Mapping of causal variants through precision genome editing
Abstract/Contents
- Abstract
- Exposure to different environments can give rise to variation in traits and disease risks, even for individuals with the same genotype. This phenomenon is referred as Gene-by-Environment (GxE) interactions. The most well-known examples of GxE interactions are Sickle Cell Disease and Lactose Persistence, in each case the phenotypic differences arise when only exposed to certain pathogens or diet. However, there are only few cases where the causal genetic variants were identified, hindering our understanding of the underpinning molecular mechanisms. Hence, there is an urgent need to systematically uncover the causal variants contributing to GxE interactions, to better predicting disease risk and drug-treatment outcomes by accounting for both genetic and environmental factors. Traditional mapping methods for identifying causal variants for a given trait involve obtaining statistical evidence for linked regions of the genome that associated with the trait. However, the resolution of association mapping is often limited and often span many tightly linked genetic variants, making the detection of causal variants a grand challenge. To address gap in the mapping resolution, I first sought to establish a strategy for effectively surveying the effect of genetic variants across the genome. In chapter 2, a pooled, precision genome editing system, termed CRISPEY, was developed to allow direct measurement of individual variant effects through allele replacement. By parallel replacement of single-nucleotide variants between two Saccharomyces cerevisiae strains, hundreds of causal variants affecting growth fitness were mapped using CRISPEY. To systematically identify GxE interactions, CRISPEY-BAR, an improved version of the CRISPEY method, was used to mapped causal genetic variants in multiple environments. In chapter 3, CRISPEY-BAR directly mapped hundreds of causal variants at nucleotide resolution and showed that GxE interactions are pervasive among natural genetic variants with fitness effects. Importantly, the mapped causal variants informed potential molecular mechanisms for GxE interactions. To generalize the precision genome editing strategy for mapping causal variants, I pursued adoption of the CRISPEY strategy to human cells. In chapter 4, the CRISPEY approach showed precision genome editing activity in human cell lines. This promising result warrants further development of the approach for mapping causal variants in humans, as well as potential for therapeutic intervention of genetic diseases. In summary, this work provided a precision genome editing strategy that allow effective mapping of causal genetic variants, as well as insights into molecular features of GxE interactions.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2022; ©2022 |
| Publication date | 2022; 2022 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Chen, Shi-An Anderson |
|---|---|
| Degree supervisor | Fraser, Hunter B |
| Thesis advisor | Fraser, Hunter B |
| Thesis advisor | Bassik, Michael |
| Thesis advisor | Petrov, Dmitri Alex, 1969- |
| Thesis advisor | Qi, Lei, (Professor of Bioengineering) |
| Degree committee member | Bassik, Michael |
| Degree committee member | Petrov, Dmitri Alex, 1969- |
| Degree committee member | Qi, Lei, (Professor of Bioengineering) |
| Associated with | Stanford University, Department of Biology |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Shi-An A. Chen. |
|---|---|
| Note | Submitted to the Department of Biology. |
| Thesis | Thesis Ph.D. Stanford University 2022. |
| Location | https://purl.stanford.edu/qk004gc3139 |
Access conditions
- Copyright
- © 2022 by Shi-An Anderson Chen
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