scholarly journals A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies

2009 ◽  
Vol 33 (3) ◽  
pp. 275-280 ◽  
Author(s):  
Chang Yu ◽  
Sanguo Zhang ◽  
Chuan Zhou ◽  
Saba Sile
Keyword(s):  
Likelihood Ratio ◽  
Likelihood Ratio Test ◽  
Case Control ◽  
Ratio Test ◽  
Case Control Studies ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

A Simple Loglinear Model for Haplotype Effects in a Case-Control Study Involving Two Unphased Genotypes

2005 ◽  
Vol 4 (1) ◽  
Author(s):  
Stuart G. Baker
Keyword(s):  
Interactive Effect ◽  
Case Control ◽  
Nuisance Parameters ◽  
Design Matrix ◽  
Case Control Studies ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium ◽  
Unphased Genotype ◽  
Unphased Genotype Data ◽  
Control Study

Because haplotypes may parsimoniously summarize the effect of genes on disease, there is great interest in using haplotypes in case-control studies of unphased genotype data. Previous methods for investigating haplotypes effects in case-control studies have not allowed for both of the following two scenarios that could have a large impact on results (i) departures from Hardy-Weinberg equilibrium in controls as well as cases, and (ii) an interactive effect of haplotypes and environmental covariates on the probability of disease. A new method is proposed that generalizes the model of Epstein and Satten to incorporate both (i) and (ii). Computations are relatively simple involving a single loglinear design matrix for parameters modeling the distribution of haplotype frequencies in controls, parameters modeling the effect of haplotypes and covariate-haplotype interactions on disease, and nuisance parameters required for correct inference. Based on simulations with realistic sample sizes, the method is recommended with data from two genotypes, a recessive or dominant model linking haplotypes to disease, and estimates of haplotype effects among haplotypes with a frequency greater than 10%. The methodology is most useful with candidate genotype pairs or for searching through pairs of genotypes when scenarios (i) and (ii) are likely. An example without a covariate illustrates the importance of modeling a departure from Hardy-Weinberg equilibrium in controls.

scholarly journals Likelihood Ratio Test for Detecting Gene (G)-Environment (E) Interactions Under an Additive Risk Model Exploiting G-E Independence for Case-Control Data

2012 ◽  
Vol 176 (11) ◽  
pp. 1060-1067 ◽  
Author(s):  
S. S. Han ◽  
P. S. Rosenberg ◽  
M. Garcia-Closas ◽  
J. D. Figueroa ◽  
D. Silverman ◽  
...  
Keyword(s):  
Likelihood Ratio ◽  
Likelihood Ratio Test ◽  
Risk Model ◽  
Case Control ◽  
Ratio Test ◽  
Control Data ◽  
Additive Risk Model ◽  
Additive Risk
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