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Different reports Genetic genie vs livewello

Discussion in 'Genetic Testing and SNPs' started by uriraha, May 12, 2015.

  1. uriraha

    uriraha

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    israel
    Hello
    I ran my raw data in livewello and received different results for my VDR TAQ gene than i received in genetic genie.
    Livewello report didn't show any mutation in this gene. but genetic genie showed i am Homozygous for this gene VDR taq +/+.
    Now i am confused, i used to take methyl B12 for a few months now for my MTR/MTRR mutations. and i have COMT V158 +/- also.
    Should i replace the methyl B12 to the hydroxy B12 form now because i don't have VDR taq mutations?
    Which report do you think it's best to follow?
    Also i don't have mthfr issues but i tried taking methyl folate in the form of Quatrefolic brand (6S)-5-Methyltetrahydrofolate 400 mcg and felt better than when i took folinic which caused me anxiety and agitation. does anyone has any idea what can cause this?
    Please help :)
    Thanks
     

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  2. Valentijn

    Valentijn Senior Member

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    @uriraha - Genetic Genie reports the same way Yasko does. And Yasko is very frequently wrong. In this case, she's definitely wrong, so the +/+ for VDR Taq from Genetic Genie really should be -/-.
     
  3. uriraha

    uriraha

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    israel
    Thank you Valentijn
    If so does it mean i can't tolerate methyl B12 well and should take hydroxy B12 instead?
    cause i have comt V158 +/- also and i rade that you need less methyl groups in this situation.
     
  4. TheChosenOne

    TheChosenOne Senior Member

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    You may need less methyl groups is because you use less BH4 to make serotonin/dopamine in this case. You still need methyl groups is you have other mutations. The reason why you should take hydroxyB12 is because methylB12 can cause mood swings.
     
  5. whodathunkit

    whodathunkit Senior Member

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    Valentjin, does that mean that if I have VDR Taq -/- and VDR Bsm +/+ in Genetic Genie that I should reverse those? I'm reading the VDR thread but still am pretty confused about it. Don't quite understand if I have the "bad" snp or the "good" one or what it means or even if it really matters all that much. Except maybe it could help explain why I seem to feel better when I increase vitamin D beyond a couple thousand I.U's per day.
     
  6. TheChosenOne

    TheChosenOne Senior Member

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    Check your raw data.
    rs1544410 - VDR Bsm (Risk Allele: T)
    rs731236 - VDR Taq (Risk Allele: A)
    rs10735810 - VDR Fok (Risk Allele: T, 23andMe: A)

    Mine is right.
     
  7. whodathunkit

    whodathunkit Senior Member

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    I'm VDR Bsm +/+ (T,T). So I guess that means I'm homo for the "risk" allele.
    Thanks.

    But I guess what I really don't understand is what the risk is. Low vit D...?

    I'm still looking around and learning but my cognition really hasn't been great for the past few months. It's hard to admit but it's a fact. It's like my physical energy is improving while simultaneously I'm declining mentally in some ways. It's harder to "hold on" to stuff than it used to be, seems like even last year it was better. I make more typing and grammar mistakes. I'm hoping it's all part of the process of healing instead of one of those dang Alzheimer's snps manifesting. ;)
     
  8. Valentijn

    Valentijn Senior Member

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    Okay, basically VDR Taq and VDR Bsm are the same thing. When someone gets certain alleles for one, you know which alleles they get for the other. They're inherited together. So theoretically, (nearly) everyone with VDR Taq +/+ should have VDR Bsm +/+. But Yasko reports one backwards, either because she can't read research or because she wants every potential patient to have a result which supposedly needs treatment.

    Basically, the VDR Bsm listing on the Yasko or Genetic Genie report is correct. The VDR Taq listing there is incorrect and redundant and should be ignored. And at any rate, the impact upon gene function is be quite small, so even +/+ isn't anything to worry about.
     
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  9. Valentijn

    Valentijn Senior Member

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    No, it isn't.

    The riskier allele for VDR Taq is G. Yasko is wrong, and the sources which are repeating her without reading the research are also wrong.

    For more information, see the debates and studies discussed in these threads:
    http://forums.phoenixrising.me/index.php?threads/interesting-vdr-variations.24480/
    http://forums.phoenixrising.me/index.php?threads/the-great-vdr-taq-bsm-debate.24474/
     
    Last edited: Jun 19, 2015
    TheChosenOne and whodathunkit like this.
  10. Valentijn

    Valentijn Senior Member

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    VDR is a receptor which Vitamin D interacts with. VDR variations don't directly cause lower Vitamin D, but might impact how much Vitamin D is needed for it to be effective.

    In the context of methylation, VDR is discussed solely as something which uses methyl groups. Theoretically, the slower +/+ version could result in less tolerance for high doses of methylB12. But in reality, there seems to be little or no connection between VDR status and whether or not people have a poor reaction to methylB12.

    But VDR Bsm/Taq is such a mild variant that it's unlikely to do anything noticeable anyhow. I think they're pretty irrelevant in general.
     
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  11. whodathunkit

    whodathunkit Senior Member

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    That's certainly been my experience. Appreciate all the clarification, @Valentjin! :)
     
  12. TheChosenOne

    TheChosenOne Senior Member

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  13. knackers323

    knackers323 Senior Member

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    hi @Valentijn how is it that genes, methylation etc. are what Yasko specialises in, yet is able to be wrong so frequently? is this still a poorly understood field? thanks
     
  14. Valentijn

    Valentijn Senior Member

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    She isn't a doctor (MD), and her primary business is selling supplements. It's a pretty good incentive to be wrong, if it's profitable. Alternatively, she just might not be very bright.
     
  15. Oci

    Oci Senior Member

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    So what does this mean for me? According inch to Genetic Genie I have VDR++ and COMT++?

    Supposedly I have low dopamine with this combination.and this was the case on the Doctors Data OAT I had done?
     
  16. Valentijn

    Valentijn Senior Member

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    It doesn't mean much, if anything. Those are common and normal variations. The VDR SNPs have very little impact, and billions of people have COMT V158M +/+ with no issues arising from it.
     
  17. knackers323

    knackers323 Senior Member

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    @Valentijn yeah right I didn't realise she wasn't a Dr. you seem pretty knowledgeable on it all, would you mind giving me your opinion on my gene results?
     
  18. Valentijn

    Valentijn Senior Member

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    Most of the SNPs being looked at are on genes which aren't directly involved in methylation, and I think methylation is a bit of a dead-end itself.

    I looked at your +/+ methylation results, and they seem pretty irrelevant. Small or no effect sizes, high p-values, and/or poor failing to correct for the increased risk of false positives when making multiple comparisons.

    The other thing that makes those reports fairly useless is that they don't distinguish between SNPs with large impacts, and those with marginal impacts.
     
  19. Oci

    Oci Senior Member

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    So, how do we distinquish between SNPs with large impacts vs marginal impact?
    Thanks for the reassurance re Comt++ and VDR++. It does seem they are very common variants.
     
  20. Valentijn

    Valentijn Senior Member

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    Mostly based on research into their effects. But usually it will be rarer missense mutations which are having an effect, not common missense mutations or SNPs in introns. And for those missense mutations, something like the BLOSUM62 matrix can roughly predict if the change will have an impact, as can more complex modeling software.
     

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