1,1])
    SAMPLE_ID
    Item
    De-identified unique Sample ID
    string
    C2348585 (UMLS CUI [1,1])
    C4684638 (UMLS CUI [1,2])
    Item
    Cell or tissue type or subtype of sample
    string
    C2347026 (UMLS CUI [1,1])
    C0007634 (UMLS CUI [1,2])
    C0332307 (UMLS CUI [1,3])
    C2347026 (UMLS CUI [2,1])
    C0007634 (UMLS CUI [2,2])
    C0449560 (UMLS CUI [2,3])
    C1292533 (UMLS CUI [3,1])
    C0332307 (UMLS CUI [3,2])
    C1292533 (UMLS CUI [4,1])
    C0449560 (UMLS CUI [4,2])
    HISTOLOGICAL_TYPE
    Code List
    Cell or tissue type or subtype of sample
    CL Item
    blood (blood)
    CL Item
    fibroblast (fibroblast)
    CL Item
    iPSC (iPSC)
    Item
    Tumor status
    text
    C0475752 (UMLS CUI [1,1])
    IS_TUMOR
    Code List
    Tumor status
    CL Item
    No (N)
    CLONE
    Item
    Original clone number from which cell line was expanded
    string
    C0205313 (UMLS CUI [1,1])
    C1522642 (UMLS CUI [1,2])
    C0007600 (UMLS CUI [1,3])
    PASSAGE
    Item
    Passage number of cell line which was analysed
    string
    C5236382 (UMLS CUI [1,1])
    C0007600 (UMLS CUI [1,2])
    C0936012 (UMLS CUI [1,3])
    UCSD_SOURCE_TISSUE_ID
    Item
    UUID Identifier for tissue sample of fibroblast, blood or iPSC
    string
    C1710569 (UMLS CUI [1,1])
    C0016030 (UMLS CUI [1,2])
    C1710569 (UMLS CUI [2,1])
    C0178913 (UMLS CUI [2,2])
    C1710569 (UMLS CUI [3,1])
    C2717959 (UMLS CUI [3,2])
    UCSD_IPSC_CLONE_ID
    Item
    UUID Identifier for iPSC clone. If the cell is an iPSC-derived cell type, this indicates the source clone.
    string
    C1710569 (UMLS CUI [1,1])
    C2717959 (UMLS CUI [1,2])
    C1522642 (UMLS CUI [1,3])
    C2717959 (UMLS CUI [2,1])
    C0449475 (UMLS CUI [2,2])
    C0449416 (UMLS CUI [2,3])
    C1522642 (UMLS CUI [2,4])
    WICELL_ID
    Item
    WiCell identifier assigned to iPSC line archived at WiCell Research Institute, Wisconsin, USA
    string
    C3846158 (UMLS CUI [1,1])
    C0600091 (UMLS CUI [1,2])
    C2717959 (UMLS CUI [1,3])
    C1301943 (UMLS CUI [1,4])
    Item
    Analyte Type
    string
    C4744818 (UMLS CUI [1,1])
    ANALYTE_TYPE
    Code List
    Analyte Type
    CL Item
    DNA (DNA)
    Item
    Organisation providing original sample
    string
    C1549759 (UMLS CUI [1,1])
    C1138603 (UMLS CUI [1,2])
    C0205313 (UMLS CUI [1,3])
    C2347026 (UMLS CUI [1,4])
    SAMPLE_SOURCE
    Code List
    Organisation providing original sample
    CL Item
    UCSD (UCSD)
    Item
    Name of the center which conducted sequencing
    text
    C1301943 (UMLS CUI [1,1])
    C0565990 (UMLS CUI [1,2])
    C1561491 (UMLS CUI [1,3])
    SEQUENCING_CENTER
    Code List
    Name of the center which conducted sequencing
    CL Item
    Human Longevity, Inc. (HLI)
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