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chen_wang_master_thesis_040819.pdf (2.87 MB)

ETD Abstract Container

Abstract Header

Novel software tool for microsatellite instability classification and landscape of microsatellite instability in osteosarcoma

Wang, Chen
http://orcid.org/0000-0002-2727-7240
http://rave.ohiolink.edu/etdc/view?acc_num=miami1554829925088174

Abstract Details

2019, Master of Science, Miami University, Cell, Molecular and Structural Biology (CMSB).
Microsatellite instability (MSI) is characterized by high degree of polymorphism in microsatellite lengths due to deficiency in mismatch repair (MMR) system. MSI is associated with several tumor types and its status can be considered as an important indicator for patient prognosis. In this work, we developed a software tool, MSIpred, to automatically infer tumor MSI status from tumor somatic mutation information by using machine learning technologies. Evaluations on MSIpred indicated that MSIpred is a robust pan-tumor MSI classification tool and can serve as a complementary diagnostic to MSI-PCR method in MSI diagnosis. We then explored the landscape of MSI events in osteosarcoma by analyzing whole exome sequencing data of a cohort of osteosarcoma patients using a series of bioinformatics and functional genomics tools. We identified microsatellite loci recurrently altered by MSI and performed functional analysis after gene-based annotation of these MSI events. Our results suggested that genes recurrently altered by MSI are related with important regulatory functions in cells. Besides, a weak association between patient MSI burden and amount of days to cancer relapse was observed, suggesting that MSI is a potential indicator for patient prognosis in osteosarcoma.
Chun Liang (Advisor)
Yoshinori Tomoyasu (Committee Chair)
Xin Wang (Committee Member)
47 p.
Bioinformatics; Biology

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Citations

  • Wang, C. (2019). Novel software tool for microsatellite instability classification and landscape of microsatellite instability in osteosarcoma [Master's thesis, Miami University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=miami1554829925088174

    APA Style (7th edition)

  • Wang, Chen. Novel software tool for microsatellite instability classification and landscape of microsatellite instability in osteosarcoma. 2019. Miami University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=miami1554829925088174.

    MLA Style (8th edition)

  • Wang, Chen. "Novel software tool for microsatellite instability classification and landscape of microsatellite instability in osteosarcoma." Master's thesis, Miami University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=miami1554829925088174

    Chicago Manual of Style (17th edition)

miami1554829925088174
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© 2019, all rights reserved.
This open access ETD is published by Miami University and OhioLINK.