# High-throughput identification of causal variants underlying neuropsychiatric disease-related GWAS hits

> **NIH NIH R01** · WASHINGTON UNIVERSITY · 2020 · $754,046

## Abstract

Project Summary
 Neuropsychiatric diseases affect millions of people world-wide. Genome-wide association studies
(GWAS) have identified a growing number of sequence variants associated with neuropsychiatric diseases and
related traits, but the majority of these GWAS hits fall within non-coding regions and their functional effects are
difficult to decipher. We hypothesize that the majority of functional non-coding variants related to
neuropsychiatric disease fall within brain cis-regulatory elements (CREs; i.e., enhancers/promoters), and exert
their effects by disrupting transcription factor (TF) binding sites and thereby altering the expression level of genes
encoding proteins expressed in the brain, particularly the cerebral cortex. To identify causal variants underlying
neuropsychiatric disease-related GWAS hits and to map neuropsychiatric disease-related CREs, we propose to
implement a technique called CRE-seq (Cis-Regulatory Element analysis by sequencing). In CRE-seq, individual
CREs are fused to reporter genes, each containing a unique DNA barcode. The resultant CRE-reporter library,
consisting of thousands of constructs, is introduced into living tissue, and reporter gene expression is quantified
by counting barcoded transcripts with RNA-seq. CRE-seq promises to greatly accelerate our ability to measure
the effects of cis-regulatory variants in neuropsychiatric disease. To achieve this goal, we propose two Specific
Aims. In Aim 1, we will use CRE-seq to identify causal cis-regulatory variants at all known GWAS loci associated
with neuropsychiatric diseases and related traits. We will measure the cis-regulatory activity of thousands of
wild-type and variant CREs in mouse cerebral cortex in vivo and in human iPSC-derived forebrain organoids via
adeno-associated virus (AAV)-mediated CRE-seq library delivery. We will then evaluate the functional effects of
selected variants on TF binding using protein-microarrays containing all known human TFs. Lastly, we will
correlate the results of our CRE-seq analyses with brain eQTL data. In Aim 2, we will establish a template for
interpreting rare neuropsychiatric disease-related variants by systematically mapping the location of human brain
CREs. We will utilize a 'capture and clone' strategy for CRE-seq library construction, which permits analysis of
long (i.e., ~500 bp) tiled reporters at each locus. In this way, we will pinpoint essential TF binding sites (TFBSs)
which are the likely targets of rare functional variants. Next, we will use CRE-seq to analyze the effects of
introducing all possible single-nucleotide substitutions into identified TFBSs. As in Aim 1, we will perform CRE-
seq in both mouse brain and human iPSC-derived cerebral organoids. Taken together, these two Aims will
enable functional interpretation of both common and rare variants in individual human genomes and thereby
facilitate assessment of neuropsychiatric disease risk in patients.

## Key facts

- **NIH application ID:** 9942610
- **Project number:** 1R01MH122451-01
- **Recipient organization:** WASHINGTON UNIVERSITY
- **Principal Investigator:** JOSEPH CORBO
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $754,046
- **Award type:** 1
- **Project period:** 2020-03-10 → 2025-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9942610

## Citation

> US National Institutes of Health, RePORTER application 9942610, High-throughput identification of causal variants underlying neuropsychiatric disease-related GWAS hits (1R01MH122451-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9942610. Licensed CC0.

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