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23andme genetic testing

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

  1. richvank

    richvank Senior Member

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    Hi, LaurieL.

    Sorry, I'm just not up-to-speed on this yet. Also, I don't understand what you are saying in these sequences of symbols. I can't tell what is from the Yasko report, what is from the 23andme report, and what is your interpretation. Are you finding that the Yasko analysis agrees with the 23andme analysis for the SNPs they both report, when the comparision is properly made, taking into account which DNA strand each lab is using? Or are there differences?

    I send my saliva sample in a few days ago, and hopefully when I get my results back in a few weeks I will be able to put in some time and figure out what it all means. But for now, I'm not much help.

    Thanks.

    Rich
  2. LaurieL

    LaurieL Senior Member

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    Thats my whole problem, when the comparison is properly made. I am looking for someone who can do exactly that because I don't think I am right on the money. I am having serious doubts to my interpretations. :)

    I think there are differences, because 23andme uses such large strands whereas Yasko uses smaller portions and can be so much more specific. Just MO.

    If you just sent it in, then it will be about a month and a half before any of us get your input. Hows about taking a few results here and there from others and trying to work this out with me? It will make good practice for when you get your results!! :)

    Laurie
  3. searcher

    searcher

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    In case this will be helpful for anyone, I wanted to list the steps I took to translate my 23andme results into Yasko SNPs:
    - I made a copy of the spreadsheet mentioned earlier in the thread-- https://spreadsheets.google.com/ccc?hl=en&key=tLJeH__1TXzdZvNnMS3Wq_A&hl=en#gid=0 .
    - You can download the google spreadsheet to excel by going to "File"->"Download As" at the top of the page.
    - Or, you can edit it in google docs by going to "File"->"Make a Copy" and then you can edit the file on your own account.
    - I made my own row beneath the "23andme" row and filled out my results there.
    - I looked up each of my SNPs in 23andme by going to "Account"->"Browse Data."
    - I then translated the SNP to Yasko notation using Row 3 of the spreadsheet.
    - For example, column F is COMT 4680 and is often referred to as V158M. It's official name is rs4680. I looked up rs4680 in 23andme. My result was AG. The A is (+) in Yasko notation, and the G is (-) So I marked this down as +/-.
    - I haven't read the Yasko books yet so can't help with the translation from Yasko->Supplements. I am MTHFR++ so this at least confirmed that methylation was a logical approach for me.

    *As a caveat, I didn't create this spreadsheet, but as far as I can tell it is an accurate translation from 23andme to Yasko.
  4. mellster

    mellster Marco

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    What is the 1-year subscription about they mention you have to commit to for the $99 offer? What about privacy? Thanks!
  5. LaurieL

    LaurieL Senior Member

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    Searcher,

    Thank you for some input. I will go back and recheck again, my interpretations with that spreadsheet.

    Laurie
  6. searcher

    searcher

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    Hi mellster-
    23andme used to charge a one-time fee and then there were no on-going charges. Recently they changed their policy so the up-front charge is lower, but there is a monthly fee for updates on their interpretations of the SNPs and for the ability to contact potential relatives. They have a pretty good demo account where you can see what you get on the website. If you only care about getting your SNPs, you can pay $99 + $9/month for 12 months and then cancel. So if you bought today the minimum cost is $207.
    If you aren't in a hurry but are interested, I recommend waiting until they have another deal. They have them at least 2-3 times a year, and they're usually pretty significant (like this last one which was $0 down, $9/month.)

    23andme has a pretty strict privacy policy, but they do use your data for aggregate research studies. And there is always a risk with any service that there will be a data breach. From my perspective, I am not concerned because I think my medical records tell a lot more personal info about me than my SNPs do. But I know that a lot of people are concerned about the privacy of their genetic records, so it definitely is a consideration.

    -fellow san franciscan
  7. mellster

    mellster Marco

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    Thanks searcher - guess I'll wait for a deal then, not really in a hurry.
  8. LaurieL

    LaurieL Senior Member

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    Searcher,

    I think the following will help clear up some confusion and help me with interpretation. On the speadsheet you referred to...

    The third line you referred to, are these then considered the normal and a difference between that and ones own results would then result in an abnormal,....or are those values representative of the abnormal, and a match would then signify a trouble mutation? An answer to that question will clear up quite a bit. TIA!

    Laurie
  9. searcher

    searcher

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    Good question-- it took me awhile to figure this out because I think her notation is the opposite of what many others use.
    I believe Yasko's notation is:
    +/+ = homozygous for the polymorphism (usually recommends supplementation)
    +/- = heterozygous for the polymorphism
    -/- "normal" SNP

    So in the MTHFR case I mentioned I am +/+ in Yasko notation, which means she recommends supplementation.

    I put quotes in normal because many SNPs have a lot of variation so it's hard to define what's normal.

    Hope this helps!
  10. searcher

    searcher

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    I realized I should have been more specific because it is hard to understand how to use line 3.

    Line 3 is telling you how to translate your results into Yasko's notation, but isn't saying anything about what's normal. So for COMT 4680, line 3 says +A/-G. This means that you should put down a + for each A or T you have at that SNP, and put down a - for each G or C.

