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Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.
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.
Affiliation
  • Bonder MJ; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK. bondermj@gmail.com.
  • Smail C; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. bondermj@gmail.com.
  • Gloudemans MJ; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany. bondermj@gmail.com.
  • Frésard L; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA. csmail@stanford.edu.
  • Jakubosky D; Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA. csmail@stanford.edu.
  • D'Antonio M; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA.
  • Li X; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
  • Ferraro NM; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.
  • Carcamo-Orive I; Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA.
  • Mirauta B; Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, USA.
  • Seaton DD; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
  • Cai N; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA.
  • Vakili D; Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
  • Horta D; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.
  • Zhao C; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.
  • Zastrow DB; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.
  • Bonner DE; Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
  • Wheeler MT; Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA.
  • Kilpinen H; Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA.
  • Knowles JW; Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA.
Nat Genet ; 53(3): 313-321, 2021 03.
Article in En | MEDLINE | ID: mdl-33664507
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genetic Variation / Quantitative Trait Loci / Induced Pluripotent Stem Cells Type of study: Diagnostic_studies / Prognostic_studies Limits: Humans Language: En Journal: Nat Genet Journal subject: GENETICA MEDICA Year: 2021 Document type: Article Affiliation country: United kingdom
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genetic Variation / Quantitative Trait Loci / Induced Pluripotent Stem Cells Type of study: Diagnostic_studies / Prognostic_studies Limits: Humans Language: En Journal: Nat Genet Journal subject: GENETICA MEDICA Year: 2021 Document type: Article Affiliation country: United kingdom