The mean of absolute differences (A) between the estimated and true QTL position of each method was considered for six different scenarios consisting of combinations of a number of markers and the most frequent haplotypes.
H1 (31%) and H3 (11%) were the most frequent haplotypes observed (Figure 1).
The most frequent haplotypes observed in patients and controls were haplotype ACAT (40.2%, 53.2%) and CAGC (31.2%, 29.2%).
H1 and H3 were the most frequent haplotypes observed in the study population and they share a cluster of mutations (Figure 1).
MM associated SNP rs17793678 is located in intron 1 and was selected as the tag for one of the five most frequent haplotypes formed at the promoter LD block in this gene (19 kb).
However, these guidelines might not be appropriate in this case, since they are based on a neutral model, in which the most frequent haplotypes are the oldest and thus more likely to give rise to tip haplotypes.
Moving now to the haplotypes containing the DXS2251 allele (Fig.2C) we observe that the most frequent haplotypes belong to a cluster composed of 1,25,18,14,11 and 1,25,17,14,10 (arrows) and a few others.
The haplotypes may represent the ARQ and ARR haplotypes, which are the most frequent haplotypes in UK Scottish Blackface sheep, and which were shown to be linked to lamb mortality in the study of Sawalha et al. [10].
Two most frequent haplotypes of VDR, FbaT and FBAT and a relatively less frequent haplotype in patients fbaT do not show any significant difference between patients and controls when studied by themselves.
