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Department of Statistical and Actuarial Sciences
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2014 Science Dean Homecoming Celebration
2014 Science Dean Homecoming Celebration

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  • PhD Thesis Proposal Defence - Bin Luo (Monday, June 01, 2015)
    Time: 4:00pm-4:30pm and Room: Room 248
    Speaker: Bin Luo
    Title: Spatial statistical tools for genome-wide mutagenic mechanism studies under microarray probe sampling system

    DNA mutations are changes in genetic contents in a genome. A new signature of clustered mutations across the genome is the K-signature, “Kataegis” or thundershower. Rapid and cost-effective detection of mutation showers is relevant to understanding genetic heterogeneity that confounds cancer diagnosis, treatment and prognosis. Genotyping array provides a cost-effective way to detect mutations across a genome. The Mouse Diversity Genotyping Array (MDGA) used in this study is designed to detect single nucleotide polymorphisms (SNPs) at about 500,000 locations across the mouse genome. A statistical approach to detect clustered SNPs in the data from the MDGA is needed urgently.

    Based on the characteristics of probe design, several test statistics are developed characterizing the spatial properties of dispersion of SNP site mutations. Monte Carlo simulations are performed to obtain the null distributions of the test statistics. To evaluate the power performance, the alternate hypothesis is proposed as a Neyman-Scott process, which is a parent-child clustering mechanism. The performance of several established test statistics are evaluated by Monte Carlo simulation in the power study. Some test statistics show good performance under various parameter settings. They are recommended as proper tools to test for the existence of mutation clusters across the genome. The test statistics are applied to a biological sample for illustration of their utility especially when visual tools become inconclusive.

    Under the microarray probe sampling system, it is also proposed in this study to investigate the identification of SNP hotspots, and explore the spatial properties between SNPs and another type of structural mutation named copy ...

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