0 Beoordelingen

ID

45640

Beschrijving

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

Trefwoorden

  1. 12-03-23 12-03-23 - Chiara Middel
Houder van rechten

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

Geüploaded op

12 maart 2023

DOI

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Licentie

Creative Commons BY 4.0

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

    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.

    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
    Beschrijving

    pht006353

    Alias
    UMLS CUI [1,1]
    C3846158 (Other Coding)
    LOINC
    LA4728-7
    De-identified unique Sample ID
    Beschrijving

    SAMPLE_ID

    Datatype

    string

    Alias
    UMLS CUI [1,1]
    C2348585 (Clinical Trial Subject Unique Identifier)
    UMLS CUI [1,2]
    C4684638 (De-identified Information)
    Cell or tissue type or subtype of sample
    Beschrijving

    HISTOLOGICAL_TYPE

    Datatype

    string

    Alias
    UMLS CUI [1,1]
    C2347026 (Biospecimen)
    UMLS CUI [1,2]
    C0007634 (Cells)
    SNOMED
    4421005
    LOINC
    LP14738-6
    UMLS CUI [1,3]
    C0332307 (Type - attribute)
    SNOMED
    261664005
    UMLS CUI [2,1]
    C2347026 (Biospecimen)
    UMLS CUI [2,2]
    C0007634 (Cells)
    SNOMED
    4421005
    LOINC
    LP14738-6
    UMLS CUI [2,3]
    C0449560 (Subtype (attribute))
    SNOMED
    260837004
    UMLS CUI [3,1]
    C1292533 (Tissue specimen)
    SNOMED
    119376003
    UMLS CUI [3,2]
    C0332307 (Type - attribute)
    SNOMED
    261664005
    UMLS CUI [4,1]
    C1292533 (Tissue specimen)
    SNOMED
    119376003
    UMLS CUI [4,2]
    C0449560 (Subtype (attribute))
    SNOMED
    260837004
    Tumor status
    Beschrijving

    IS_TUMOR

    Datatype

    text

    Alias
    UMLS CUI [1,1]
    C0475752 (Tumor status)
    SNOMED
    277058005
    Original clone number from which cell line was expanded
    Beschrijving

    CLONE

    Datatype

    string

    Alias
    UMLS CUI [1,1]
    C0205313 (Original)
    SNOMED
    19535007
    LOINC
    LA9505-4
    UMLS CUI [1,2]
    C1522642 (Clone)
    UMLS CUI [1,3]
    C0007600 (Cultured Cell Line)
    Passage number of cell line which was analysed
    Beschrijving

    PASSAGE

    Datatype

    string

    Alias
    UMLS CUI [1,1]
    C5236382 (Passage Number)
    UMLS CUI [1,2]
    C0007600 (Cultured Cell Line)
    UMLS CUI [1,3]
    C0936012 (Analysis)
    UUID Identifier for tissue sample of fibroblast, blood or iPSC
    Beschrijving

    UCSD_SOURCE_TISSUE_ID

    Datatype

    string

    Alias
    UMLS CUI [1,1]
    C1710569 (Universally Unique Identifier)
    UMLS CUI [1,2]
    C0016030 (Fibroblasts)
    SNOMED
    52547004
    LOINC
    LP7234-0
    UMLS CUI [2,1]
    C1710569 (Universally Unique Identifier)
    UMLS CUI [2,2]
    C0178913 (Blood specimen)
    SNOMED
    119297000
    UMLS CUI [3,1]
    C1710569 (Universally Unique Identifier)
    UMLS CUI [3,2]
    C2717959 (Induced Pluripotent Stem Cells)
    UUID Identifier for iPSC clone. If the cell is an iPSC-derived cell type, this indicates the source clone.
    Beschrijving

    UCSD_IPSC_CLONE_ID

    Datatype

    string

    Alias
    UMLS CUI [1,1]
    C1710569 (Universally Unique Identifier)
    UMLS CUI [1,2]
    C2717959 (Induced Pluripotent Stem Cells)
    UMLS CUI [1,3]
    C1522642 (Clone)
    UMLS CUI [2,1]
    C2717959 (Induced Pluripotent Stem Cells)
    UMLS CUI [2,2]
    C0449475 (cell type)
    SNOMED
    246238003
    UMLS CUI [2,3]
    C0449416 (Source)
    SNOMED
    260753009
    LOINC
    LP21212-3
    UMLS CUI [2,4]
    C1522642 (Clone)
    WiCell identifier assigned to iPSC line archived at WiCell Research Institute, Wisconsin, USA
    Beschrijving

    WICELL_ID

    Datatype

    string

    Alias
    UMLS CUI [1,1]
    C3846158 (Other Coding)
    LOINC
    LA4728-7
    UMLS CUI [1,2]
    C0600091 (Identifier)
    SNOMED
    118522005
    LOINC
    LP31795-5
    UMLS CUI [1,3]
    C2717959 (Induced Pluripotent Stem Cells)
    UMLS CUI [1,4]
    C1301943 (Institution name)
    SNOMED
    398321007
    Analyte Type
    Beschrijving

    ANALYTE_TYPE

    Datatype

    string

    Alias
    UMLS CUI [1,1]
    C4744818 (Analyte Type)
    Organisation providing original sample
    Beschrijving

    SAMPLE_SOURCE

    Datatype

    string

    Alias
    UMLS CUI [1,1]
    C1549759 (Organization Identifier)
    UMLS CUI [1,2]
    C1138603 (Provider)
    LOINC
    LP7504-6
    UMLS CUI [1,3]
    C0205313 (Original)
    SNOMED
    19535007
    LOINC
    LA9505-4
    UMLS CUI [1,4]
    C2347026 (Biospecimen)
    Name of the center which conducted sequencing
    Beschrijving

    SEQUENCING_CENTER

    Datatype

    text

    Alias
    UMLS CUI [1,1]
    C1301943 (Institution name)
    SNOMED
    398321007
    UMLS CUI [1,2]
    C0565990 (Medical center)
    SNOMED
    288565001
    UMLS CUI [1,3]
    C1561491 (Sequencing)

    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.

    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)
    Datatype
    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])
    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])
    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])
    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])
    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])
    Code List
    Name of the center which conducted sequencing
    CL Item
    Human Longevity, Inc. (HLI)

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