ID

46002

Beskrivning

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.

Länk

dbGaP study=phs000924

Nyckelord

Versioner (1)
  1. 2024-04-28 2024-04-28 - Madita Rudolph
Rättsinnehavare

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

Uppladdad den

28 april 2024

DOI

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Licens

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

Engelsk

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 Formulär  
  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
Beskrivning

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
Beskrivning

SUBJECT_ID

Datatyp

string

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

iPSCORE_ID

Datatyp

string

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

SEX

Datatyp

text

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

AGE

Datatyp

text

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

REPORTED_RACE_ETHNICITY

Datatyp

string

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

RACE_ETHNICITY_GROUPING

Datatyp

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".
Beskrivning

GENETICALLY_SIMILAR_POPULATION_GROUP

Datatyp

text

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

HEART_DISEASE_CATEGORY

Datatyp

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
Beskrivning

PRIMARY_HEART_DIAGNOSES

Datatyp

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
Beskrivning

OTHER_HEART_DIAGNOSES

Datatyp

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
Beskrivning

HEART_DISEASE_COMMENT

Datatyp

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/
Beskrivning

DISEASE_ONTOLOGY_CODE

Datatyp

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)
Beskrivning

SUBSTUDY_iPSCORE_RESOURCE

Datatyp

float

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

SUBSTUDY_ABERRANT_METHYLATION

Datatyp

float

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

SUBSTUDY_WHOLE_GENOME_SEQUENCING

Datatyp

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)
Beskrivning

SUBSTUDY_IPSC_EQTL

Datatyp

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)
Beskrivning

SUBSTUDY_IPSC_CM_NKX25

Datatyp

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)
Beskrivning

SUBSTUDY_IPSC_CM_HIC

Datatyp

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)
Beskrivning

SUBSTUDY_IPSC_SOMATIC

Datatyp

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
Beskrivning

SUBSTUDY_RPE_PILOT

Datatyp

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
Beskrivning

SUBSTUDY_IPSCORE_SV

Datatyp

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
Beskrivning

SUBSTUDY_CM_LNCRNA

Datatyp

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 Formulär
  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
Typ
Description | Question | Decode (Coded Value)
Datatyp
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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