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23andme genetic testing

Discussion in 'Genetic Testing and SNPs' started by rwac, Apr 10, 2011.

  1. searcher

    searcher

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    biophile-
    I wanted to let you know that your translations all look correct. The order of the nucleotides doesn't matter. And I think the +A/-T for rs2303080 has to be a mistake.
  2. rwac

    rwac Senior Member

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    I also created the snpedia articles.
    Glad to be of help!
  3. LaurieL

    LaurieL Senior Member

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    Well then, its a small world isn't it. I almost emailed you from the snpedia site but then I finally had my ah-hah moment.

    Your contributions to the site are much appreciated!!

    Laurie
  4. topaz

    topaz Senior Member

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    Hi

    Re: "orange" people

    Im a newbie to this forum and have been reading a lot of the threads here.

    Not wanting to dumb-down the SNP discussion, I can make a brief comment on "orange people".

    Taking high doses of beta carotene to "tan" ones skin was common in the 1980's(??). The resulting "tan" was characterised by an orange tinge (ie orange-brown/tan). I googled this again now to confirm my recollection and there are a plethora of "tanning pills" on the market which use beta carotene or beta carotene and canthaxanthin to create a tan. Ofcourse one could just use natural beta carotene as in carrot juice.

    I suspect the issue of "orange people" comes from how orange a person is (on the orange to brown scale). From what I recall, taking beta carotene to tan does produce that fake orange/brown tan colour, and not just the brown/tan colour. This is what I recall from the 80's. Maybe todays pills have improved the colour one turns (via canthaxanthin maybe???).

    Google "beta carotene and tanning" and you will see the info yourself.

    From one article: "All our experts agreed that beta carotene can turn the skin a yellowy/orange colour in high enough doses"

    So, prima facie, as the orange tinged skin effect of high doses of beta carotene appears to be common and frequent/expected, I would guess that this orange colouring of skin is not a result of having this SNP - just a likely side-effect of high doses of beta carotene (it is the beta carotene that gives certain vegetables their colour so it appears that this also translates to the colouring human skin). [I will ofcourse refrain from joking that it does appear that you are what you eat!]

    Over to greater minds and higher level discussion....
  5. richvank

    richvank Senior Member

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    Hi, Topaz.

    Thanks for the information. It may be that people who have the SNP get oranger, sooner, on less carrot juice! It would be interesting to quantify this, though I don't know how vital an issue it is, unless a person has this SNP and is a vegan. Then they might have problems with their eyes and other issues because of vitamin A deficiency.

    Best regards,

    Rich
  6. LaurieL

    LaurieL Senior Member

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    Here's a couple of more thoughts on the orange color. I do know that 23andme flags the most common SNP's found in populations and not necessarily the abnormal SNP's in active disease, like we are used to in Dr. Yasko's results. So the use of beta-carotene for "tanning" purposes could very well have to do with the fact that most people would have that mutation or particular SNP. The really orange people could very well have an unidentified "set" of SNP's and explain the two really orange people Rich has met. As well as some of us, whom seem to turn "really" orange.

    I like the humor. :Sign Good one:

    Laurie
  7. LaurieL

    LaurieL Senior Member

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    rwac,

    Have you put together a list of SNP's involved in the common supplementation and nutritionals surrounding autism and CFS/ME populations? Perhaps a list of these could also help and explain why sometimes the supplementation and nutritionals just don't "work" like they should.

    For example: http://www.ncbi.nlm.nih.gov/pubmed/18374198

    SNP's in warfarin are found in Vitamin K pathways. VKORC1, CYP2C9

    This might be an interesting avenue for all of us to contribute to sometime.

    Laurie
  8. rwac

    rwac Senior Member

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    Laurie, Thanks for pointing that out, somehow I missed that although I was actually looking for stuff related to vit K status.
  9. camas

    camas Senior Member

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    Thank you, Laurie! Well done! :thumbsup::victory: :thumbsup:

    I think I may finally get it now, despite fairly significant brain fog. Thought I'd share my results (in bold) in case I went awry somewhere. Comments or corrections are welcome.

