Contrary to G-BLUP, a multilocus association model uses the marker information directly by assigning different, possibly zero, effects to the marker genotypes.
G-BLUP uses the marker information in estimating realized relationships between the individuals, and then uses the marker-estimated genomic relationship matrix in a mixed model context (e.g., VanRaden 2008; Powell et al. 2010).
Using the marker genotype information from the HMDP and RNA expression data from hippocampus and striatum, we performed a genome-wide association test for each of the 25,697 probes (genes) on the microarray compared to each of the 101,629 SNP markers using the software package EMMA.
A number of authors have demonstrated that combining pedigree EBV from large national data sets and marker derived breeding values gave more accurate GEBV than just using the marker derived information alone [ 2- 4].
Criteria are needed to a) identify markers that have the promise to be clinically useful; b) assess the best methodology for clinical evaluation of the markers in question and c) confirm or validate that using the marker adds useful information compared to using standard prognostic factors alone.
triM will be able to use all the marker information in such large datasets and complete the analyses rapidly.
In independent validation, the prediction model developed using the marker and phenotype data in one population (C×H, training population) was used to predict the phenotypes in the other population using only the marker information (S×A, testing population).
