The extent of linkage disequilibrium between selected SNPs (Table 1) lying in the 6p21 area is shown in Figures 2, and Figure S1 and Figure S2.
The extent of linkage disequilibrium between the polymorphisms has been calculated using the Arlequin program.
Although linkage disequilibrium is strong across the PTGS2 gene, differences in the degree and extent of linkage disequilibrium between populations may explain variation in risk estimates from one study to another.
Interpretations regarding the position of QTL which segregate across breeds must be treated with caution, as this will depend on the extent of linkage disequilibrium between breeds with causative mutations.
To measure the extent of linkage disequilibrium between any pairwise markers, we first inferred phase and reconstructed haplotypes using the PHASE software (http://www.stat.washington. edu/stephens/phase.html) developed by Stephens et al, 2001).
Even though the extent of linkage disequilibrium between HLA-A3 and HLA-DRB1*1501 is modest (D′ = 0.3, r = 0.14) the original study by Naito et al. (1972), which included 94 cases and 871 controls, had >50% power to identify association with A3 at the 5% level.
A further difference between CNV subtypes has been observed in the extent of linkage disequilibrium (LD) between a CNV and the surrounding single nucleotide polymorphisms (SNPs); stronger LD was found between SNPs and common deletions [15], [16] than with CNVs in duplication-rich regions [17].
In crossbred populations, effects of SNPs may be breed-specific because the extent of linkage disequilibrium (LD) between SNPs and quantitative trait loci (QTL) can differ between breeds.
The design and feasibility of whole-genome association studies are critically dependent on the extent of linkage disequilibrium (LD) betwhole-genome association