    ACE Del16, rs1799754, +D/-l (not tested)
    CBS A360A, rs1801181, +T/-C (AG) +/-
    CBS Y233Y (C699T), rs234706, +A/-G (AG) +/-
    COMT (H62H), rs4633, +T/-C (CC) -/-
    COMT (V158M), rs4680, +A/-G (GG) -/-
    COMT (L136L), rs4618, +C/-G (not tested)
    COMT -61 (P199P), rs769224, +A/-G (GG) -/-
    MAO-A (R297R), rs6323, +T/-G (GT) +/-
    MTHFR A222V (C677T), rs1801133, +T/-C (AG) +/-
    MTHFR E429A (A1298C), rs1801131, +C/-A (GT) +/-
    MTHFR P39P, rs2066470, +T/-C (GG) -/-
    MTR A9196 or A27566, rs1805087, +G/-A (AG) +/-
    MTRR H595Y, rs10380, +T/-C (CC) -/-
    MTRR K350A, rs162036, +G/-A (AA) -/-
    MTRR S257T, rs2303080, +A/-T (not tested)
    MTRR A9196G (A66G), rs1801394, +G/-A (AA) -/-
    MTRR A664A, rs1802059, +A/-G (AG) +/-
    NOS D298E (G894T), rs1799983, +T/-G (not tested)
    SOUX S370S, no rs#, +C/-T
    SOUX A628G, rs7297662, +G/-A (not tested)
    VDR Bsm/Taq, rs1544410, +A/-G (CC) -/-
    VDR fok1, rs10735810, +T/-C (not tested)
    ACAT-02, rs3741049, +T/-C (GG) -/-
    AHCY-01, rs819147, +G/-A (TT) -/-
    AHCY-02, rs819134, +G/-A (AA) -/-
    AHCY-19, rs819171, +G/-A (TT) -/-
    BHMT-01, rs585800, +T/-A (not tested)
    BHMT-02, rs567754, +T/-C (CT) +/-
    BHMT-04, rs617219, +C/-A (AC) +/-
    BHMT-08, rs651852, +T/-C (CT) +/-
    SHMT, rs1979277, +A/-G (no call)
  10. LaurieL

    LaurieL Senior Member

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    :Sign Good Job: Nothing awry, did good. I was hoping this would help others in trying to get info from their 23andme results.....and thank you!!

    Laurie
  11. camas

    camas Senior Member

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    Oh, good. Maybe I'm not quite as foggy as I thought. Thanks for looking over my results. Much appreciated!
  12. biophile

    biophile Places I'd rather be.

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    Earlier I posted my results for the 32 relevant values.

    A "non-ME/CFS" friend of mine also had their results back from 23andme and sent me the raw data to check for comparison.

    Friend: 0 x (+/+), 1 x (+), 8 x (+/-) or (-/+), 15 x (-/-), 8 x missing data.

    Me: 5 x (+/+), 1 x (+), 5 x (+/-) or (-/+), 13 x (-/-), 8 x missing data.

    2/4 of COMT were +/+ for me (the other 2 were either missing data or -/-). For my friend, all 3 AHCY were (+/-) or (-/+). I really have no idea if any of this means anything, but I do have a question for richvank if he is interested.

    Last year I tried 1/4 dose FolaPro and 1/4 dose hydroxy-B12 for roughly 2 months. I couldn't tolerate a higher dosage of FolaPro as that seemed responsible for most side-effects (which did not appear straight away). I stopped altogether because I got impatient or perhaps just forgot 3 months is the suggested minimum. That was about 12 months ago and I regret not staying on it because I have recently become interested in trying it again due to the 23andme results and painful reminders of how pathetic my medication intolerance has become. I am also considering purchasing folinic acid and perhaps methyl-B12 drops as well. I am reluctant to get all the other peripheral cofactors. Also, several years ago I had a very bad experience with SAM-e and would not dare to try it again.

    Would differences in individual profiles offer insight into fine-tuning the methylation protocol by studying the mechanisms behind these processes?

    http://www.knowyourgenetics.com/The Methylation Pathway_files/diagram-1.jpg

    http://www.knowyourgenetics.com/The Methylation Pathway_files/supplmentation-1.jpg

    On the general issue of beta-carotene, this could be mere coincidence, but the last 2 times I had juiced carrots to drink I got a bad headache.

