The power and pitfalls of omics part 2: epigenomics, transcriptomics and ME/CFS
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Livewello and Pubmed saying different things?

Discussion in 'Genetic Testing and SNPs' started by Paralee, Jan 24, 2017.

  1. Paralee

    Paralee Senior Member

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    Livewello is showing rs492602 in gene FUT2 that B12 is low for the homozygous GG, but the pubmed 1876911 reference number is saying it's high? It seems like a secretor difference but I can't figure it out. In case someone wants to help? Thank you If so.

    Paralee
     
  2. alicec

    alicec Senior Member

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    Livewello doesn't do genetic research, it collates the research of others. It is quite possible that there are mistakes in some reports.

    Better to actually read the research when there appears to be a discrepancy and go with the research obviously.

    I'm not sure what pubmed reference you mean but here is the original study which correlated B12 levels with FUT2 status. Look at Table 1.

    You will see that there are three closely linked SNPs which all closely correlate with B12. The actual non-secretor status is determined by the premature termination of the FUT2 protein coded for by SNP rs602662. If you are +/+ for this it is highly likely you will be +/+ for the other two.

    The non-secretor phenotype correlates with slightly higher B12 levels. For rs492602, the relevant allele is GG.

    Note the difference in B12 is small.
     
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  3. sarah darwins

    sarah darwins I told you I was ill

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    This thread will interest you: http://forums.phoenixrising.me/index.php?threads/fut2-genetics.30929/
     
  4. Paralee

    Paralee Senior Member

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    @alicec and @sarah darwins , thank you. It looks like I have

    rs492602 (position 49206417) GG so that's a +/+ ?
    rs602662 (position 49206985) AA ++ ?
    rs601338 (position 49206674) AA +/+ ?

    So this means I'm a non-secretor with slightly higher B12 levels, but the effect is not worth much all in all?
    I have had IBS since late teens off and on and read other places my gut flora is probably not very good, but the dbSNP page is as far as I've been able to understand as far as to what the variant is (and using the position), which usually agrees with the MAF but not always.

    On a lighter note I've noticed in the gene diagrams there's p's and q's reminding me of the old saying "you need to watch your p's and q's". Probably showing my age as this was some time ago so I'm pretty sure it meant for proper English instead of genetic readings. :)
     
    Last edited: Jan 25, 2017
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  5. sarah darwins

    sarah darwins I told you I was ill

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    I have the same. I've been getting interested in this from the point of view of gut flora, not B12 (that does seem to be only a marginal effect, as pointed out above). There is some evidence to suggest that this 'non-secretor' status, which seems to involve things like H antigen in the gut, might be significant in making it more difficult for healthy bacteria, especially bifidos, to colonize the gut wall.

    I've had two gut flora profiles, the first showed zero bifidobacteria. Then after some pretty intensive gut treatment and a lengthy probiotic probiotic regimen, I had another profile done that showed only a tiny percentage of bifidos.

    I've seen suggestions that this non-secreting issue in the gut can be remediated with Beta 1,3 glucans and galactooligosaccharides. There's a product called BioImmune that contains both, I think, as well as a probiotic, but I didn't get on with that one. But I've been taking Beta 1,3 glucans alone for a couple of months, with a 1-week break each month, and I've had a major improvement in gut motility and regularity of bowel movements. It's definitely doing something and so far it's all been good. I regard it as a self-experiement still in progress, but I'm quietly quite excited about it. Since I started on it I've been much more tolerant of probiotics, some of which were triggering nasty reactions before. Feels like it might just be a missing part of the puzzle for me, but it's still early days. I'll report more somewhere on PR if the good effects continue.
     
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  6. Paralee

    Paralee Senior Member

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    @sarah darwins , please do let us/me/whoever would like to know. One thing I read that surprised me was I shouldn't take the acidopholus (sp?) but should take 3 different other kinds, I hope I can find where I wrote those names.
     
  7. alicec

    alicec Senior Member

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    Yes you are a non secretor. The B12 effect seems to be real but in itself is unlikely to be of great significance.

    There are other studies looking at the effect of secretor status on microbiota composition and correlation with IBD, as @sarah darwins has indicated.

    Here is fairly comprehensive analysis which is trying to explain mechanisms.

    They took samples (endoscopic lavage, so from the epithelial mucosa, not lumen as would be the case with faecal samples) from 12 -/-, 18 +/- and 9 +/+ individuals and analysed microbial composition as well as microbial and human metabolites.

    Their overall conclusion was

    Interestingly they saw metabolic differences in +/- as well as +/+ individuals.

    Essentially they are saying that the presence or absence of secreted H antigen in colonic mucous has a significant effect on microbiota composition (the antigen acts as a carbon source for some bacteria) which in turns affects energy metabolism in the microbiome of +/+ and +/- individuals. These changes are associated with sub-clinical local inflammation in the host mucosa.
     
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  8. sarah darwins

    sarah darwins I told you I was ill

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    Thanks, alicec, for providing an actual scientific counterpoint to my waffle! I can just about follow these papers but my attempts to summarise them are always about what you would expect from an arts grad ;-)
     
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  9. Paralee

    Paralee Senior Member

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    Thank you, @sarah darwins , I'll check those out. I've heard for so long "fix your gut" but have remained in the dark on how to do so.
     
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  10. Paralee

    Paralee Senior Member

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    Thank you, @alicec , crohn's disease is one of our family's "gifts". My mother had it really bad and my cousin's son has it, better controlled, though.
     
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  11. Paralee

    Paralee Senior Member

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    @sarah darwins , could you please tell me what you are taking? I have no idea on my own where to begin.
     
  12. sarah darwins

    sarah darwins I told you I was ill

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    What I said — Beta 1,3 glucans. Solgar do it, available from Amazon etc.

    But I'm not at the point of recommending it. Just letting anyone interested know that I'm experimenting with it and encouraged by the results so far.
     
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  13. Paralee

    Paralee Senior Member

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    I know, @sarah darwins , I just needed something to do a search on, and didn't realize that was the name, I thought it was maybe a category. Gives me a chance to at least check something out. Thanks again.
     
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