Bayesian models for population-based case-control studies when the population is in Hardy-Weinberg equilibrium

2005 ◽  
Vol 28 (2) ◽  
pp. 183-192 ◽  
Author(s):  
K.F. Cheng ◽  
J.H. Chen
Keyword(s):  
Bayesian Models ◽  
Population Based ◽  
Case Control ◽  
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 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

scholarly journals Population-Based Estimates of the Age-Specific Cumulative Risk of Breast Cancer for Pathogenic Variants in CHEK2: Findings from the Australian Breast Cancer Family Registry

Cancers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1378
Author(s):  
Tú Nguyen-Dumont ◽  
James G. Dowty ◽  
Jason A. Steen ◽  
Anne-Laure Renault ◽  
Fleur Hammet ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cumulative Risk ◽  
Population Based ◽  
Case Control ◽  
Cancer Information ◽  
Case Control Studies ◽  
Breast Cancer Family ◽  
Pathogenic Variants ◽  
Increased Risk ◽  
Control Family

Case-control studies of breast cancer have consistently shown that pathogenic variants in CHEK2 are associated with about a 3-fold increased risk of breast cancer. Information about the recurrent protein-truncating variant CHEK2 c.1100delC dominates this estimate. There have been no formal estimates of age-specific cumulative risk of breast cancer for all CHEK2 pathogenic (including likely pathogenic) variants combined. We conducted a population-based case-control-family study of pathogenic CHEK2 variants (26 families, 1071 relatives) and estimated the age-specific cumulative risk of breast cancer using segregation analysis. The estimated hazard ratio for carriers of pathogenic CHEK2 variants (combined) was 4.9 (95% CI 2.5–9.5) relative to non-carriers. The HR for carriers of the CHEK2 c.1100delC variant was estimated to be 3.5 (95% CI 1.02–11.6) and the HR for carriers of all other CHEK2 variants combined was estimated to be 5.7 (95% CI 2.5–12.9). The age-specific cumulative risk of breast cancer was estimated to be 18% (95% CI 11–30%) and 33% (95% CI 21–48%) to age 60 and 80 years, respectively. These findings provide important information for the clinical management of breast cancer risk for women carrying pathogenic variants in CHEK2.

Significance of Hardy-Weinberg Equilibrium in Case Control

2004 ◽  
Vol 73 (1) ◽  
pp. 95-95
Author(s):  
Hemant Kumar Bid ◽  
Rama D. Mittal
Keyword(s):  
Case Control ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

scholarly journals Impact of the introduction of pneumococcal conjugate vaccination on pneumonia in The Gambia: population-based surveillance and case-control studies

2017 ◽  
Vol 17 (9) ◽  
pp. 965-973 ◽  
Author(s):  
Grant A Mackenzie ◽  
Philip C Hill ◽  
Shah M Sahito ◽  
David J Jeffries ◽  
Ilias Hossain ◽  
...  
Keyword(s):  
Population Based ◽  
Case Control ◽  
The Gambia ◽  
Case Control Studies ◽  
Conjugate Vaccination
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