0 Ratings
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.

Link

dbGaP study=phs000924

Keywords

Versions (1)
  1. 4/28/24 4/28/24 - Madita Rudolph
Copyright Holder

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

Uploaded on

April 28, 2024

DOI

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License

Creative Commons BY 4.0
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    dbGaP phs000924 NextGen Consortium: The iPSCORE (iPSC Collection for Omic Research) Resource

    English

    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 forms  
    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.
    pht006323
    Description

    pht006323

    Alias
    UMLS CUI [1,1]
    C3846158
    De-identified unique Subject ID with the format of either a universally unique identifier (UUID) for subjects with data or the iPSCORE_ID for those that are only in pedigree file
    Description

    SUBJECT_ID

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C4684638
    UMLS CUI [1,2]
    C1299222
    De-identified Subject ID
    Description

    iPSCORE_ID

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C4684638
    UMLS CUI [1,2]
    C2348585
    Subject sex
    Description

    SEX

    Data type

    text

    Alias
    UMLS CUI [1,1]
    C0079399
    Subject age at enrollment
    Description

    AGE

    Data type

    text

    Measurement units
    • years
    Alias
    UMLS CUI [1,1]
    C5236162
    years
    Reported race/ethnicity of participant as recorded by fill in the blank
    Description

    REPORTED_RACE_ETHNICITY

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C0015031
    Race/ethnicity category as grouped by researcher
    Description

    RACE_ETHNICITY_GROUPING

    Data type

    text

    Alias
    UMLS CUI [1,1]
    C0015031
    Most similar super population group as estimated by comparing the individuals SNPs to the 1KG dataset by PCA. This value is the super population values from 1KG, not eg "Asian".
    Description

    GENETICALLY_SIMILAR_POPULATION_GROUP

    Data type

    text

    Alias
    UMLS CUI [1,1]
    C1257890
    Classification of primary heart diagnoses for individuals recruited through the UCSD Sulpizio Cardiovascular Center
    Description

    HEART_DISEASE_CATEGORY

    Data type

    text

    Alias
    UMLS CUI [1,1]
    C0205225
    UMLS CUI [1,2]
    C0011900
    UMLS CUI [1,3]
    C0018799
    UMLS CUI [1,4]
    C0008902
    Primary heart diagnosis for individuals recruited through the UCSD Sulpizio Cardiovascular Center
    Description

    PRIMARY_HEART_DIAGNOSES

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C0205225
    UMLS CUI [1,2]
    C0011900
    UMLS CUI [1,3]
    C0018799
    Other (non-primary) heart diagnoses for individuals recruited through the UCSD Sulpizio Cardiovascular Center
    Description

    OTHER_HEART_DIAGNOSES

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C0011900
    UMLS CUI [1,2]
    C0018799
    UMLS CUI [1,3]
    C0205394
    Comment on heart diagnoses for individuals recruited through the UCSD Sulpizio Cardiovascular Center
    Description

    HEART_DISEASE_COMMENT

    Data type

    string

    Alias
    UMLS CUI [1,1]
    C0947611
    UMLS CUI [1,2]
    C0011900
    UMLS CUI [1,3]
    C0018799
    Disease ontology (DO) code for primary heart diagnoses as described http://www.disease-ontology.org/ and obtained through http://www.malacards.org/
    Description

    DISEASE_ONTOLOGY_CODE

    Data type

    float

    Alias
    UMLS CUI [1,1]
    C0805701
    UMLS CUI [1,2]
    C1518584
    UMLS CUI [1,3]
    C0011900
    UMLS CUI [1,4]
    C0018799
    Indicator for whether subject was part of iPSCORE resource paper (PMID 28410642)
    Description

    SUBSTUDY_iPSCORE_RESOURCE

    Data type

    float

    Alias
    UMLS CUI [1,1]
    C2348568
    Indicator for whether subject was part of paper studying aberrant iPSC methylation in twins (PMID 28388429)
    Description

    SUBSTUDY_ABERRANT_METHYLATION

    Data type

    float

    Alias
    UMLS CUI [1,1]
    C2348568
    Indicator for whether subject has whole genome sequence data
    Description

