Evidence map›Paper›PMID 28017796›Full record

ArticleCell stem cell2017

Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity.

Ivan Carcamo-Orive, Gabriel E Hoffman, Paige Cundiff, Noam D Beckmann, Sunita L D'Souza, Joshua W Knowles, Achchhe Patel, Dimitri Papatsenko, Fahim Abbasi, Gerald M Reaven and 12 more

Erratum issuedAbstract read
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In one paragraph

Article in Cell stem cell, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 173 papers.

0numbers the graph read from it
0cells of the map it votes in
173citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

173 citing papers in PubMed.

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  18. Dynamic changes in mRNA isoform usage during human retinal development.bioRxiv : the preprint server for biology · 2025
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113 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

22 authors.

Ivan Carcamo-OriveDepartment of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
Gabriel E HoffmanDepartment of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Paige CundiffDepartment of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Noam D BeckmannDepartment of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Sunita L D'SouzaDepartment of Developmental and Regenerative Biology, Experimental Therapeutics Institute, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Joshua W KnowlesDepartment of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
Achchhe PatelDepartment of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Dimitri PapatsenkoDepartment of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Skolkovo Institute of Science and Technology, Nobel Street, Building 3, Moscow 143026, Russia.
Fahim AbbasiDepartment of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
Gerald M ReavenDepartment of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
Sean WhalenGladstone Institutes, University of California, San Francisco, San Francisco, CA 94148, USA.
Philip LeeDepartment of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
Mohammad ShahbaziDepartment of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
Marc Y R HenrionDepartment of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Kuixi ZhuDepartment of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Sven WangDepartment of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Panos RoussosDepartment of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY 10468, USA.
Eric E SchadtDepartment of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Gaurav PandeyDepartment of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Rui ChangDepartment of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: rui.r.chang@mssm.edu.
Thomas QuertermousDepartment of Medicine and Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: tomq1@stanford.edu.
Ihor LemischkaDepartment of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

Funding

Higher Order Chromatin and Genetic Risk for Alzheimer's DiseaseR01AG050986 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ROUSSOS, PANAGIOTIS · 2015 to 2025
$11.2M
Integrative translational discovery of vascular risk factors in aging and dementiaRF1AG051504 · NIA · MAYO CLINIC JACKSONVILLE · PI BU, GUOJUN, ERTEKIN-TANER, NILUFER · 2015 to 2019
$9.8M
Identifying the gene networks of insulin resistance: the GENESIPS studyU01HL107388 · NHLBI · STANFORD UNIVERSITY · PI QUERTERMOUS, THOMAS, SCHADT, ERIC E · 2011 to 2015
$8.8M
1/3-Networks from Multidimensional Data for Schizophrenia and Related DisordersR01MH097276 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI SCHADT, ERIC E, SKLAR, PAMELA · 2012 to 2014
$2.5M
Building Novel Predictive Networks for high-throughput, in-silico Key Driver Prioritization to Enhance Drug Target Discovery in AMP-AD and M2OVE-ADRF1AG057457 · NIA · UNIVERSITY OF ARIZONA · PI BRADSHAW, ELIZABETH M, CHANG, RUI · 2017 to 2019
$2.3M
Molecular Mechanisms of Insulin Resistance Associated LociR01DK107437 · NIDDK · STANFORD UNIVERSITY · PI QUERTERMOUS, THOMAS · 2016 to 2019
$2.2M
Transforming Genomics with 5 PB Big Omics Data Engine Cray CS300-AC SupercomputerS10OD018522 · OD · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI KOVATCH, PATRICIA · 2014 to 2014
$1.9M
Constructing gene-regulatory networks to reveal the metabolic basis of lifespan in yeastR01AG043076 · NIA · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI HARTMAN, JOHN L · 2012 to 2016
$1.9M
Identification of causal coronary heart disease variation in smooth muscle cellsR33HL120757 · NHLBI · STANFORD UNIVERSITY · PI QUERTERMOUS, THOMAS · 2016 to 2018
$1.6M
Boosting the Translational Impact of Scientific Competitions by Ensemble LearningR01GM114434 · NIGMS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI PANDEY, GAURAV · 2015 to 2017
$1.3M
NHLBI NIH HHS R33 HL120757NHLBI NIH HHS U01 HL107388NIA NIH HHS R01 AG043076NIA NIH HHS R01 AG050986NIA NIH HHS RF1 AG051504NIA NIH HHS RF1 AG057457NIDDK NIH HHS R01 DK107437NIGMS NIH HHS R01 GM114434NIH HHS S10 OD018522NIMH NIH HHS R01 MH097276
6 · The paper itself

Abstract

Variability in induced pluripotent stem cell (iPSC) lines remains a concern for disease modeling and regenerative medicine. We have used RNA-sequencing analysis and linear mixed models to examine the sources of gene expression variability in 317 human iPSC lines from 101 individuals. We found that ∼50% of genome-wide expression variability is explained by variation across individuals and identified a set of expression quantitative trait loci that contribute to this variation. These analyses coupled with allele-specific expression show that iPSCs retain a donor-specific gene expression pattern. Network, pathway, and key driver analyses showed that Polycomb targets contribute significantly to the non-genetic variability seen within and across individuals, highlighting this chromatin regulator as a likely source of reprogramming-based variability. Our findings therefore shed light on variation between iPSC lines and illustrate the potential for our dataset and other similar large-scale analyses to identify underlying drivers relevant to iPSC applications.

Indexed as

Genetic HeterogeneityTranscription, GeneticAllelesBayes TheoremCell DifferentiationCell LineGene Expression Regulation, DevelopmentalGene Regulatory NetworksGenetic Association StudiesHumansInduced Pluripotent Stem CellsPolycomb-Group ProteinsQuantitative Trait LociReproducibility of ResultsPolycomb-Group Proteinsallelic imbalancedifferentiation variabilityeQTLiPSC librarykey driversnetwork analysisPolycomb targetstranscriptional variabilityvariance partition

Identifiers

PMID28017796
PMCPMC5384872

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.