    So if your SNP is AA, then you mark it down as +/+. If you are AG, then you are +/-. If you are GG, then you are -/-. And, as you mentioned earlier, A=T and G=C.

    Let me know if this makes sense or if there is any area I can help clarify.
  11. LaurieL

    LaurieL Senior Member

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    :victory: I just had an ah-ha moment. Sheesh.

    You will notice in all the categories of SNP's she lists in that table, even though the alleles may differ, all the results are +/-.

    To add some more detail to what you already have....

    In Yasko-speak:

    A '-' means you have the 'normal' genetic variant
    A '+' means you may have issues with that enzyme
    A '+/+ is abnormal
    A '+/- is one you may still want to pay attention to and may derive benefit from
    supplementation
    A '-/-' is normal

    C=G and T=A.

    Simple as that, just plug them into your own spreadsheet, and whallah.....

    :Retro smile:

    Laurie
  12. LaurieL

    LaurieL Senior Member

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    I learned a few things and wanted to address the information in the following post on page one, post #3.

    http://snptips.5amsolutions.com/
    With this link, you must have the firefox browser in order to use this add on.

    I noticed this link is incomplete in their listing, and some of the rs#'s for Yasko's are incorrect. I suggest not using this list, as it is why it caused so much confusion in my own quest. Will post a complete list to follow.

    I also have this one. Interesting, I wonder how many of us do?

    Laurie
  13. LaurieL

    LaurieL Senior Member

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    Here is a list in which correlates the 23andme rs#s with Dr. Yasko's references.

    Out of the 32 SNP's Dr. Yasko tests for in the methylation cycle, 23andme gave me 26 out of the 32. The six I got a 'no call or no result' are in blue, but the info still in that line is correct for others to use. I don't know if these six will be across the board for everyone. I do know there are some of which were discussed somewhere around here.

    ACE Del16, rs1799754, +D/-l

    CBS A360A, rs1801181, +T/-C
    CBS Y233Y (C699T), rs234706, +A/-G

    COMT (H62H), rs4633, +T/-C
    COMT (V158M), rs4680, +A/-G
    COMT (L136L), rs4618, +C/-G
    COMT -61 (P199P), rs769224, +A/-G

    MAO-A (R297R), rs6323, +T/-G

    MTHFR A222V (C677T), rs1801133, +T/-C
    MTHFR E429A (A1298C), rs1801131, +C/-A
    MTHFR P39P, rs2066470, +T/-C

    MTR A9196 or A27566, rs1805087, +G/-A

    MTRR H595Y, rs10380, +T/-C
    MTRR K350A, rs162036, +G/-A
    MTRR S257T, rs2303080, +A/-T
    MTRR A9196G (A66G), rs1801394, +G/-A
    MTRR A664A, rs1802059, +A/-G

    NOS D298E (G894T), rs1799983, +T/-G

    SOUX S370S, no rs#, +C/-T
    SOUX A628G, rs7297662, +G/-A


    VDR Bsm/Taq, rs1544410, +A/-G
    VDR fok1, rs10735810, +T/-C

    ACAT-02, rs3741049, +T/-C

    AHCY-01, rs819147, +G/-A
    AHCY-02, rs819134, +G/-A
    AHCY-19, rs819171, +G/-A

    BHMT-01, rs585800, +T/-A
    BHMT-02, rs567754, +T/-C
    BHMT-04, rs617219, +C/-A
    BHMT-08, rs651852, +T/-C

    SHMT, rs1979277, +A/-G

    Commas seperate, Yasko name, 23andme rs#, Yasko variant (+/-). It is the Yasko variant that one would use to compare to their variant given by 23andme.

    For example, CBS A360A, rs1801181, +T/-C. 23andme result is a GG, which translates to CC, remember, G=C and T=A. So translated to CC and C is '-' in Yasko variant, then the 23andme would read as -/- or normal.

    Laurie
  14. richvank

    richvank Senior Member

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    Hi, LaurieL.

    I was interested to see that you have the BCMO1 SNP. Do you find that if you eat a lot of carotene, such as in carrot juice, that your skin turns orange readily? I've encountered one case like that, and it would be interesting to know if he has that SNP.

    Rich
  15. LaurieL

    LaurieL Senior Member

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    SO, my +/+ are MTHFR C677T and MAO-A R297R.

    My +/- are then CBS A360A, COMT L136L, MTR A9196 or A27586, MTRR A66G, MTRR A664A, VDR Bsm/Taq, VDR fok1, ACAT-02, and my SHMT C1420T.

    The rest are -/- or "normal".

    Whew! Going to bed.

    Laurie
  16. LaurieL

    LaurieL Senior Member

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    Yes, especially the bottoms of my feet and my hands. My son is the same way. I will be interested to get his results as well.

    Laurie
  17. rwac

    rwac Senior Member

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    I have one of the BCMO1 snps and I can't tolerate carotene supplements. The soles of my feet are also orange.
  18. LaurieL

    LaurieL Senior Member

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    rwac,

    I wanted to make sure you knew how important your post was in me learning as well as instigating the ah-hah moment I had above, and wanted to say a hearty thank you.

