Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics

Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human...

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Published in:Nature genetics Vol. 53; no. 3; pp. 313 - 321
Main Authors: Bonder, Marc Jan, Smail, Craig, Gloudemans, Michael J., Frésard, Laure, Jakubosky, David, D’Antonio, Matteo, Li, Xin, Ferraro, Nicole M., Carcamo-Orive, Ivan, Mirauta, Bogdan, Seaton, Daniel D., Cai, Na, Vakili, Dara, Horta, Danilo, Zhao, Chunli, Zastrow, Diane B., Bonner, Devon E., Wheeler, Matthew T., Kilpinen, Helena, Knowles, Joshua W., Smith, Erin N., Frazer, Kelly A., Montgomery, Stephen B., Stegle, Oliver
Format: Journal Article
Language:English
Published: New York Nature Publishing Group US 01.03.2021
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ISSN:1061-4036, 1546-1718, 1546-1718
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Abstract Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of new colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases. Integrative data analysis of 1,367 human iPSC lines maps common and rare regulatory variants that colocalize with loci associated with human traits and diseases.
AbstractList Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of new colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases.Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of new colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases.
Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of new colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases.
Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of novel colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases.
Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of new colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases. Integrative data analysis of 1,367 human iPSC lines maps common and rare regulatory variants that colocalize with loci associated with human traits and diseases.
Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental contexts. However, in their pluripotent state, the disease impact of genetic variants is less well known. Here, we integrate data from 1,367 human iPSC lines to comprehensively map common and rare regulatory variants in human pluripotent cells. Using this population-scale resource, we report hundreds of new colocalization events for human traits specific to iPSCs, and find increased power to identify rare regulatory variants compared with somatic tissues. Finally, we demonstrate how iPSCs enable the identification of causal genes for rare diseases. Integrative data analysis of 1,367 human iPSC lines maps common and rare regulatory variants that colocalize with loci associated with human traits and diseases.
Audience Academic
Author Jakubosky, David
Bonner, Devon E.
Mirauta, Bogdan
Smith, Erin N.
Gloudemans, Michael J.
Seaton, Daniel D.
Stegle, Oliver
Li, Xin
Ferraro, Nicole M.
Cai, Na
Wheeler, Matthew T.
Frésard, Laure
Zastrow, Diane B.
Bonder, Marc Jan
D’Antonio, Matteo
Carcamo-Orive, Ivan
Kilpinen, Helena
Montgomery, Stephen B.
Zhao, Chunli
Vakili, Dara
Horta, Danilo
Frazer, Kelly A.
Smail, Craig
Knowles, Joshua W.
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5 Genomic Medicine Center, Children’s Mercy Research Institute and Children’s Mercy Kansas City, Kansas City, MO 64108, USA
17 Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
9 Department of Pediatrics and Rady Children’s Hospital, University of California, San Diego, La Jolla, CA 92093, USA
11 Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
12 Wellcome Sanger Institute, Wellcome Trust Genome Campus, CB10 1SA Cambridge, UK
15 Faculty of Medicine, Imperial College London, London, UK
16 Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA 94305, USA
19 Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093 USA
20 Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
7 Biomedical Science
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/33664507$$D View this record in MEDLINE/PubMed
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Jan Bonder, Marc
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Copyright The Author(s), under exclusive licence to Springer Nature America, Inc. 2021
COPYRIGHT 2021 Nature Publishing Group
Copyright Nature Publishing Group Mar 2021
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Shared first authors, contributed equally to this work
Shared last authors, contributed equally to this work
The main analyses and data preparations were performed by M.J.B. and C.S.; D.J. and M.D. performed structural variant calling and analysis; N.M.F. performed GTEx v7 data processing; L.F. and X.L. performed rare variant annotation and interpretation; H.K. and D.V. annotated and validated the rare disease variants and genes for the HipSci rare disease samples; M.J.G. performed the colocalization analysis; M.J.B., D.S., B.M. and D.H. developed the eQTL software; C.Z. generated iPSC lines for UDN rare disease samples; N.C., I.C.-O., Y.P. assisted with data processing and analysis; M.J.B., C.S., M.J.G., S.B.M., O.S. wrote the manuscript; I.C.-O., N.C., N.M.F., K.A.F., L.F., M.J.G., D.J., M.T.W., D.B.Z., B.M. assisted in editing the manuscript; M.J.B., C.S., E.S., K.A.F., O.S., S.B.M. conceived and oversaw the study.
Author contributions
ORCID 0000-0002-6060-8902
0000-0001-5844-6433
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0000-0001-8045-6021
0000-0002-9924-9943
0000-0003-1922-7240
0000-0002-5200-3903
0000-0001-8251-0589
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Snippet Induced pluripotent stem cells (iPSCs) are an established cellular system to study the impact of genetic variants in derived cell types and developmental...
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proquest
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SourceType Open Access Repository
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StartPage 313
SubjectTerms 38/39
38/91
45/100
631/208/191/2018
631/208/200
631/532
Agriculture
Animal Genetics and Genomics
Bardet-Biedl Syndrome - genetics
Biomedical and Life Sciences
Biomedicine
Calcium Channels - genetics
Cancer Research
Cell Line
Cerebellar Ataxia - genetics
Disease
DNA Methylation
Gene Expression
Gene Function
Genetic aspects
Genetic diversity
Genetic regulation
Genetic research
Genetic variance
Genetic Variation
Genomes
Genotype & phenotype
Human Genetics
Humans
Induced Pluripotent Stem Cells - cytology
Induced Pluripotent Stem Cells - physiology
Pluripotency
Polymorphism, Single Nucleotide
Proteins - genetics
Quantitative Trait Loci
Rare diseases
Rare Diseases - genetics
Regulatory Sequences, Nucleic Acid
Sequence Analysis, RNA
Stem cells
Whole Genome Sequencing
Title Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics
URI https://link.springer.com/article/10.1038/s41588-021-00800-7
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