    SUBSTUDY_WHOLE_GENOME_SEQUENCING

    Data type

    float

    Alias
    UMLS CUI [1,1]
    C0470187
    UMLS CUI [1,2]
    C3640076
    UMLS CUI [1,3]
    C1511726
    Indicator for whether subject was part of paper studying expression quantitative trait loci (eQTL) in iPSC (PMID 28388430)
    Description

    SUBSTUDY_IPSC_EQTL

    Data type

    float

    Alias
    UMLS CUI [2,1]
    C1522602
    UMLS CUI [2,2]
    C1292711
    UMLS CUI [2,3]
    C0282420
    UMLS CUI [2,4]
    C3826857
    UMLS CUI [2,5]
    C2717959
    Indicator for whether subject was part of paper studying allele-specific NKX2-5 binding in iPSC-derived cardiomyocytes (bioRxiv 351411; doi: https://doi.org/10.1101/351411)
    Description

    SUBSTUDY_IPSC_CM_NKX25

    Data type

    float

    Alias
    UMLS CUI [2,1]
    C1522602
    UMLS CUI [2,2]
    C1292711
    UMLS CUI [2,3]
    C0282420
    UMLS CUI [2,4]
    C1413784
    UMLS CUI [2,5]
    C1624609
    UMLS CUI [2,6]
    C2717959
    UMLS CUI [2,7]
    C0225828
    Indicator for whether subject was part of paper studying Hi-C in iPSCs and iPSC-derived cardiomyocytes (bioRxiv 352682; doi: https://doi.org/10.1101/352682)
    Description

    SUBSTUDY_IPSC_CM_HIC

    Data type

    float

    Alias
    UMLS CUI [2,1]
    C1522602
    UMLS CUI [2,2]
    C1292711
    UMLS CUI [2,3]
    C0282420
    UMLS CUI [2,4]
    C0872186
    UMLS CUI [2,5]
    C2717959
    UMLS CUI [2,6]
    C0225828
    Indicator for whether subject was part of paper studying the mutational burden of iPSCs (bioRxiv 334870; doi: https://doi.org/10.1101/334870)
    Description

    SUBSTUDY_IPSC_SOMATIC

    Data type

    float

    Alias
    UMLS CUI [2,1]
    C1522602
    UMLS CUI [2,2]
    C1292711
    UMLS CUI [2,3]
    C0282420
    UMLS CUI [2,4]
    C0026882
    UMLS CUI [2,5]
    C2828008
    UMLS CUI [2,6]
    C2717959
    Indicator for whether subject was part of paper examining the utility of iPSC-derived retinal pigment epithelium to study the genetics of eye diseases
    Description

    SUBSTUDY_RPE_PILOT

    Data type

    float

    Alias
    UMLS CUI [2,1]
    C1522602
    UMLS CUI [2,2]
    C1292711
    UMLS CUI [2,3]
    C0282420
    UMLS CUI [2,4]
    C1524063
    UMLS CUI [2,5]
    C2717959
    UMLS CUI [2,6]
    C4540048
    UMLS CUI [2,7]
    C2603343
    UMLS CUI [2,8]
    C0017399
    UMLS CUI [2,9]
    C0015397
    Indicator for whether subject was part of paper examining structural variation in iPSCORE
    Description

    SUBSTUDY_IPSCORE_SV

    Data type

    float

    Alias
    UMLS CUI [1,1]
    C1522602
    UMLS CUI [1,2]
    C1292711
    UMLS CUI [1,3]
    C0282420
    UMLS CUI [1,4]
    C2717924
    UMLS CUI [1,5]
    C2717959
    Indicator for whether subject was part of paper examining lncrnas in iPSC-CMs
    Description

    SUBSTUDY_CM_LNCRNA

    Data type

    float

    Alias
    UMLS CUI [1,1]
    C1522602
    UMLS CUI [1,2]
    C1292711
    UMLS CUI [1,3]
    C0282420
    UMLS CUI [1,4]
    C2982391
    UMLS CUI [1,5]
    C2717959
    UMLS CUI [1,6]
    C0225828
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    Similar models

