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APPLICATIONS OF THE HARDY-WEINBERG PRINCIPLE TO DETECTION OF LINKAGE DISEQUILIBRIUM AND GENOTYPING ERRORS IN THE CONTEXT OF ASSOCIATION STUDIES

Londono-Vasquez, Douglas
http://rave.ohiolink.edu/etdc/view?acc_num=case1181247657

Abstract Details

2007, Doctor of Philosophy, Case Western Reserve University, Epidemiology and Biostatistics.
The Hardy-Weinberg (HW) principle is a theorem about the independence of alleles at a single locus. Nevertheless, as it has been shown elsewhere (Feder et al. 1996; Jiang et al. 2001; Nielsen, Ehm, and Weir 1998), this principle can also be used to detect association between marker and disease-susceptibility alleles in samples collected based on a phenotype. Song and Elston (Song and Elston 2006) exploited this fact by introducing the WA statistic, a mapping tool that combines a test based on the difference in deviation from the HW proportions between cases and controls (termed the HW trend test, HWTT) with the Cochran-Armitage trend test of association (CATT) (Armitage 1955). In this dissertation, we present a modification and an extension of the WA statistic. First, we modify the WA statistic by showing that using population allele frequencies yields a more powerful HWTT and, consequently, a more powerful WA statistic. Second, we propose an extension of the WA statistic to a quantitative framework by introducing the concept of sliding window of a test of HW proportions. We show that even though under several scenarios the test shows good performance, the CATT is overall a better test and that the power of the WA statistic basically reduces to that of the CATT. The HW principle has also been suggested as a tool to perform genotype quality control (Bardoczy et al. 2004; Gomes et al. 1999; Gyorffy, Kocsis, and Vasarhelyi 2004b; Kocsis et al. 2004a; Nemeth et al. 2004). Here, in the context of case-control designs, we present a novel method for the detection of genotyping errors. This test measures the difference between the largest and second largest deviation from HW proportions in a set of markers. We evaluate the Type I error rate and power of this method and show that although it can detect 6% to 80% of the true error rate, in general, genotyping errors do not induce enough allelic correlation to be detected by a test of Hardy-Weinberg proportions.
Katrina Goddard (Advisor)
141 p.
Biology, Genetics; Statistics
Association; Case-control; WA-statistic; Genotyping Errors

Recommended Citations

Citations

  • Londono-Vasquez, D. (2007). APPLICATIONS OF THE HARDY-WEINBERG PRINCIPLE TO DETECTION OF LINKAGE DISEQUILIBRIUM AND GENOTYPING ERRORS IN THE CONTEXT OF ASSOCIATION STUDIES [Doctoral dissertation, Case Western Reserve University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=case1181247657

    APA Style (7th edition)

  • Londono-Vasquez, Douglas. APPLICATIONS OF THE HARDY-WEINBERG PRINCIPLE TO DETECTION OF LINKAGE DISEQUILIBRIUM AND GENOTYPING ERRORS IN THE CONTEXT OF ASSOCIATION STUDIES. 2007. Case Western Reserve University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=case1181247657.

    MLA Style (8th edition)

  • Londono-Vasquez, Douglas. "APPLICATIONS OF THE HARDY-WEINBERG PRINCIPLE TO DETECTION OF LINKAGE DISEQUILIBRIUM AND GENOTYPING ERRORS IN THE CONTEXT OF ASSOCIATION STUDIES." Doctoral dissertation, Case Western Reserve University, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=case1181247657

    Chicago Manual of Style (17th edition)

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© 2007, all rights reserved.
This open access ETD is published by Case Western Reserve University School of Graduate Studies and OhioLINK.