CChi: An efficient cloud epistasis test model in human genome wide association studies

2013 ◽  
Author(s):  
Zhihui Zhou ◽  
Guixia Liu ◽  
Lingtao Su ◽  
Lun Yan ◽  
Liang Han
Keyword(s):  
Human Genome ◽  
Association Studies ◽  
Genome Wide Association ◽  
Test Model ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals The mouse QTL map helps interpret human genome-wide association studies for HDL cholesterol

2011 ◽  
Vol 52 (6) ◽  
pp. 1139-1149 ◽  
Author(s):  
Magalie S. Leduc ◽  
Malcolm Lyons ◽  
Katayoon Darvishi ◽  
Kenneth Walsh ◽  
Susan Sheehan ◽  
...  
Keyword(s):  
Human Genome ◽  
Association Studies ◽  
Hdl Cholesterol ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Qtl Map

Detecting Epistasis by LASSO-Penalized-Model Search Algorithm in Human Genome-Wide Association Studies

2014 ◽  
Vol 989-994 ◽  
pp. 2426-2430
Author(s):  
Zhi Hui Zhou ◽  
Gui Xia Liu ◽  
Ling Tao Su ◽  
Liang Han ◽  
Lun Yan
Keyword(s):  
Human Genome ◽  
Search Algorithm ◽  
Association Studies ◽  
Simulated Data ◽  
Penalized Regression ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Model Search ◽  
Number Of Factors ◽  
Genome Wide

Extensive studies have shown that many complex diseases are influenced by interaction of certain genes, while due to the limitations and drawbacks of adopting logistic regression (LR) to detect epistasis in human Genome-Wide Association Studies (GWAS), we propose a new method named LASSO-penalized-model search algorithm (LPMA) by restricting it to a tuning constant and combining it with a penalization of the L1-norm of the complexity parameter, and it is implemented utilizing the idea of multi-step strategy. LASSO penalized regression particularly shows advantageous properties when the number of factors far exceeds the number of samples. We compare the performance of LPMA with its competitors. Through simulated data experiments, LPMA performs better regarding to the identification of epistasis and prediction accuracy.

scholarly journals Approximately independent linkage disequilibrium blocks in human populations

2015 ◽  
Author(s):  
Tomaz Berisa ◽  
Joseph K. Pickrell
Keyword(s):  
Linkage Disequilibrium ◽  
Human Genome ◽  
Association Studies ◽  
Automated Analysis ◽  
Genome Wide Association ◽  
Human Populations ◽  
Genome Wide Association Studies ◽  
Multiple Genome ◽  
Genome Wide

We present a method to identify approximately independent blocks of linkage disequilibrium (LD) in the human genome. These blocks enable automated analysis of multiple genome-wide association studies.

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