# Comprehensive approaches for understanding the functional impact of genetic variation and genetic complexity

> **NIH NIH R01** · PACIFIC NORTHWEST RESEARCH INSTITUTE · 2020 · $179,518

## Abstract

Project Summary/ Abstract:
Our limited ability to relate genotype to phenotype is a major obstacle for biomedical research and
personalized medicine. Currently only ~2% of germline missense variants have clinical interpretations, and the
remainder, variants of uncertain significance (VUS), offer no information to inform diagnosis or guide treatment.
As the clinical use of whole exome and genome sequencing increases, the number of VUS will skyrocket.
Large-scale functional assays are the only methods for variant interpretation currently poised to match the
pace of variant discovery, and here we propose to extend their use to interpret genetic complexity. Our
approach leverages the advent of low-cost, large-scale gene synthesis and the development of high
throughput in vivo assays of protein function in model organisms, such as yeast. We propose a generalizable
approach for determining the functional consequences of polymorphisms in human disease genes, including
individual alleles, combinations of alleles in the same gene, and combinations of alleles in multiple genes in a
pathway, on a massively parallel scale. The quantitative nature of our assay and the structure of our
experimental design will allow us to compare the impact of allele combinations with their individual effects, and
thus detect genetic epistasis (nonlinear genetic interactions) arising from naturally occurring human genetic
variation outside the limits of outbred human populations. Through this novel approach, we will not only explore
the extent to which nonlinear interactions between human genes are pervasive or rare, but by placing them in
the context of protein and metabolic pathway structure, we will gain insight into their molecular underpinnings.
Our study will also provide an unprecedented amount of information about the contribution of individual amino
acids to the function of the three disease-relevant enzymes in our study, and we will analyze our results in the
context of their published crystal structures. Finally, we will develop new methods and assays that will expand
the throughput, combinatorics, and number of assays available for functional analysis of human variation.
We will pilot our approach using three human genes (OTC, ASS1, and ASL) associated with a class of
metabolic disorders known as urea cycle disorders (UCD). Neonatal UCD is associated with severe enzyme
deficiency. These infants rapidly develop high levels of ammonia, cerebral edema, and symptoms that can
include seizures, coma, and death. Less severe forms may remain undiagnosed into childhood or adulthood.
Late onset UCDs generally involve an environmental trigger (e.g. surgery, pregnancy, or chemical exposure) in
individuals with reduced enzyme function. Diagnosis of the adult onset form is hampered by the fact that it
often presents with symptoms such as episodic psychosis, bipolar disorder and major depression, and without
treatment, prognosis is poor. Thus, knowledge of the functional implicat...

## Key facts

- **NIH application ID:** 10135728
- **Project number:** 3R01GM134274-02S1
- **Recipient organization:** PACIFIC NORTHWEST RESEARCH INSTITUTE
- **Principal Investigator:** AIMEE M DUDLEY
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $179,518
- **Award type:** 3
- **Project period:** 2019-09-19 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10135728

## Citation

> US National Institutes of Health, RePORTER application 10135728, Comprehensive approaches for understanding the functional impact of genetic variation and genetic complexity (3R01GM134274-02S1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10135728. Licensed CC0.

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