The results in Table 2 show that improved IBD detection due to increased marker density has the potential to significantly expand the range of scenarios in which IBD mapping has more power than standard single-marker association testing.
We performed single marker association tests using all three ES measures on the WTCCC CAD GWAS data.
However, existing single-marker association tests are underpowered for detecting rare risk variants.
We develop family-based functional principal-component analysis (FPCA) with or without smoothing, a generalized T2, combined multivariate and collapsing (CMC) method, and single-marker association test statistics.
We conducted a single-marker association test and a gene-based analysis of rare variants.
For a random selection of 40 genic SSRs, single-marker association tests (240; 40 SSRs × 6 traits) were conducted using MLM.
For multi-marker association tests, haplotype analysis was only conducted when nominal association existed in the single-marker analyses and significance was corrected by 5,000 permutations using Haploview software.
In addition, as GWAS focus on single-marker association tests, the obtained results may not provide clear insights into which genes have significant association, how they interact with other genes and/or environment, and what is the underlying disease mechanism.
For the commercial Hy-Line, microsatellite marker associations were tested with a non-parametric Kruskal –Wallis test, because the genotyping data comprised a single generation and linkage analysis could not be applied.
For autosomal markers association was tested using a Cochrane Armitage test (SNPtest) assuming an additive model, using the top 4 principal components as covariates.
Among those, 334 SSR/STS and 623 DArT markers could be projected onto the consensus linkage map and were used for LD and marker-phenotype association tests (957 markers).
