scholarly journals Inference on Haplotype Effects in Case-Control Studies Using Unphased Genotype Data

2003 ◽  
Vol 73 (6) ◽  
pp. 1316-1329 ◽  
Author(s):  
Michael P. Epstein ◽  
Glen A. Satten
Keyword(s):  
Case Control ◽  
Genotype Data ◽  
Case Control Studies ◽  
Unphased Genotype ◽  
Unphased Genotype Data

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 Data supporting the high-accuracy haplotype imputation using unphased genotype data as the references

Data in Brief ◽  
2016 ◽  
Vol 8 ◽  
pp. 1412-1415 ◽  
Author(s):  
Wenzhi Li ◽  
Wei Xu ◽  
Shaohua He ◽  
Li Ma ◽  
Qing Song
Keyword(s):  
High Accuracy ◽  
Genotype Data ◽  
Unphased Genotype ◽  
Unphased Genotype Data

scholarly journals Search for Haplotype Interactions That Influence Susceptibility to Type 1 Diabetes, through Use of Unphased Genotype Data

2003 ◽  
Vol 73 (6) ◽  
pp. 1385-1401 ◽  
Author(s):  
Jian Zhang ◽  
Faming Liang ◽  
Willem R.M. Dassen ◽  
Pieter A. Doevendans ◽  
Mathisca de Gunst
Keyword(s):  
Type 1 Diabetes ◽  
Genotype Data ◽  
Unphased Genotype ◽  
Unphased Genotype Data

scholarly journals Using imputed genotype data in the joint score tests for genetic association and gene-environment interactions in case-control studies

2017 ◽  
Vol 42 (2) ◽  
pp. 146-155 ◽  
Author(s):  
Minsun Song ◽  
William Wheeler ◽  
Neil E. Caporaso ◽  
Maria Teresa Landi ◽  
Nilanjan Chatterjee
Keyword(s):  
Genetic Association ◽  
Case Control ◽  
Genotype Data ◽  
Case Control Studies ◽  
Score Tests ◽  
Gene Environment

Choosing Haplotype-Tagging SNPS Based on Unphased Genotype Data Using a Preliminary Sample of Unrelated Subjects with an Example from the Multiethnic Cohort Study

2003 ◽  
Vol 55 (1) ◽  
pp. 27-36 ◽  
Author(s):  
Daniel O. Stram ◽  
Christopher A. Haiman ◽  
Joel N. Hirschhorn ◽  
David Altshuler ◽  
Laurence N. Kolonel ◽  
...  
Keyword(s):  
Cohort Study ◽  
Genotype Data ◽  
Multiethnic Cohort ◽  
Unphased Genotype ◽  
Unphased Genotype Data

scholarly journals High-accuracy haplotype imputation using unphased genotype data as the references

Gene ◽  
2015 ◽  
Vol 572 (2) ◽  
pp. 279-284 ◽  
Author(s):  
Wenzhi Li ◽  
Wei Xu ◽  
Guoxing Fu ◽  
Li Ma ◽  
Jendai Richards ◽  
...  
Keyword(s):  
High Accuracy ◽  
Genotype Data ◽  
Unphased Genotype ◽  
Unphased Genotype Data
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