# Development of scalable methods for rapid phenotyping and functional testing of variants

> **NIH NIH R24** · OKLAHOMA MEDICAL RESEARCH FOUNDATION · 2024 · $607,682

## Abstract

Project Summary
Advances in sequencing have greatly improved our capacity to discover the genetic causes of human diseases.
Many genome-wide association studies (GWAS) and exome sequencing projects have uncovered thousands of
candidate genes linked to human diseases. However, how these genes contribute to disease pathology is still
unclear. Researchers use zebrafish to validate these candidate genes and identify pathologically relevant genes
to understand the pathophysiology better. CRISPR/Cas9 technology has significantly impacted functional
studies in zebrafish, enabling the generation of loss-of-function alleles. Gene knockout generation is efficient,
but point mutations remain challenging to create in a high-throughput manner. Understanding disease
pathophysiology through knockout alleles is informative but hypomorphic, and gain-of-function alleles require
advanced methods like CRISPR base editors. These tools are underutilized due to limited targeting coverage
and low efficiency, but expanding their coverage would benefit the research community. In the first aim, we will
use a knockout library of 80 mutants to develop a high-throughput phenotyping pipeline. Then in the second aim,
we will optimize and expand the targeting coverage of CRISPR-based base editors that can induce single
nucleotide changes in the genome in a targeted manner. We will then use the candidate genes and phenotype
data from the Aim 1 to test these base editors on a larger number of loci. These aims will generate 80 disease
models and robust base editing tools tested on a diverse set of genes. Completing these aims will result in 80
disease models and improved base editing tools that will be accessible to the research community via the
Zebrafish International Resource Center (ZIRC).

## Key facts

- **NIH application ID:** 10782895
- **Project number:** 1R24OD034438-01A1
- **Recipient organization:** OKLAHOMA MEDICAL RESEARCH FOUNDATION
- **Principal Investigator:** Gaurav K Varshney
- **Activity code:** R24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $607,682
- **Award type:** 1
- **Project period:** 2024-07-15 → 2028-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10782895

## Citation

> US National Institutes of Health, RePORTER application 10782895, Development of scalable methods for rapid phenotyping and functional testing of variants (1R24OD034438-01A1). Retrieved via AI Analytics 2026-05-21 from https://api.ai-analytics.org/grant/nih/10782895. Licensed CC0.

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