ArticleStem cell reports2017
iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.
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Article in Stem cell reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers, 2 of them syntheses that pooled it.
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112citing papers in PubMed, 2 pooled it
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Who cites it
112 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Genetic analyses of inflammatory polyneuropathy and chronic inflammatory demyelinating polyradiculoneuropathy identified candidate genes.HGG advances · 2024Pooled it
- Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes as an in vitro model in toxicology: strengths and weaknesses for hazard identification and risk characterization.Expert opinion on drug metabolism & toxicology · 2021Pooled it
- LPS stimulation reveals male and female dimorphism in human iPSC-derived macrophages.iScience · 2026Article
- A panel of Diversity Outbred mouse embryonic stem cells: enabling the functional characterization of natural genetic variationbioRxiv : the preprint server for biology · 2026Article
- Progressive suppression of DNA repair genes with persistent p53 target activation in doxorubicin-treated cardiomyocytes.G3 (Bethesda, Md.) · 2026Article
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- HIV heart inflammation is mediated by HIV infected myeloid cells, HIV-tat secretion, and aberrant function of Connexin43-containing channels.Scientific reports · 2026Article
- CX-5461 and doxorubicin activate a shared DNA damage-associated transcriptional response in human cardiomyocytes.G3 (Bethesda, Md.) · 2026Article
- Polygenic backgrounds influence phenotypic consequences of variants in cells, individuals, and populations.Cell genomics · 2026Review
- Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq.bioRxiv : the preprint server for biology · 2026Article
- Early considerations for village-in-a-dish platform: a multidisciplinary perspective.Frontiers in bioengineering and biotechnology · 2026Review
- Review
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.Nucleic acids research · 2025Article
- Article
- Anthracyclines induce global changes in cardiomyocyte chromatin accessibility that overlap with cardiovascular disease loci.PLoS genetics · 2025Article
- Article
- Systems genetics reveals the influence of expression QTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells.G3 (Bethesda, Md.) · 2025Article
- Article
- DNA-damage-associated protein co-expression network in cardiomyocytes informs on tolerance to genetic variation and disease.iScience · 2025Article
- Developing a general AI model for integrating diverse genomic modalities and comprehensive genomic knowledge.bioRxiv : the preprint server for biology · 2025Article
52 more citing papers are in PubMed but not listed here.
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Authors and funding
48 authors.
Athanasia D PanopoulosGene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Matteo D'AntonioInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Paola BenaglioDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Roy WilliamsDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
Sherin I HashemDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Bernhard M SchuldtZentrum für Integrative Psychiatrie, Universitätsklinikum Schleswig-Holstein, 24105 Kiel, Germany.
Christopher DeBoeverBioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Angelo D AriasDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Melvin GarciaInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Bradley C NelsonDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Olivier HarismendyDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
David A JakuboskyBiomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Margaret K R DonovanBioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
William W GreenwaldBioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
KathyJean FarnamInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Megan CookInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Victor BorjaInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Carl A MillerInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Jonathan D GrinsteinDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Frauke DreesDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Jonathan OkuboInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Kenneth E DiffenderferStem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Yuriko HishidaGene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Veronica ModestoStem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Carl T DargitzStem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Rachel FeiringStem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Chang ZhaoInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Aitor AguirreDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Thomas J McGarryDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Hiroko MatsuiInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
He LiInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Joaquin ReynaInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Fangwen RaoDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Daniel T O'ConnorDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Gene W YeoInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Sylvia M EvansDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Neil C ChiInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Kristen JepsenInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Naoki NariaiDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Franz-Josef MüllerZentrum für Integrative Psychiatrie, Universitätsklinikum Schleswig-Holstein, 24105 Kiel, Germany.
Lawrence S B GoldsteinDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Juan Carlos Izpisua BelmonteGene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Eric AdlerDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Jeanne F LoringCenter for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
W Travis BerggrenStem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Agnieszka D'Antonio-ChronowskaInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Erin N SmithDepartment of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
Kelly A FrazerInstitute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: kafrazer@ucsd.edu.
