Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay.
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.
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA. Electronic address: rtewhey@broadinstitute.org.
Ryan
R
Tewhey
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA.
Dylan
D
Kotliar
Broad Institute, Cambridge, MA 02142, USA.
Daniel S
DS
Park
Broad Institute, Cambridge, MA 02142, USA.
Brandon
B
Liu
Broad Institute, Cambridge, MA 02142, USA.
Sarah
S
Winnicki
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA.
Steven K
SK
Reilly
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA.
Kristian G
KG
Andersen
Broad Institute, Cambridge, MA 02142, USA.
Tarjei S
TS
Mikkelsen
Broad Institute, Cambridge, MA 02142, USA.
Eric S
ES
Lander
Broad Institute, Cambridge, MA 02142, USA.
Stephen F
SF
Schaffner
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA. Electronic address: pardis@broadinstitute.org.
Pardis C
PC
Sabeti
D000483:Alleles; D005786:Gene Expression Regulation; D015723:Gene Library; D017930:Genes, Reporter; D030342:Genetic Diseases, Inborn / Q000235:genetics*; D005821:Genetic Techniques; D014644:Genetic Variation; D056945:Hep G2 Cells; D006801:Humans; D040641:Quantitative Trait Loci; D012680:Sensitivity and Specificity; D013167:Spondylitis, Ankylosing / Q000235:genetics