Harnessing Cancer Omics to Inform Precision Oncology

<p>The development of high-throughput technologies greatly facilities precision oncology in the era of big data. With the growing size of pan-cancer genomic, transcriptomic and proteomic profiling data, there is imperative need for integrative analysis of molecular and clinical information in an efficient way. Here, we conducted omics analysis on three different cancer studies and developed an LLM-based bioinformatics chatbot, DrBioRight, that can perform cancer omics data mining based on natural language. We identified ultraconserved elements (UCE) that can be enhancers of tumor suppressor and silencers of oncogene in colon cancer via whole genome and targeted UCE sequencing from two cohorts. We characterized the tumor microenvironment of melanoma brain metastasis (MBM) during anti-PD1 therapy using single cell RNA sequencing (scRNA-seq) of patients’ cerebrospinal fluid (CSF) samples. We profiled functional proteomics from kidney tumor samples using reverse phase protein array (RPPA) and formulated an MTOR score that improves prognosis prediction of recurrent risk given Leibovich risk scoring. Finally, we selected high quality user queries to finetune the LLM modules of DrBioRight, evaluated its responses and improved its performances. Our results not only provide unique resources to the cancer research community, but also an online bioinformatics chatbot which helps users get access and conduct integrative analysis on cancer omics data efficiently.</p>

Name thesis:degree_name

Doctor of Philosophy (PhD)

Level thesis:degree_level

Dissertation (PhD)

Year dc:date.available

2025

Authors dc:creator

• Tang, Yitao
• <p>0000-0002-5340-1890</p>

Contributors dc:contributor

• Han Liang
• Traver Hart
• Li Ma

• RPPA
• genomics
• scRNA-seq
• cancer
• LLM
• Computational Biology

Repository record dc:identifier

https://digitalcommons.library.tmc.edu/utgsbs_dissertations/1490

OAI identifier oai:identifier

oai:digitalcommons.library.tmc.edu:utgsbs_dissertations-2547