|
The efficiency of single SNP and SNP-set analysisin genome-wide association studies |
|---|---|
| รหัสดีโอไอ | |
| Creator | 1. Sirikanlaya Sookkhee 2. Pianpool Kirdwichai 3. M. Fazil Baksh |
| Title | The efficiency of single SNP and SNP-set analysisin genome-wide association studies |
| Publisher | Research and Development Office, Prince of Songkla University |
| Publication Year | 2564 |
| Journal Title | Songklanakarin Journal of Science and Technology (SJST) |
| Journal Vol. | 43 |
| Journal No. | 1 |
| Page no. | 243-251 |
| Keyword | single SNP analysis, Sequence Kernel Association Test, Generalized Higher Criticism, permutation test |
| URL Website | https://rdo.psu.ac.th/sjstweb/index.php |
| ISSN | 0125-3395 |
| Abstract | The objective of this research is to compare and identify effective methods for the identification of gene loci associatedwith a disease outcome in the analysis of genome-wide data. We evaluate three methods, namely single SNP analysis, SequenceKernel Association Test (SKAT) and the recently proposed Generalized Higher Criticism (GHC). The simulated data used in thisresearch were constructed from a control data set in a study of Crohn's disease. True positive (TP) and false positive rate (FP) wereevaluated under different genetic models for disease with significant thresholds adjusted for multiple hypothesis testing based onthe permutation method. The findings are mixed with all three methods giving similar TP rates under some disease models anddifferent rates for other models. Overall, GHC is shown to be preferable in terms of error rates but it is disadvantageous in termsof computational efficiency. |
