However, it is worth noting that this allele was found, in most cases, in linkage with DRB1*15, whereas in the controls, a larger proportion of DQB1*0602 was found in linkage with DRB1*11 alleles.
However, in most cases the linkage phase is unknown and has to be estimated jointly.
For Norway and Odense, Denmark, linkage was possible for most cases, as the linkage used personal identification (ID) numbers, while the linkage success was lower for the other registries.
Among them, the largest linkage group was found to belong to Chromosome 9. None of the chromosomes is fully covered by linkage groups, but in most cases a small number of linkage groups represent each chromosome (details in Tables 1 and 2).
In most cases these rely on linkage analysis using naturally-occuring genetic variants.
In addition, where there was overlap between QTLs and PASS regions, the majority of PASS regions were localized at or close to the peak of the QTL linkage, in most cases suggesting candidates for these QTLs and in some cases single genes.
Most interacting SNPs were found on different genes, and significant LD was therefore not likely due tight physical linkage in most cases, though our markers were not genetically mapped and we therefore do not know the physical proximity of the candidate genes.
The reason a failure in initiating recombination induces chromosome missegregation is because a subset of DSBs are repaired into crossovers, and, in most cases, it is the physical linkage (chiasmata) of the homologs by crossovers that ensures chromosomes segregate properly at the first meiotic division (Page and Hawley, 2003).
Cases and controls showed the same prevalence for the two variants, which were found in linkage disequilibrium in most cases and controls.
Moreover, QTL linkage designs have in most cases been based on a limited number of families from crosses between divergent populations [ 4], resulting in limited mapping accuracy and QTL results that are not directly transferable to commercial populations.
