Cancer gene fusion discovery through integrative genomic analysis
- Craig Patrick Giacomini.
- May 2013.
- Physical description
- online resource (x, 143 pages) : illustrations (some color)
- Giacomini, Craig Patrick.
- Kuo, Calvin Jay. thesis advisor.
- Lipsick, Joseph Steven, 1955- thesis advisor.
- Pollack, Jonathan R. thesis advisor (primary).
- West, Robert (Pathologist). thesis advisor.
- Stanford University. Program in Cancer Biology.
- Stanford University. Committee on Graduate Studies. degree grantor.
- Includes bibliographical references.
- ["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."]
- Gene Fusion
- Genomics > methods
- Neoplasms > genetics
- Oncogene Proteins, Fusion > genetics
- Breast Neoplasms > genetics
- Gene Rearrangement
- Oligonucleotide Array Sequence Analysis > methods
- Publication date
- Submitted to the Interdisciplinary Cancer Biology Program and the Committee on Graduate Studies of Stanford University.
- Thesis (Ph.D.)--Stanford University, 2013.