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In addition, it has become clear that a small number of regions associated with many traits harbor multiple independent association signals (a classic example of which is the Chr8q24 region centromeric to MYC, which is associated with many forms of cancer including PrCa).
In addition, a locus may show strongly associated variants that are weakly correlated, suggesting the presence of multiple independent association signals.
Moreover, our analysis on 5p13.1, an extensively reported region of association, shows evidence for the presence of multiple independent association signals in the region.
At present, there is no consensus on the appropriate threshold of significance for multiple, independent association signals (in terms of p values or Bayes' factors).
Multiple independent association signals within the IL2RA region confer risk to type 1 diabetes and are associated with sCD25 concentrations [ 38, 47, 48].
The two large and comprehensive SLE studies of the 6q23 region have yielded multiple independent association signals, including polymorphisms in the TNFAIP3 gene [ 6, 7].
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The forward selection approach was used when multiple independent associations were available in the conditional tests: to select the most associated SNP or SNP pair (i.e. with the lowest conditional P/ Pint), fit into the background and test the remaining, repeating until no more significant conditional associations were found.
There is now also clear evidence of multiple, independent associations with MS across the major histocompatibility complex (MHC), as is the case for other autoimmune diseases [15], [16].
Both regression models identified multiple independent associations, reflecting the complexity of this region.
Linkage disequilibrium (LD) among SNPs rs8110925, rs2307276, and rs11564620 was very low (r2 < 0.1) in the three populations studied (Additional file 5 Figure S1), suggesting multiple independent associations were observed.
Common genetic variation in this region should be further explored for independent evidence of association with prostate cancer; a precedent has already been set for multiple independent associations in close proximity from prostate cancer GWAS, including 8q24 (Gudmundsson et al. 2007a; Haiman et al. 2007; Yeager et al. 2007) and HNF1B (Sun et al. 2008).
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