Genomics Commons^™

Investigating The Ecology And Evolution Of Normal Breast Tissues And Breast Cancer With Single Cell Genomics, Tapsi Kumar, Tapsi Kumar

Dissertations & Theses (Open Access)

There is vast cellular heterogeneity in human breast tissues, with different transcriptional programs in the stromal, epithelial, and immune components, however, it remains unclear how their reprogramming and interplay leads to the progression of invasive phenotypes such as Triple- Negative Breast cancer (TNBC). To do define the microenvironmental alterations that occur during cancer, we first established a human breast cell atlas, a reference of normal breast cell types from disease free women. We profiled 535,941 cells from 62 women and 124,024 nuclei from 20 women revealing 11 major cell types and 52 cell states that reflect different biological functions that …

Computational Approaches To Understand Chemoresistance & Tumor Evolution Using Longitudinal Clinical Data And Lineage Tracing, Sahil Seth

Dissertations & Theses (Open Access)

Tumors are highly heterogeneous and dynamic, continually adapting and evolving in response to their microenvironment as well as external perturbations. Multi-region (spatial) and single cell sequencing has enabled us to anatomize the heterogeneity further and provide evidence of its association with chemo and drug resistance. To investigate this further we took two different approaches to understand the chemo-resistance, and functional heterogeneity in Triple negative breast cancer (TNBC) and Pancreatic ductal carcinoma in situ (PDAC) from an evolutionary perspective.

The first approach was to leverage tumor profiling from an ongoing randomized clinical trial in triple-negative breast cancer (ARTEMIS) to assess mechanisms …

Economic Evaluation Of Potential Applications Of Gene Expression Profiling In Clinical Oncology, Malek Hannouf

Electronic Thesis and Dissertation Repository

Histopathological analysis of tumor is currently the main tool used to guide cancer management. Gene expression profiling may provide additional valuable information for both classification and prognostication of individual tumors. A number of gene expression profiling assays have been developed recently to inform therapy decisions in women with early stage breast cancer and help identify the primary tumor site in patients with metastatic cancer of unknown primary. The impact of these assays on health and economic outcomes, if introduced into general practice, has not been determined. I aimed to conduct an economic evaluation of regulatory-approved gene expression profiling assays for …