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The second PCA was expected to show the general population relationships with less functional effects, while the first one was supposed to be affected by the functional variant.
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It is therefore likely that a different SNP tagged by these variants is the functional variant, and this is further supported by the haplotypic association we identified for SNPs surrounding rs3822086, which persists even when this SNP is excluded.
Note that by applying this parameter, the functional variant known to increase dependence on dietary choline is the minor allele for all 3 CD SNPs in all cohorts.
Additionally, the population-based design of GWAS will produce low OR estimates if disease in only a small portion of the sampled population is mediated by this locus, even if the functional variant were genotyped.
This process of defining the functional variant will by itself de-emphasize the broad framework of race/ethnicity.
To identify the functional variant tagged by the associated single-nucleotide polymorphism (SNP), we performed comprehensive genetic mapping of the region to identify the most plausible causal SNP for spontaneous HCV clearance.
The precise identity and mode of action of the functional variant tagged by rs6465657 is at present unknown, but It is reasonably easy to postulate that the 'C' allele at rs6465657 could be marking a loss-of-function variant with effects on LMTK2 half-life or function.
The functional variant was associated by GWAS with multiple sclerosis, but not with other autoimmune diseases, and mechanistically it was found to result in a novel soluble form of TNFR1 that can block TNF.
The results from our study are very promising and we expect our strategy will help validate the functional variants identified by the GWAS and Cancer Genome Projects.
Moreover, as with all studies of this nature, the presence of linkage disequilibrium prevents us from conclusively identifying the functional variants nor the mechanisms by which they exert their effects.
However, identifying the functional variants is difficult.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com