Three of these SNPs are reportedly highly predictive of a favorable treatment response among HCV genotype 1 infected patients: rs12979860 [8], [8], rs12980275 [10], and rs8099917 [9], [10] [10], with a strong linkage disequilibrium noted between rs12979860 and rs8099917 [6].
Because of strong linkage disequilibrium noted between rs12979860 and rs12980275 (R2 = 0.86 assuming Hardy-Weinberg equilibrium, as compared to R2 = 0.42 for rs12979860 and rs8099917 as well as R2 = 0.41 for rs12980275 and rs8099917) and because rs8099917 was not significantly associated with SVR, only SNP variants for rs12979860 were included in the multivariate analyses.
By using nonparametric analysis, significant evidence for linkage was noted for chromosome 4 [ 83].
No significant linkage was noted for the SNPs genotyped on 19q.
Our data point to an appreciable linear component to variation in this 4-bar linkage system noted for its non-linear evolutionary dynamics [ 25, 26].
We treated RYHyb20 as two separate linkage groups, noted as RYHyb20(Omy20) and RYHyb20(Omy28), because Omy20 and Omy28 are not fused in RBT.
The high levels of synteny, collinearity and similar ranges of linkage distances noted between the spruce and pine genomes will provide opportunities to transfer genomic information between these genera, especially if such conservation is maintained at a finer scale.
With regard to the studies discussed above, which used linkage methods, it should be noted that linkage and association methods test for different things; while linkage methods find regions that may harbor genes involved in a disease, association methods test for the statistical correlation between genetic variants and a disease.
We noted linkage in fourteen regions of the genome for eleven factors; interestingly, only one single linkage signal was found for factors representing baseline platelet function.
When this particular family was analyzed individually, marginal linkage signals were noted at nine loci (Miller, unpublished data, 2014).
