Wednesday, January 12, 2011

Genes Redux

After preliminary research yesterday, W. L. Karns and I suspect that the G allele is not a mutation in Bsm/Taq in the Vitamin D Receptor gene (VDR), and that, instead, A is the mutation. (See the Gene Chart and post from Monday.)  This adds more confusion to the already complex and perplexing genetic findings in ME/CFS.  Autism expert Dr. Amy Yasko has said that G is the mutation in Bsm/Taq (which she indicates with a + sign), but we suspect this is incorrect. We assumed Yasko was correct when we created the Gene Chart.

Once we're certain that A is the mutation, the chart will be changed to reflect what we suspect is correct: that G is the wild type and A is the mutation.

Assuming that G is the wild type and A is the mutation, those who respond best to the drug GcMAF are still those with GG.  GcMAF expert Dr. Nobuto Yamamoto appears to be calling those with the double G allele “bb.”

The G allele in snp RS 1544410, which is what Yasko and some others refer to as Bsm/Taq, is the ancestral allele.

We will check the VDR Fok mutation as well.


On another note, ME/CFS patient Gerwyn Morris had a letter published in which he critiqued the methodology of the recent Hohn PLoS ONE paper, "No Evidence for XMRV in German CFS and MS Patients with Fatigue Despite the Ability of the Virus to Infect Human Blood Cells In Vitro."


  1. I saw Gerwyn's post and have read other posts of his online, but I am unfamiliar with who this gentleman is. I did notice his comments created heated debate by one person on the PLoS forum, however. Wow, Gerwyn's analysis sure butted up against someone's views about XMRV science! I haven't read anything that sarcastic except on a ameteur science blog.

    Truth be told, as a patient I do not read heated debates steeped in sarcasim and insults about XMRV science that reveal subjective bias hidden behind a thin veil of scientific data. I turn to other forums that moderate that kind of thing. I do get science can be competative and debate messy, but when it denegrates into mud slinging, forget it. There are better places for information that are more balanced.

    Many thanks to Gerwyn for his balanced comments on PLoS. Too bad others cannot claim the same.

  2. Mindy in the Yasko-based spreadsheet you posted, in the Bsm/Taq column, 14.9% of CFS patients are -/- and 34% are +/+.

    Conversely for controls 19.6% are -/- and 43.2% are +/+.

    So based on these percentages I would have thought it is more likely that Yasko is correct (14.9 being closer to 19.6, and 34 being closer to 43.2).

    Be interested to know what you think.

  3. John, Yasko is saying that the smaller percentages are the wild type and the larger percentages are the mutations, but we suspect--but do not know for sure--that the larger percentages (both with patients and controls) are the wild type and the smaller percentages are the mutations.

    It's very confusing, and I'm determined to get to the bottom of it. The terminology is not consistent in the studies we looked at, which is why searching for the answers is so frustrating.

  4. Ok, thanks Amy. Here is my current thinking then:

    For BSM the standard terminology is reversed. So bb refers to -/- (wild-type) and BB refers to +/+ (mutation).

    [See Figure 2 from here for confirmation of the above:]

    Yasko is saying -/- less common than +/+
    Yakso is saying wild-type less common than mutation
    Yasko is saying bb less common than BB

    From the literature I have searched, bb is way more common than BB, so I think you may be right!

    For example:

    "In the patients with sarcoidosis, the BB, Bb, and bb genotypes accounted for 1.0%, 37.6%, and 61.4%, whereas in healthy control subjects the figures were 1.0%, 20.0%, and 79.0%, respectively."

    So in other words what Yasko calls -/- for BSM is in fact +/+ (and vice versa).

    From Yasko my results for BSM/Taq are +/+. So if you are correct I am really -/- (according to standard terminology), or bb. In other words I am a strong gc-maf responder for BSM (which is what redlabs belgium say I am too).

    Joey Tuan suspected this a while back when he noted most CFS patients were coming back as BB (low responders) from the Yasko test.

    Many thanks for investigating this issue. I hope this is good news for us!

  5. Oops Mindy, sorry called you Amy by mistake! Had Amy Yasko on my mind (blame the brain-fog) ...

    I'd be interested to know Mindy what you think of the Fok gene? Do you think Yasko is right about that one? I ask because again Yasko and Red-labs are telling people opposite things about their VDR-Fok status.

    Many thanks!

  6. Forgive me for resurrecting an older blog post, but has this VDR Bsml issue ever been resolved? I used the spreadsheet together with 23andme results for my own benefit (thanks!) but I am stuck with the VDR thingy. Basically, I still don't know if my AA alleles are a good or bad thing. Any new ideas? Thanks!

    1. Some of these genetic SNPs are different in their percentages across the world and races.
      For example a vitD SNP might be advantageous in sunny Africa but not so in Norway.
      which gives some info
      and has a distribution map for the different countries
      by GcMAF Australia

    2. Also this NIH site which is abit more complicated but at the bottom shows how the frequency can vary in different countries

  7. does anyone have a complete list of rs# for all 30 Yasko genes ?


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