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Extract SNPs from 23andme data to yasko/nutrigenomics notation

Discussion in 'Genetic Testing and SNPs' started by hixxy, Mar 26, 2012.

  1. adreno

    adreno 3% neanderthal

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    Tundras of Europa
    I'm a slow metabolizer. And please make the thread you mentioned; I'm interested :)
  2. Calico13

    Calico13

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    I started working on the new thread, offline for now until I get everything together. If you can think of any SNP's you want added, let me know! For now I'm focusing on things like liver pathways, APOE status and whatever else I think is interesting. I want to do more research and add collagen genes and anything related to the detoxification systems and the immune system.

    I have to say going through and looking at each gene, I have some weird genotypes. One that hasn't been seen in Caucasians, so I dunno what to think about that. It is on the CYP3A5 gene. Of course there's very little information on it...lol
  3. hixxy

    hixxy Woof woof

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    Russell Island, Australia
    The way we tend to look at these genes on this forum is as though they are static, making the assumption that all of them are expressed. I guess gene expression is the difference between all these other people with the well known MTHFR polymorphisms and no disease and those of us with disease.

    I guess you could say, whatever it was that caused these nasty genes to become expressed is the cause of our disease, while the genes themselves are our potential for disease.

    I'm a slow caffeine metaboliser. I've never been able to tolerate much caffeine.

    New thread sounds interesting. Be sure to post back here when you create it, so I don't overlook it.
  4. adreno

    adreno 3% neanderthal

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    I guess you're right about that, hixxy. It's all about epigenetics. That's why I'm starting to think that metabolic testing will provide more useful info than genotype testing.
  5. hixxy

    hixxy Woof woof

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    Russell Island, Australia
    Indeed. Have you had the HDRI Methylation Panel done yet? I have a consult with my doctor this week, so will be discussing it with him.
  6. adreno

    adreno 3% neanderthal

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    No, but I will look into it, once I have the funds.
  7. adreno

    adreno 3% neanderthal

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    I realize this is getting OT, but I wanted to add that slow metabolizers of caffeine have an increased risk of myocardial infarction, when consuming coffee:

    Coffee, CYP1A2 genotype, and risk of myocardial infarction.
    http://www.ncbi.nlm.nih.gov/m/pubmed/16522833/
  8. hixxy

    hixxy Woof woof

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    I remember right about the time my health was starting to deteriorate (6 or so years ago) I took some caffeine tablets and ended up at ER with heart instability / crush chest pain. The dose of caffeine tablets was far lower than what should have had that effect.
  9. nandixon

    nandixon Senior Member

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    Hi hixxy,

    I'm curious to see your GSTM1 results. Here are mine ("normal" call in square brackets):

    GSTM1 -/- (CC)[CC] rs12068997
    GSTM1 +/+ (GG)[AA] rs4147565
    GSTM1 -/- (AA)[AA] rs4147567
    GSTM1 +/+ (TT)[AA] rs4147568
    GSTM1 -/- (CC)[CC] rs1056806
    GSTM1 +/+ (TT)[AA] rs12562055
    GSTM1 +/+ (AA)[GG] rs2239892

    A lot of positives, too, like you mentioned, but such a grouping may simply represent a haplotype. Perhaps someone knows.

    I had a MetaMetrix panel done in 2000. For detoxification of acetaminophen, the glutathione conjugation was only 50% of the lowest normal reference value ("acetaminophen mercapturate" was measured). I'm not sure how much influence GSTM1 has relative to the other glutathione-S-transferases in that particular case.

    For anyone else interested, here is a recent (2011) listing of genes for the "glutathione pathway": GSH synthesis (GSS, GCLC, and GCLM); GSH redox status (GSR, GPX1, GPX2, GPX3, GPX4, GPX5, GPX6, and GPX7); GSH S-transferases (GSTA1, GSTA2, GSTA3, GSTA4, GSTA5, GSTM1, GSTM2, GSTM3, GSTM4, GSTM5, GSTO1, GSTO2, GSTP1, GSTT1, GSTT2, and GSTZ1); and GSH conjugate transporters (ABCC1, ABCC2, ABCC3, and ABCC4). From: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044203/

    (BTW, hixxy, 23andMe is reporting VDR Taq with the call letters A and G in my report. You have CC . . .?)
  10. qofmiwok

    qofmiwok

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    Interesting. I have exactly the same results as nandixon.

    GSTM1 -/- (CC)[CC] rs12068997
    GSTM1 +/+ (GG)[AA] rs4147565
    GSTM1 -/- (AA)[AA] rs4147567
    GSTM1 +/+ (TT)[AA] rs4147568
    GSTM1 -/- (CC)[CC] rs1056806
    GSTM1 +/+ (TT)[AA] rs12562055
    GSTM1 +/+ (AA)[GG] rs2239892

    Question, how did you find what is considered "normal"?

    Thanks
  11. nandixon

    nandixon Senior Member

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    Hi qofmiwok,

    I'm so glad you asked that - in double-checking my results I found that the word processor on my phone inadvertently shifted a column. So my previous post isn't correct. I don't have any variant alleles. The correct results, I hope(!) are:

    GSTM1 -/- (CC)[CC] rs12068997
    GSTM1 -/- (GG)[GG] rs4147565
    GSTM1 -/- (AA)[AA] rs4147567
    GSTM1 -/- (TT)[TT] rs4147568
    GSTM1 -/- (CC)[CC] rs1056806
    GSTM1 -/- (TT)[TT] rs12562055
    GSTM1 -/- (AA)[AA] rs2239892

    The "normal" calls in square brackets are the ancestral (wild type) alleles from NCBI, e.g., http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=12068997 (I also checked each one with openSNP, too).

    So it must be some other glutathione-S-transferase that's causing problems in the MetaMetrix results I mentioned, since all those ancestral alleles seem very dominant in the general population.

    If Rich happens to see this maybe he might have an idea. (My GSTA2 rs2608615 is CC, same as Rich's, from a post he made in April, so I guess that one is ok, too.)

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