Title |
Genome-wide association analyses of the 15th QTL-MAS workshop data using mixed model based single locus regression analysis
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Published in |
BMC Proceedings, May 2012
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DOI | 10.1186/1753-6561-6-s2-s5 |
Pubmed ID | |
Authors |
Wei-Xuan Fu, Chong-Long Wang, Xiang-Dong Ding, Zhe Zhang, Pei-Pei Ma, Zi-Qing Weng, Jian-Feng Liu, Qin Zhang |
Abstract |
The mixed model based single locus regression analysis (MMRA) method was used to analyse the common simulated dataset of the 15th QTL-MAS workshop to detect potential significant association between single nucleotide polymorphisms (SNPs) and the simulated trait. A Wald chi-squared statistic with df =1 was employed as test statistic and the permutation test was performed. For adjusting multiple testing, phenotypic observations were permutated 10,000 times against the genotype and pedigree data to obtain the threshold for declaring genome-wide significant SNPs. Linkage disequilibrium (LD) in term of D' between significant SNPs was quantified and LD blocks were defined to indicate quantitative trait loci (QTL) regions. |
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