title: A prevalence-based association test for case-control studies.
abstract: Genetic association is often determined in case-control studies by the differential distribution of alleles or genotypes. Recent work has demonstrated that association can also be assessed by deviations from the expected distributions of alleles or genotypes. Specifically, multiple methods motivated by the principles of Hardy-Weinberg equilibrium (HWE) have been developed. However, these methods do not take into account many of the assumptions of HWE. Therefore, we have developed a prevalence-based association test (PRAT) as an alternative method for detecting association in case-control studies. This method, also motivated by the principles of HWE, uses an estimated population allele frequency to generate expected genotype frequencies instead of using the case and control frequencies separately. Our method often has greater power, under a wide variety of genetic models, to detect association than genotypic, allelic or Cochran-Armitage trend association tests. Therefore, we propose PRAT as a powerful alternative method of testing for association.
authors.affiliation: Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee 37232, USA.
authors.forename: Kelli K
authors.initials: KK
authors.lastname: Ryckman
authors.forename: Lan
authors.initials: L
authors.lastname: Jiang
authors.forename: Chun
authors.initials: C
authors.lastname: Li
authors.forename: Jacquelaine
authors.initials: J
authors.lastname: Bartlett
authors.forename: Jonathan L
authors.initials: JL
authors.lastname: Haines
authors.forename: Scott M
authors.initials: SM
authors.lastname: Williams
mesh_terms: D000375:Aging; D000483:Alleles; D016022:Case-Control Studies; D003198:Computer Simulation; D005787:Gene Frequency; D005828:Genetics, Population; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D008268:Macular Degeneration / Q000235:genetics; D008957:Models, Genetic; D015233:Models, Statistical; D015995:Prevalence; D015203:Reproducibility of Results; D012107:Research Design