Cancer gene fusion discovery through integrative genomic analysis

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Recurrent gene fusions and chromosomal translocations have long been recognized for their roles in oncogenesis. This dissertation employs genomic approaches to discover and characterize novel gene fusions in several cancer types. First we developed a "breakpoint analysis" pipeline for gene fusion discovery and applied this method to a collection of nearly 1,000 human cancer samples profiled on DNA microarrays. This approach led to the discovery and characterization of twelve new gene fusions in diverse cancer types including angiosarcoma, pancreatic cancer, and colon cancer. Separately, we performed RNA Sequencing on a series of 36 breast cancer specimens and used a suite of computational tools developed in-house to discover ~350 candidate gene rearrangements. Notably, we discovered recurrent fusions of the sterile 20 (STE20)-like kinase TAOK1, and functional studies suggest that these fusions encode potent oncoproteins that drive breast carcinogenesis. Many of the alterations discovered in this dissertation represent the first gene fusions reported to date in the corresponding cancer type, and many represent potentially druggable targets with therapeutic implications for patients.


Type of resource text
Form electronic; electronic resource; remote
Extent 1 online resource.
Publication date 2013
Issuance monographic
Language English


Associated with Giacomini, Craig Patrick
Associated with Stanford University, Cancer Biology Program.
Primary advisor Pollack, Jonathan D
Thesis advisor Pollack, Jonathan D
Thesis advisor Kuo, Calvin Jay
Thesis advisor Lipsick, Joseph Steven, 1955-
Thesis advisor West, Robert
Advisor Kuo, Calvin Jay
Advisor Lipsick, Joseph Steven, 1955-
Advisor West, Robert


Genre Theses

Bibliographic information

Statement of responsibility Craig Patrick Giacomini.
Note Submitted to the Interdisciplinary Cancer Biology Program.
Thesis Thesis (Ph.D.)--Stanford University, 2013.
Location electronic resource

Access conditions

© 2013 by Craig Patrick Giacomini
This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).

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