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Research Article

Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue

  • Federico Innocenti equal contributor,

    equal contributor Contributed equally to this work with: Federico Innocenti, Gregory M. Cooper

    Affiliation: Cancer Research Center, Committee on Clinical Pharmacology and Pharmacogenomics, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America

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  • Gregory M. Cooper equal contributor,

    equal contributor Contributed equally to this work with: Federico Innocenti, Gregory M. Cooper

    Affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America

    Current address: Hudson Alpha Institute, Huntsville, Alabama, United States of America

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  • Ian B. Stanaway,

    Affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America

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  • Eric R. Gamazon,

    Affiliation: Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America

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  • Joshua D. Smith,

    Affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America

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  • Snezana Mirkov,

    Affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America

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  • Jacqueline Ramirez,

    Affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America

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  • Wanqing Liu,

    Affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America

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  • Yvonne S. Lin,

    Affiliations: Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington, United States of America, Department of Pharmaceutics, University of Washington, Seattle, Washington, United States of America

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  • Cliona Moloney,

    Affiliation: Merck Research Laboratories, Boston, Massachusetts, United States of America

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  • Shelly Force Aldred,

    Affiliation: SwitchGear Genomics, Menlo Park, California, United States of America

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  • Nathan D. Trinklein,

    Affiliation: SwitchGear Genomics, Menlo Park, California, United States of America

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  • Erin Schuetz,

    Affiliation: Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America

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  • Deborah A. Nickerson,

    Affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America

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  • Ken E. Thummel,

    Affiliations: Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington, United States of America, Department of Pharmaceutics, University of Washington, Seattle, Washington, United States of America

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  • Mark J. Rieder,

    Affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America

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  • Allan E. Rettie,

    Affiliation: Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington, United States of America

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  • Mark J. Ratain,

    Affiliation: Cancer Research Center, Committee on Clinical Pharmacology and Pharmacogenomics, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America

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  • Nancy J. Cox,

    Affiliation: Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America

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  • Christopher D. Brown mail

    caseybrown@uchicago.edu

    Affiliations: Institute for Genomics and Systems Biology, The University of Chicago and Argonne National Laboratory, Chicago, Illinois, United States of America, Departments of Human Genetics and Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America

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  • Published: May 26, 2011
  • DOI: 10.1371/journal.pgen.1002078

About the Authors

Federico Innocenti, Mark J. Ratain
Cancer Research Center, Committee on Clinical Pharmacology and Pharmacogenomics, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
Gregory M. Cooper, Ian B. Stanaway, Joshua D. Smith, Deborah A. Nickerson, Mark J. Rieder
Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
Eric R. Gamazon, Nancy J. Cox
Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
Snezana Mirkov, Jacqueline Ramirez, Wanqing Liu
Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
Yvonne S. Lin, Ken E. Thummel, Allan E. Rettie
Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington, United States of America
Yvonne S. Lin, Ken E. Thummel
Department of Pharmaceutics, University of Washington, Seattle, Washington, United States of America
Cliona Moloney
Merck Research Laboratories, Boston, Massachusetts, United States of America
Shelly Force Aldred, Nathan D. Trinklein
SwitchGear Genomics, Menlo Park, California, United States of America
Erin Schuetz
Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
Christopher D. Brown
Institute for Genomics and Systems Biology, The University of Chicago and Argonne National Laboratory, Chicago, Illinois, United States of America
Christopher D. Brown
Departments of Human Genetics and Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America

Corresponding Author

Email: caseybrown@uchicago.edu

Competing Interests

The authors ND Trinklein and SF Aldred are employees of and hold stock in SwitchGear Genomics. SwitchGear Genomics sells reporter vectors commercially and is the owner by assignment of patents or patent applications related to the reporter platform. The author C Moloney is an employee of Merck Research Labs.

Author Contributions

Conceived and designed the experiments: F Innocenti, GM Cooper, E Schuetz, DA Nickerson, KE Thummel, MJ Rieder, AE Rettie, MJ Ratain, NJ Cox, CD Brown. Wrote the paper: GM Cooper, CD Brown. Initiated and administered tissue collection, storage, and sample data collection: YS Lin, E Schuetz, KE Thummel. Provided assistance with Merck data: C Moloney. Provided molecular biology technical support: JD Smith, S Mirkov, J Ramirez, W Liu. Provided bioinformatic support: IB Stanaway, ER Gamazon. Performed genotype imputation and regression analyses: GM Cooper, IB Stanaway, CD Brown. Generated and analyzed gene expression and genotyping data: GM Cooper, IB Stanaway, JD Smith, MJ Rieder, CD Brown. Performed replication analyses: GM Cooper, CD Brown. Generated and analyzed probe, promoter, and UTR resequencing data: GM Cooper, JD Smith, DA Nickerson, MJ Rieder. Performed SGG cloning and reporter assays: SF Aldred, ND Trinklein. Incorporated data into SCAN database: ER Gamazon, NJ Cox. Edited the paper: F Innocenti, GM Cooper, IB Stanaway, ER Gamazon, JD Smith, S Mirkov, J Ramirez, W Liu, YS Lin, C Moloney, SF Aldred, ND Trinklein, E Schuetz, DA Nickerson, KE Thummel, MJ Rieder, AE Rettie, MJ Ratain, NJ Cox, CD Brown.