Funding
VIRAL MALIGNANCYP30CA023100 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Jesse Nodora · 1985 to 2026
$124.9MUC San Diego Clinical and Translational Research InstituteUL1TR001442 · NCATS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FIRESTEIN, GARY S, HOGARTH, MICHAEL · 2015 to 2024
$88.3MViral Vector Core (VVC)P30CA014195 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI Reuben Shaw · 1985 to 2026
$82.8MSan Diego Clinical and Translational Research InstituteUL1TR000100 · NCATS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FIRESTEIN, GARY S · 2012 to 2015
$19.7MREGULATORY GENOMIC STUDIES IN A COHORT OF IPS CELL DERIVED CARDIOMYOCYTESU01HL107442 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI EVANS, SYLVIA M, FRAZER, KELLY A · 2011 to 2016
$9.8MSan Diego Biomedical Informatics Education & Research (SABER)T15LM011271 · NLM · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SHAMIM NEMATI · 2012 to 2026
$9.7MTraining Program in Basic Clinical GeneticsT32GM008666 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI HAMILTON, BRUCE A · 1998 to 2021
$8.6MGRADUATE TRAINING PROGRAM IN BIONFORMATICST32GM008806 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BAFNA, VINEET, REN, BING · 2001 to 2020
$6.2MMolecular Basis of Hereditary Retinal DegenerationsR01EY021237 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AYYAGARI, RADHA · 2011 to 2020
$5.6MFunctional Analysis of T2D Associated Non-coding SNPsU01DK105541 · NIDDK · LUDWIG INSTITUTE FOR CANCER RES LTD · PI FRAZER, KELLY A, REN, BING · 2015 to 2019
$4.6MDevelopmental Regulatory Genomics of Human Cardiovascular LineagesUM1HL128773 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CHI, NEIL C, EVANS, SYLVIA M · 2015 to 2019
$3.8MFine-mapping and functional analysis of T1D-associated variantsDP3DK112155 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI FRAZER, KELLY A, SANDER, MAIKE · 2016 to 2016
$3.3MNCATS NIH HHS UL1 TR000100NCATS NIH HHS UL1 TR001442NCI NIH HHS P30 CA014195NCI NIH HHS P30 CA023100NEI NIH HHS R01 EY021237NHGRI NIH HHS R41 HG008118NHGRI NIH HHS R44 HG008118NHLBI NIH HHS U01 HL107442NHLBI NIH HHS UM1 HL128773NIDDK NIH HHS DP3 DK112155NIDDK NIH HHS U01 DK105541NIGMS NIH HHS T32 GM008666NIGMS NIH HHS T32 GM008806NLM NIH HHS T15 LM011271
Abstract
Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants) as determined using high-throughput RNA-sequencing and genotyping arrays, respectively. Using iPSCs from a family of individuals, we show that iPSC-derived cardiomyocytes demonstrate gene expression patterns that cluster by genetic background, and can be used to examine variants associated with physiological and disease phenotypes. The iPSCORE collection contains representative individuals for risk and non-risk alleles for 95% of SNPs associated with human phenotypes through genome-wide association studies. Our study demonstrates the utility of iPSCORE for examining how genetic variants influence molecular and physiological traits in iPSCs and derived cell lines.
Indexed as
Databases, FactualGenetic Association StudiesGenetic VariationArrhythmias, CardiacCell DifferentiationCell LineCellular ReprogrammingGenotypeHigh-Throughput Nucleotide SequencingHumansInduced Pluripotent Stem CellsMultigene FamilyMyocytes, CardiacOligonucleotide Array Sequence AnalysisPhenotypePolymorphism, Single Nucleotidecardiac diseaseGWASiPSCiPSC-derived cardiomyocytesiPSCOREKCNH2LQT2molecular traitsNHLBI Next Genphysiological traits
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