    Thanks, two brain fogged minds are better than one!
    geesiddiqui likes this.
  13. determined

    determined Senior Member

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    I'm also interested in the ACHY SNPS, if anyone has any insight. So, I'm speculating here, but if someone has a problem with ACHY, will they react badly to SAMe?
  14. camas

    camas Senior Member

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    It is interesting to compare results with others. My partner has 6 +/+ and 4 +/- compared to my 10 +/-. On the surface his results look worse than mine, but I need to look at it more closely. He does not have ME/CFS, but is a type 1 diabetic which might partially explain his results. Despite his illness, he's considerably more functional than me.
  15. biophile

    biophile Places I'd rather be.

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    Interesting. I agree it is hard to know what all this means. I don't expect the hypothesis of a partial block in the methylation cycle to explain all my symptoms, but I will be impressed if it helped restore me to the illness state I was at before the additional complications became obvious.
  16. determined

    determined Senior Member

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    It would be really interesting to get information about the methylation SNPs of a large number of healthy people. I think Rich has stressed that the methylation deficits are functional rather than specific genetic flaws.

    I believe that our condition is mainly autoimmune. Perhaps there are antibodies preventing the proper functioning of the methylation cycle. Other than altering my immune system's reaction to methylfolate and mB12, I really can't explain why my tiny tiny does of both of these has had such a dramatic effect. Surely I am not taking enough to really supplement the actual levels of these molecules in a significant way.....
  17. LaurieL

    LaurieL Senior Member

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    I was also interested in the ACHY mutations, so I'll give what I have on it which isn't much. I look forward to a response from Rich.

    I believe it has an link to the CBS and COMT mutations.

    In CBS A360A, the ACHY mutation can actually make the CBS mutation better.

    For COMT V158M, ACHY + VDR Bsm/Taq is prone to mood swings/aggression when given things that increase dopamine.

    AHCY S-Adenosylhomocysteine Hydrolase:

    S-Adenosyl Methionine (SAMe), the key methyl donor generated from methionine, is metabolized in to S-Adenosyl Methionine, and then on to homocysteine by AHCY. Individuals (+) for both AHCY and CBS often have low baseline urine sulfate levels, which then rise and fall in response to treatment. Early on the levels rise, as the bottle neck abnormal AHCY enzyme has been limiting the supply of homocysteine. Once the cycle starts to spin, homocysteine is made available to CBS, and urine sulfate will rise. Later, in response to a low animal protein/low sulfur diet, urine sulfate levels will fall. Defects in AHCY are addressed by measures designed to improve overall Methyl Cycle function, such as Methyl support RNA 1/8th dropper per day.

    http://www.heartfixer.com/AMRI-Nutrigenomics.htm#VDR Taq: Vitamin D Receptor Taq Abnormality

    Depending on what other mutations exist, then ACHY could make things worse or improve things, i was thinking MTR, or MTRR mutations may also figure in this somewhere.

    Laurie
  18. LaurieL

    LaurieL Senior Member

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    The chart that rwac posted the link to earlier in this thread is a chart of Dr. Yaskos, in which features a large control group versus CFS patients. It shows the percentage of +/+, +/-, and -/- in the control group as well as CFS patients.

    I found it really interesting in that 93% of those tested in the CFS arena had atleast one + for the MAO-A enzyme versus 78% of the controls.

    Those mutations figuring over 80% include the ACE, MAO-A, BHMT, SOUX, and AHCY. In the case of the SOUX mutation, 100% of CFS patients tested positive for this mutation, but I believe the control group also tested in around 90%.

    Laurie
  19. LaurieL

    LaurieL Senior Member

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    Could it depend on MTRR, and BHMT mutations?

    Laurie
  20. determined

    determined Senior Member

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    Is Yasko published? I find very little information about all these SNPs that seems well-established.

    FWIW, I am homozygous +/+ for MTRR A66G, but I am homozygous normal -/- for all the BHMT SNPs. I am heterogyzous for all the AHCY SNPs.

    I am also +/+ for the MTHFRA1298C.

    When I get more time, I want to continue listening to some MIT lectures on Genomics.

    http://ocw.mit.edu/courses/health-s...2-genomic-medicine-spring-2004/lecture-notes/

    I have listened to a few, and one of the lecturers said that much of the information "out" on SNPs is incorrect.

    All of this is interesting to be sure, but perhaps we are hoping for information beyond what is really available now. I continue to think of this as primarily autoimmune. But I really like thinking about all of these pieces to the puzzle. I hope we find "the answer" in my lifetime.

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