    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 forms
    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)
    Data type
    Alias
    Item Group
    pht006323
    C3846158 (UMLS CUI [1,1])
    SUBJECT_ID
    Item
    De-identified unique Subject ID with the format of either a universally unique identifier (UUID) for subjects with data or the iPSCORE_ID for those that are only in pedigree file
    string
    C4684638 (UMLS CUI [1,1])
    C1299222 (UMLS CUI [1,2])
    iPSCORE_ID
    Item
    De-identified Subject ID
    string
    C4684638 (UMLS CUI [1,1])
    C2348585 (UMLS CUI [1,2])
    Item
    Subject sex
    text
    C0079399 (UMLS CUI [1,1])
    SEX
    Code List
    Subject sex
    CL Item
    Female (F)
    C0086287 (UMLS CUI [1,1])
    CL Item
    Male (M)
    C0086582 (UMLS CUI [1,1])
    AGE
    Item
    Subject age at enrollment
    text
    C5236162 (UMLS CUI [1,1])
    REPORTED_RACE_ETHNICITY
    Item
    Reported race/ethnicity of participant as recorded by fill in the blank
    string
    C0015031 (UMLS CUI [1,1])
    Item
    Race/ethnicity category as grouped by researcher
    text
    C0015031 (UMLS CUI [1,1])
    RACE_ETHNICITY_GROUPING
    Code List
    Race/ethnicity category as grouped by researcher
    CL Item
    African American (African American)
    CL Item
    Asian (Asian)
    CL Item
    European (European)
    CL Item
    Hispanic (Hispanic)
    CL Item
    Indian (Indian)
    CL Item
    Middle Eastern (Middle Eastern)
    CL Item
    Multiple ethnicities reported (Multiple ethnicities reported)
    Item
    Most similar super population group as estimated by comparing the individuals SNPs to the 1KG dataset by PCA. This value is the super population values from 1KG, not eg "Asian".
    text
    C1257890 (UMLS CUI [1,1])
    GENETICALLY_SIMILAR_POPULATION_GROUP
    Code List
    Most similar super population group as estimated by comparing the individuals SNPs to the 1KG dataset by PCA. This value is the super population values from 1KG, not eg "Asian".
    CL Item
    AFR (AFR)
    CL Item
    AMR (AMR)
    CL Item
    EAS (EAS)
    CL Item
    EUR (EUR)
    CL Item
    SAS (SAS)
    Item
    Classification of primary heart diagnoses for individuals recruited through the UCSD Sulpizio Cardiovascular Center
    text
    C0205225 (UMLS CUI [1,1])
    C0011900 (UMLS CUI [1,2])
    C0018799 (UMLS CUI [1,3])
    C0008902 (UMLS CUI [1,4])
    HEART_DISEASE_CATEGORY
    Code List
    Classification of primary heart diagnoses for individuals recruited through the UCSD Sulpizio Cardiovascular Center
    CL Item
    Arrhythmia (Arrhythmia)
    CL Item
    Cardiomyopathy (Cardiomyopathy)
    CL Item
    Structural (Structural)
    PRIMARY_HEART_DIAGNOSES
    Item
    Primary heart diagnosis for individuals recruited through the UCSD Sulpizio Cardiovascular Center
    string
    C0205225 (UMLS CUI [1,1])
    C0011900 (UMLS CUI [1,2])
    C0018799 (UMLS CUI [1,3])
    OTHER_HEART_DIAGNOSES
    Item
    Other (non-primary) heart diagnoses for individuals recruited through the UCSD Sulpizio Cardiovascular Center
    string
    C0011900 (UMLS CUI [1,1])
    C0018799 (UMLS CUI [1,2])
    C0205394 (UMLS CUI [1,3])
    HEART_DISEASE_COMMENT
    Item
    Comment on heart diagnoses for individuals recruited through the UCSD Sulpizio Cardiovascular Center
    string
    C0947611 (UMLS CUI [1,1])
    C0011900 (UMLS CUI [1,2])
    C0018799 (UMLS CUI [1,3])
    DISEASE_ONTOLOGY_CODE
