dorsal/arxiv
View SchemaGenotype-based Case-Control Analysis, Violation of Hardy-Weinberg Equilibrium, and Phase Diagrams
| Authors | Young Ju Suh, Wentian Li |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611092 |
| URL | https://arxiv.org/abs/q-bio/0611092 |
| Journal | Proceedings of the 5th Asia-Pacific Bioinformatics Conference, eds. David Shankoff, Lusheng Wang, Francis Chin, pp.185-194 (Imperial College Press, 2007) |
Abstract
We study in detail a particular statistical method in genetic case-control analysis, labeled "genotype-based association", in which the two test results from assuming dominant and recessive model are combined in one optimal output. This method differs both from the allele-based association which artificially doubles the sample size, and the direct chi-square test on 3-by-2 contingency table which may overestimate the degree of freedom. We conclude that the comparative advantage (or disadvantage) of the genotype-based test over the allele-based test mainly depends on two parameters, the allele frequency difference delta and the Hardy-Weinberg disequilibrium coefficient difference delta_epsilon. Six different situations, called "phases", characterized by the two X^2 test statistics in allele-based and genotype-based test, are well separated in the phase diagram parameterized by delta and delta_epsilon. For two major groups of phases, a single parameter theta = tan^-1 (delta/delta_epsilon) is able to achieves an almost perfect phase separation. We also applied the analytic result to several types of disease models. It is shown that for dominant and additive models, genotype-based tests are favored over allele-based tests.
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"abstract": "We study in detail a particular statistical method in genetic case-control\nanalysis, labeled \"genotype-based association\", in which the two test results\nfrom assuming dominant and recessive model are combined in one optimal output.\nThis method differs both from the allele-based association which artificially\ndoubles the sample size, and the direct chi-square test on 3-by-2 contingency\ntable which may overestimate the degree of freedom. We conclude that the\ncomparative advantage (or disadvantage) of the genotype-based test over the\nallele-based test mainly depends on two parameters, the allele frequency\ndifference delta and the Hardy-Weinberg disequilibrium coefficient difference\ndelta_epsilon. Six different situations, called \"phases\", characterized by the\ntwo X^2 test statistics in allele-based and genotype-based test, are well\nseparated in the phase diagram parameterized by delta and delta_epsilon. For\ntwo major groups of phases, a single parameter theta = tan^-1\n(delta/delta_epsilon) is able to achieves an almost perfect phase separation.\nWe also applied the analytic result to several types of disease models. It is\nshown that for dominant and additive models, genotype-based tests are favored\nover allele-based tests.",
"arxiv_id": "q-bio/0611092",
"authors": [
"Young Ju Suh",
"Wentian Li"
],
"categories": [
"q-bio.QM",
"q-bio.SC"
],
"journal_ref": "Proceedings of the 5th Asia-Pacific Bioinformatics Conference,\n eds. David Shankoff, Lusheng Wang, Francis Chin, pp.185-194 (Imperial College\n Press, 2007)",
"title": "Genotype-based Case-Control Analysis, Violation of Hardy-Weinberg Equilibrium, and Phase Diagrams",
"url": "https://arxiv.org/abs/q-bio/0611092"
},
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