Cited by 483Genetic Associations and EpidemiologyGenomics and Chromatin DynamicsGenetic Mapping and Diversity in Plants and Animals

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Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

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Tewhey, Ryan, Kotliar, Dylan, Park, Daniel S., Liu, Brandon, Winnicki, Sarah, Reilly, Steven K., Andersen, Kristian G., Mikkelsen, Tarjei S., Lander, Eric S., Schaffner, Stephen F., Sabeti, Pardis C.·2016·Cell

DOI 10.1016/j.cell.2016.04.027PMC PMC4957403

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Abstract

Although studies have identified hundreds of loci associated with human traits and diseases, pinpointing causal alleles remains difficult, particularly for non-coding variants. To address this challenge, we adapted the massively parallel reporter assay (MPRA) to identify variants that directly modulate gene expression. We applied it to 32,373 variants from 3,642 cis-expression quantitative trait loci and control regions. Detection by MPRA was strongly correlated with measures of regulatory function. We demonstrate MPRA's capabilities for pinpointing causal alleles, using it to identify 842 variants showing differential expression between alleles, including 53 well-annotated variants associated with diseases and traits. We investigated one in detail, a risk allele for ankylosing spondylitis, and provide direct evidence of a non-coding variant that alters expression of the prostaglandin EP4 receptor. These results create a resource of concrete leads and illustrate the promise of this approach for comprehensively interrogating how non-coding polymorphism shapes human biology.

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Identifying non-coding variant effects at scale via machine learning models of cis-regulatory reporter assays
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VarNexus: an integrative database for interpreting disease-associated regulatory variants through multimodal predictions and functional evidence
Gong, L., Tan, C., Zhang, J., Shu, R., Guo, S., Xiao, T., Shi, J., Wang, J., Ni, T., & Ding, R. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag1056

Authors: Tewhey, R., Kotliar, D., Park, D. S., Liu, B., Winnicki, S., Reilly, S. K., Andersen, K. G., Mikkelsen, T. S., Lander, E. S., Schaffner, S. F., & Sabeti, P. C.
Affiliations: Broad Institute (US)
Corresponding author: Tewhey, Ryan
Sabeti, Pardis C.
ORCID: Tewhey, Ryan
Kotliar, Dylan
Park, Daniel S.
Reilly, Steven K.
Andersen, Kristian G.
Mikkelsen, Tarjei S.
Lander, Eric S.
Schaffner, Stephen F.
Sabeti, Pardis C.
Venue: Cell
Publisher: Elsevier BV
Published: 2016-06
Volume: 165
Issue: 6
Pages: 1519-1529
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2016.04.027
PMC: PMC4957403
OpenAlex: W2412481123
Cited by: 480
References: 37
Citations by year: 2026: 39 · 2025: 50 · 2024: 66 · 2023: 39 · 2022: 42 · 2021: 46 · 2020: 53 · 2019: 51 · 2018: 39 · 2017: 42 · 2016: 13
FWCI: 39.05
Type: journal article
Language: en
Update notices: erratum (2018-02-22)
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 366 d)
Locations: Cell (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-nd)
Funders: Howard Hughes Medical Institute
National Institutes of Health (1dp2od006514-01)
National Human Genome Research Institute (F32HG009226, K99HG008179, R01HG006785)
National Institute of General Medical Sciences (T32GM007753)
National Institute of Allergy and Infectious Diseases (U19AI110818, R01AI114855)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords: massively parallel reporter assay, cis-eQTL, non-coding variants, gene expression regulation, regulatory function, ankylosing spondylitis, non-coding polymorphisms
MeSH terms: Alleles, Gene Expression Regulation, Genetic Techniques, Humans, Sensitivity and Specificity, Spondylitis, Ankylosing, Genetic Variation, Gene Library, Genes, Reporter, Genetic Diseases, Inborn, Quantitative Trait Loci, Hep G2 Cells

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Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

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