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Published on Jun 5, 2013
Population structure and inbreeding can confound results from a standard genome-wide association test. Accounting for the random effect of relatedness can lead to lower false discovery rates and identify the causative markers without over-correcting and dampening the true signal.
This presentation will review four different methods of analyzing genotype data while accounting for random effects of relatedness. Methods include PCA analysis with Linear Regression, GBLUP, EMMAX, and MLMM. Comparisons will be made using data from the Sheep HapMap project and a simulated phenotype. After presenting the various methods, we will discuss how these results can be obtained using Golden Helix SNP & Variation Suite (SVS) software and how SVS can be used to compare and contrast the results.