    You know, when being treated by my environmental toxicologist, one of the supplements he used regulary was Beta-carotene. Now I realize that it was that, in which could have very well caused our orange color. I had connected it then to either anemia or Diabetes related symptoms, even though I wasn't diagnosed. It is interesting in that I have that SNP, and I also have SNP's indicating megoblastic anemia tendencies as well as Diabetes tendencies. Or increased risks. Hows about you guys?

    Laurie
  19. biophile

    biophile Places I'd rather be.

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    Time consuming stuff!

    I received my 23andme results recently as well. Over the years I have acquired additional symptoms which suggest to me some sort of "methylation" issue or equivalent. That's a long story for another time, but according to LaurieL's sleuthing (thanks BTW) which I applied to my results with the help of the spreadsheet from http://www.cfscentral.com/2011/01/gene-pool.html, out of those 32 SNPs, 6 were (+/+) or (+), 5 were (+/-) or (-/+), 13 were (-/-), and there was missing data for 8.

    However, I don't understand the interchangeability of the nucleotides T=A and C=G? For example, when looking at "(MTRR) rs2303080 [S257T +A/-T]" (which I was missing data for), if A=T, how can A count as (+) and T count as (-) if they are interchangeable? Also, does the order of the nucleotides matter?

    I haven't been in the best cognitive shape recently so I wonder if I've done something wrong below. Anyway, below are the results for the 32 SNPs, my results in bold after each colon, red colour for (+/+) or (+), blue for (+/-) or (-/+), green for (-/-), as far as I can tell anyway ...

    (ACE) rs1799752 [Del 16 +D/-I]: missing data

    (CBS) rs1801181 [A360A +T/-C]: AA=TT? | (+/+)
    (CBS) rs234706 [Y233Y (C699T) +A/-G]: GG (-/-)

    (COMT) rs4633 [H62H +T/-C]: TT | (+/+)
    (COMT) rs4680 [V158M +A/-G]: AA | (+/+)
    (COMT) rs4818 [L136L +C/-G]: missing data
    (COMT-61) rs769224 [P199P +A/-G]: GG | (-/-)

    (MAO A) rs6323 [R297R +T/-G ]: T | (+)

    (MTHFR) rs1801133 [A222V (C677T) +T/-C]: GG=CC?| (-/-)
    (MTHFR) rs1801131 [E429A A1298C +C/-A]: GT=CA? | (+/-)
    (MTHFR 03) rs2066470 [P39P +T/-C]: AG=TC? | (+/-)

    (MTR) rs1805087 [A919G A2756G +G/-A]: AG | (-/+)?

    (MTRR) rs10380 [H595Y +T/-C]: CC | (-/-)
    (MTRR) rs162036 [K350A +G/-A]: AA | (-/-)
    (MTRR) rs2287780 [R415T +T/-C]: CC | (-/-)
    (MTRR) rs2303080 [S257T +A/-T]: missing data
    (MTRR) rs1801394 [A919G (A66G) +G/-A]: GG | (+/+)
    (MTRR-11) rs1802059 [A664A +A/-G]: GG | (-/-)

    (NOS 3) rs1799983 [D298E (G894T) +T/-G]: missing data

    (SUOX) none [S370S +C/-T]: missing data
    (SUOX) rs7297662 [A628G +G/-A]: missing data

    (VDR) rs1544410 [Bsm/Taq +A/-G]: TT=AA? | (+/+)
    (VDR) rs10735810 [Fok I +T/-C]: missing data

    (ACAT1-02) rs3741049 [N/A +T/-C]: AG=TC? | (+/-)

    (AHCY-01) (rs?)819147 [N/A +G/-A]: TT=AA? | (-/-)
    (AHCY-02) rs819134 [N/A +G/-A]: AA | (-/-)
    (AHCY-19) rs819171 [N/A +G/-A]: TT=AA? | (-/-)

    (BHMT-01) rs585800 [N/A +T/-A]: missing data
    (BHMT-02) rs567754 [N/A +T/-C]: CC | (-/-)
    (BHMT-04) rs617219 [N/A +C/-A]: AA | (-/-)
    (BHMT-08) rs651852 [N/A +T/-C]: CC | (-/-)

    (SHMT) rs1979277 [C1420T +A/-G]: AG | (+/-)
  20. richvank

    richvank Senior Member

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    Hi, all.

    I just want to note that people whose bodies are not able to convert beta carotene to vitamin A very readily may be low in vitamin A unless they are eating foods that are high in actual vitamin A (such as liver, dairy products, eggs, and fish, for examples). Vitamin A deficiency can produce dry eyes and night blindness, as well as other problems.

    I've met two "orange people." Both told me that they were ingesting a lot of carrot juice. I don't know if they had this SNP.

    Years ago I read of a rare case of a person whose conversion of beta carotene to vitamin A was uncontrolled and too rapid. This is sort of the opposite of what we are discussing here. This person died of vitamin A toxicity, similar to what has happened to people who ate polar bear liver, which is very high in vitamin A.

    Best regards,

    Rich

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