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THE PROBABILITY OF SNPS ASSOCIATED WITH A DISEASE

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2015, Doctor of Philosophy, Case Western Reserve University, Epidemiology and Biostatistics.
Multiple inferences are widely used in genome-wide association studies, but there are problems existing in family wise error control (FWER). Benjamini & Hochberg (1995) introduced a new point of view to control errors, the false discover rate (FDR), which is the expected ratio of the number of false rejections to the total number of rejections. FDR is conservative when the unknown number of true null hypotheses is less than the total number of hypotheses. To solve this bias, many methods exist to estimate the number of true null hypotheses. In this dissertation, we develop a simple nonparametric empirical model to help select SNPs that are associated with a disease. This model is connected with the theory of the FDR. The distribution of null hypothesis p-values is estimated by the permutation p-values. The distribution of alternative hypothesis p-values is estimated by the distribution of the original p-values after subtracting the proportion of the null hypothesis p-values. Thus the model can produce a useful posterior probability of effect for each individual SNP with a minimum of prior assumptions. For the Wellcome Trust Case Control Consortium (WTCCC) Crohn’s disease dataset, the highest posterior probabilities are consistent with the most significant p-values. For the colon cancer data, the SNPs with the highest posterior probabilities are quite different from the SNPs with the most significant p-values.
Robert Elston (Advisor)
Sanford Markowitz (Committee Member)
Xiaofeng Zhu (Committee Member)
Nora Nock (Committee Member)
124 p.

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Citations

  • zhang, L. (2015). THE PROBABILITY OF SNPS ASSOCIATED WITH A DISEASE [Doctoral dissertation, Case Western Reserve University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=case1413540577

    APA Style (7th edition)

  • zhang, lu. THE PROBABILITY OF SNPS ASSOCIATED WITH A DISEASE. 2015. Case Western Reserve University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=case1413540577.

    MLA Style (8th edition)

  • zhang, lu. "THE PROBABILITY OF SNPS ASSOCIATED WITH A DISEASE." Doctoral dissertation, Case Western Reserve University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=case1413540577

    Chicago Manual of Style (17th edition)