Author ORCID Identifier


Date of Graduation


Document Type

Dissertation (PhD)

Program Affiliation

Biostatistics, Bioinformatics and Systems Biology

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Nicholas Navin

Committee Member

Bora Lim

Committee Member

Ken Chen

Committee Member

Peter Van Loo

Committee Member

Scott Kopetz


Aneuploidy is a prominent feature in Triple-Negative Breast Cancers (TNBC), however, the evolution of genotypes during tumor expansion remains poorly understood. The prevalent model of TNBC evolution is the Punctuated Copy Number Evolution (PCNE), in which tumors undergo a period of elevated genomic instability, acquiring complex genomic rearrangements within a short timeframe followed by clonal stasis. However, these observations rely on limited cell numbers and inherent experimental bias from first-generation single cell technologies. Therefore, the evolutionary trajectory after the punctuated burst remains unknown. To address this question, we sequenced 9,765 cells from 8 primary TNBCs and 6,413 cells from 4 TNBC cell lines using a novel single cell DNA sequencing method, Acoustic Cell Tagmentation. Our results show that TNBCs maintain a reservoir of subclonal diversity during expansion and go through a period of transient instability after the punctuated burst. We also demonstrate this diversity in TNBC cell lines that quickly re-diversify their genotypes. Lastly, the advances in single cell copy number methods require analytical tools that can scale up with cell throughput. To address this problem, we present CopyKit, an end-to-end tool for analyzing single cell copy number datasets. We show that CopyKit can resolve the clonal substructure of two metastatic liver samples. We also apply CopyKit to determine the metastatic lineages of a primary breast tumor with metastasis to the liver and pleural effusion and two matched colorectal carcinoma and its matched metastatic tumors.


single cell, copy number, tumor heterogeneity, copykit, triple negative breast cancer.



To view the content in your browser, please download Adobe Reader or, alternately,
you may Download the file to your hard drive.

NOTE: The latest versions of Adobe Reader do not support viewing PDF files within Firefox on Mac OS and if you are using a modern (Intel) Mac, there is no official plugin for viewing PDF files within the browser window.