    Item
    Disease ontology (DO) code for primary heart diagnoses as described http://www.disease-ontology.org/ and obtained through http://www.malacards.org/
    float
    C0805701 (UMLS CUI [1,1])
    C1518584 (UMLS CUI [1,2])
    C0011900 (UMLS CUI [1,3])
    C0018799 (UMLS CUI [1,4])
    SUBSTUDY_iPSCORE_RESOURCE
    Item
    Indicator for whether subject was part of iPSCORE resource paper (PMID 28410642)
    float
    C2348568 (UMLS CUI [1,1])
    SUBSTUDY_ABERRANT_METHYLATION
    Item
    Indicator for whether subject was part of paper studying aberrant iPSC methylation in twins (PMID 28388429)
    float
    C2348568 (UMLS CUI [1,1])
    SUBSTUDY_WHOLE_GENOME_SEQUENCING
    Item
    Indicator for whether subject has whole genome sequence data
    float
    C0470187 (UMLS CUI [1,1])
    C3640076 (UMLS CUI [1,2])
    C1511726 (UMLS CUI [1,3])
    SUBSTUDY_IPSC_EQTL
    Item
    Indicator for whether subject was part of paper studying expression quantitative trait loci (eQTL) in iPSC (PMID 28388430)
    float
    C1522602 (UMLS CUI [2,1])
    C1292711 (UMLS CUI [2,2])
    C0282420 (UMLS CUI [2,3])
    C3826857 (UMLS CUI [2,4])
    C2717959 (UMLS CUI [2,5])
    SUBSTUDY_IPSC_CM_NKX25
    Item
    Indicator for whether subject was part of paper studying allele-specific NKX2-5 binding in iPSC-derived cardiomyocytes (bioRxiv 351411; doi: https://doi.org/10.1101/351411)
    float
    C1522602 (UMLS CUI [2,1])
    C1292711 (UMLS CUI [2,2])
    C0282420 (UMLS CUI [2,3])
    C1413784 (UMLS CUI [2,4])
    C1624609 (UMLS CUI [2,5])
    C2717959 (UMLS CUI [2,6])
    C0225828 (UMLS CUI [2,7])
    SUBSTUDY_IPSC_CM_HIC
    Item
    Indicator for whether subject was part of paper studying Hi-C in iPSCs and iPSC-derived cardiomyocytes (bioRxiv 352682; doi: https://doi.org/10.1101/352682)
    float
    C1522602 (UMLS CUI [2,1])
    C1292711 (UMLS CUI [2,2])
    C0282420 (UMLS CUI [2,3])
    C0872186 (UMLS CUI [2,4])
    C2717959 (UMLS CUI [2,5])
    C0225828 (UMLS CUI [2,6])
    SUBSTUDY_IPSC_SOMATIC
    Item
    Indicator for whether subject was part of paper studying the mutational burden of iPSCs (bioRxiv 334870; doi: https://doi.org/10.1101/334870)
    float
    C1522602 (UMLS CUI [2,1])
    C1292711 (UMLS CUI [2,2])
    C0282420 (UMLS CUI [2,3])
    C0026882 (UMLS CUI [2,4])
    C2828008 (UMLS CUI [2,5])
    C2717959 (UMLS CUI [2,6])
    SUBSTUDY_RPE_PILOT
    Item
    Indicator for whether subject was part of paper examining the utility of iPSC-derived retinal pigment epithelium to study the genetics of eye diseases
    float
    C1522602 (UMLS CUI [2,1])
    C1292711 (UMLS CUI [2,2])
    C0282420 (UMLS CUI [2,3])
    C1524063 (UMLS CUI [2,4])
    C2717959 (UMLS CUI [2,5])
    C4540048 (UMLS CUI [2,6])
    C2603343 (UMLS CUI [2,7])
    C0017399 (UMLS CUI [2,8])
    C0015397 (UMLS CUI [2,9])
    SUBSTUDY_IPSCORE_SV
    Item
    Indicator for whether subject was part of paper examining structural variation in iPSCORE
    float
    C1522602 (UMLS CUI [1,1])
    C1292711 (UMLS CUI [1,2])
    C0282420 (UMLS CUI [1,3])
    C2717924 (UMLS CUI [1,4])
    C2717959 (UMLS CUI [1,5])
    SUBSTUDY_CM_LNCRNA
    Item
    Indicator for whether subject was part of paper examining lncrnas in iPSC-CMs
    float
    C1522602 (UMLS CUI [1,1])
    C1292711 (UMLS CUI [1,2])
    C0282420 (UMLS CUI [1,3])
    C2982391 (UMLS CUI [1,4])
    C2717959 (UMLS CUI [1,5])
    C0225828 (UMLS CUI [1,6])
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