Author ORCID Identifier


Date of Graduation


Document Type

Dissertation (PhD)

Program Affiliation

Quantitative Sciences

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Traver Hart, Ph.D.

Committee Member

Hsiming (Sidney) Wang, Ph.D.

Committee Member

Guillermina Lozano, Ph.D.

Committee Member

Eduardo Vilar-Sanchez, M.D., Ph.D.

Committee Member

Jeffrey Chang, Ph.D.

Committee Member

John Paul Shen, M.D.


Discovering synthetic lethal interactions between genes holds the key to uncovering cancer vulnerabilities, enabling the development of more effective drugs for patients. However, identifying these vulnerabilities in the complex genome of human, which comprises thousands of genes, poses a significant challenge. One alternative approach to investigate these interactions involves exploring enriched sources of synthetic lethal interactions, such as paralog pairs. In recent years, a couple of studies have conducted dual-gene knockout experiments on paralog pairs using different approaches to identify synthetic lethal interactions. In this study, we conducted a meta-analysis of CRISPR genetic interaction screens. We identified a candidate set of synthetic lethals that are independent of background, and showed that the Cas12a platform exhibited enhanced sensitivity and consistency. Building on this knowledge, we developed a platform capable of expressing four independent enCas12a guide RNAs from a single promoter. Using this platform, we designed a whole-genome library that targets not only all protein coding genes but also targets ~5,000 paralog pairs, triples and quads. This library is 30% smaller than current whole-genome libraries and requires fivefold fewer reagents than other dual-gene knockout studies to assess genetic interactions between gene pairs. We screened this library in different cell lines and showed its high sensitivity and efficiency.


CRISPR, enCas12a, Paralog Pairs, Synthetic lethal interactions, Gene Editing, Whole-genome CRISPR library, Dual-gene knockout

Available for download on Saturday, March 22, 2025