VDR Genetics Part 3: Fok

If you recall from the previous post, we were looking at the VDR SNPs Bsm and Fok that are used to predict the potential response to treatment with GcMAF. Two labs (Yasko's lab & Red labs) test for these SNPs, and they are both producing directly opposite results.

The previous post looked at the evidence to show which lab was producing the correct answer for the Bsm SNP. This post will look at the Fok SNP for the two labs.

The Fok SNP is a lot easier to deal with than Bsm.

For example this table here shows the distribution of Fok genotypes across various populations:

http://www.bioline.org.br/showimage?hg/photo/hg03011t2.jpg

As can be seen the wildtype -/- genotype, FF, is much more common across all populations than the double mutation +/+, ff, genotype (between 2 and 10 times more common).

Also this study mentioned in a previous post which looked at white non-Hispanic Americans shows that FF is over 3 times more common than ff:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938035/table/T3/

In particular the frequency of FF is 40.9% and that of ff is 12.0% for healthy controls (N=805).

According to Yasko's testing the FF genotype has a frequency of 38.3% and the ff genotype a frequency of 12.8% amongst ME/CFS patients (N=47). As can be seen these are very similar to the VDR Fok frequencies published in the literature.

Again, the above argument suffers from a potential flaw. It is possible that the most common allele in ME/CFS differs from controls for the VDR Fok SNP, and that therefore Yasko's reporting for this SNP is wrong.

To counter this argument we look at call letters.

Yasko's call letters for the Fok SNP are +T/-C as can be verified from the example test here:

http://i1186.photobucket.com/albums/z380/John_Garcia/genetics.jpg


The call letters for Fok reported in the literature are also +T/-C:

http://jid.oxfordjournals.org/content/197/3/405/F4.large.jpg

We can therefore conclude that as far as the Fok SNP is concerned Yasko's results seem to be accurate, and Red labs results seem to be in doubt.

Conclusion: Given all available evidence, right now I would trust Yasko's results for the Fok SNP, and redlabs results for the Bsm SNP.