Biomedical Sciences ETDs

Publication Date

Summer 7-13-2021

Abstract

Virtually all fields of biology have benefited from the advancements in comparative genomics technologies, specifically in the study of evolution. In this dissertation I develop and use comparative genomic technologies to investigate the novel SARS-CoV-2 virus, assembly the first genome of the black lace domestic angelfish and identify germline genetic variants associated with altered breast cancer-specific survival. Our genome tiling array for the novel coronavirus presents a rapid and cost-effective method to sequence the entire viral genome and can be used to track the rapid evolution of viral variants in the population. The domestic angelfish is a member of the Pterophyllum genus but due to decades of selective breeding and the acquisition of mutations, this species is largely uncategorized. Utilizing multi-species comparative genomics were able to identify that the source species for the black lace domestic angelfish is the P. altum with potential introgression from the P. leopoldi as well. Additionally, we investigated the genes responsible for the striking and unique appearance of each angelfish species by performing subfamily clustering of these genes among cichlid species. Finally, we investigated the multiplicative effects of germline genetic variants and the use of adjuvant therapy on breast cancer-specific survival. Our case cohort study revealed that women who inherit one of seven germline genetic variants have an altered risk of breast cancer-specific mortality. Further, we identified three variants whose joint effects with either estrogen receptor status, endocrine therapy receipt, or use of chemotherapy result in altered survival. Taken together, the chapters presented in my dissertation illustrate the impacts of comparative genomics methods on a wide range of biological fields.

Keywords

comparative genomics, covid-19, breast cancer, pterophyllum spp., phylogenetics, bioinformatics

Document Type

Dissertation

Language

English

Degree Name

Biomedical Sciences

Level of Degree

Doctoral

Department Name

Biomedical Sciences Graduate Program

First Committee Member (Chair)

Dr. Jeremy Edwards

Second Committee Member

Dr. Mara Steinkamp

Third Committee Member

Dr. Deirdre Hill

Fourth Committee Member

Dr. Jessica Weber

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