Advancing Software Tools for Designing Oligonucleotide FISH Probes: Enabling Visualization of Repetitive DNA in Varied Genomes

Abstract

Genomes are organized in a specific and hierarchical manner that influences cell function and fate. The perturbation of genomic stability has been shown to mediate the rise of human diseases. While numerous tools have been developed to better understand the relationship of the non- repetitive genome toward preserving genomic stability, our understanding of the functional consequences of highly repetitive DNA is limited. During my thesis work, I have contributed to the development of software tools that may be used to support fluorescent in situ hybridization (FISH) assays to visualize highly repetitive DNA at the scale of diverse and fully assembled genome builds. The work I describe here includes the development of Tigerfish, a software tool to design oligonucleotides that target unique repetitive DNA intervals at the scale of genomes. Additionally, I also curated numerous scientific communications and advocacy resources to facilitate building more inclusive research spaces in genomics within and outside of the University of Washington. Through my work, I also created a curriculum that may be used to teach others in PhD programs about the importance of fostering supportive academic environments for those with diverse lived experiences beyond scientific learning spaces.