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23andme genetic testing

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

  1. drex13

    drex13 Senior Member

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    Columbus, Ohio
    Not yet. I was looking specifically for rs1801394 which is for MTRR A66G. I got the result from 23andMe as GG. According to the mothering link posted earlier in this thread, normal is the "A" type. So I think think GG is not good, but I can't find it in Promethease.
  2. drex13

    drex13 Senior Member

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    Columbus, Ohio
    LOL....sorry. Yeah, you have to download it . You can do it for free, or pay $2 through Amazon, for a supposedly much faster result. I paid the $2, but so far I really havn't gotten anything useful from the info. It would help if I knew what I was looking at.
  3. determined

    determined Senior Member

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    Okay, now I'm looking at my report (thanks, rwac!) but now, how do I save all these results? I'm confused. Are they on my computer or do I have to log in to see them somewhere? Certainly this is not something I can read all at once. Thanks if you can help. I am a technophobe.... : (
  4. penny

    penny Senior Member

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    Southern California
    It saves the file on your computer, the location of mine is like this:
    file:///C:/Documents and Settings/penny/My_Promethease_2011_05_11/My_Promethease_2011_05_11.html

    So you could move it someplace easier to access or just bookmark it in your browser (this is what I did).
  5. determined

    determined Senior Member

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    Sorry for another question, but is the saved version searchable like the report I'm looking at now? It is linked to the internet.

    When you say "bookmark in your browser" that's on online link, yes?

    Again, I do apologize for my ignorance.
  6. rwac

    rwac Senior Member

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  7. camas

    camas Senior Member

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    Oregon
    The report you are looking at has been saved on your hard drive as an html file, so you view it using your browser whether you are online or not.

    Here's how to find your report assuming you are using Windows.

    1. Click on the Windows icon on the bottom left of your screen. You'll see a box that says "search programs and files."

    2. In this box type "my_promethease" or just "my_" without the quote marks. You'll see some folders and files listed above.

    3. Click on the file/document (not the folder) that says simply "my_promethese_2011_05_16" It might read 15, 16, or 17 depending on what date you originally ran it.

    4. Now clicking on this document will bring up your browser and show your report.

    5. To view it more easily the next time, just bookmark it and you can bring up your report whenever you have your browser open and want to look at it.

    6. If you are using Internet Explorer, you bookmark by clicking on the star on the upper right and then clicking on Add to Favorites.

    If you are using Firefox you click on Bookmarks in the menu bar and click Bookmark this page.

    I don't know how bookmarking is done in other browsers, but I suspect you are probably using IE?

    I hope that helped!
  8. determined

    determined Senior Member

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    USA: Deep South
    You guys are just awesome, thanks so much!

    I have to get away from all the data for a while, but there is a lot there to explain many components of this disease. I wish I had done this years ago.
  9. camas

    camas Senior Member

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    Oregon
    Hmmm. This SNP showed up in both mine and my partner's Promethease reports just as it does on 23andMe. I'm AA which it says is normal. My partner's showed up as GG and says he's at 1.4x higher risk for meningiomas whatever that is! So I'm assuming GG is probably not good?
  10. determined

    determined Senior Member

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    USA: Deep South
    Okay, I think I've got all the tech problems worked out. Thanks again.

    Now, next problem: promethease said that I have a SNP in gs231 (which would suggest that I do need the methylfolate). But they don't give the corresponding "rs" version that applies to the 23andme data. That was one that they didn't give the "rs" number for, and of course it's the one that I really want.

    I've googled it with no luck either.

    This is fun, but also frustrating.
  11. camas

    camas Senior Member

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    Oregon
    It looks like you can look these up in SNPedia. Here's where this genotype is discussed:

    http://www.snpedia.com/index.php/Gs231

    If you click on Criteria on the right, it shows the associated SNPs. Is this what you are looking for?
  12. determined

    determined Senior Member

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    USA: Deep South
    Yes, I do see that now, thanks! But it is giving me results as if I am C/C, but my 23andme results list me as G/G for both. I think G/G is normal but C/C is the mutated version. So I guess I don't understand why promethease said I have this mutation.

    Thanks again for your help! All day long I've felt like I had somewhere to turn with this - it's hard to overestimate the value of THAT! :victory:
  13. camas

    camas Senior Member

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    As I understand it, 23andMe is reporting it as GG and Promethease translated it to CC. They both mean the same thing. SNPedia and Promethease are following the government standard. You can read more about it here: http://tinyurl.com/3zen6hl
  14. drex13

    drex13 Senior Member

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    Columbus, Ohio
    Right. I think G=C and A=T. I have this written down in my notebook, which I can't find at the moment because I think I left it at work. So some SNP's in Yasko might be listed using C or T and 23andME use A and G. Check out some of the links posted earlier in this thread and you can kind of figure out the translations on some. But some are still confusing.
  15. drex13

    drex13 Senior Member

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    Columbus, Ohio
    I think this SNP (A66G) has something to do with converting B12. Not sure I'm still trying to figure it out, but pretty sure GG means I don't something right.
  16. determined

    determined Senior Member

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    USA: Deep South
    Thanks so much for the help. I need to read the FAQs very thoroughly!
  17. richvank

    richvank Senior Member

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    Hi, drex and the group.

    I haven't yet had time to pull together the Yasko nutrigenomics results and the 23andme panel in my head, but I do want to point out something. These letters, G,C,A, and T represent nucleotides in the DNA molecule (guanine, cytosine, adenine and thymine). A single nucleotide polymorphism or SNP occurs when one of these is substituted for another. For a particular SNP, the letter designating the nucleotide that is actually present in the person's DNA is designated the "call letter."

    The confusion between the results from different labs that characterize SNPs is that there is not always agreement on which nucleotide is the normal or "norm" for this SNP. The reason is that some SNPs are very common, and could be near 50% frequency in the population. Also, the frequency of a particular SNP can vary quite a lot between different ethnic groups, because of their differing genomic heritage. So one lab could consider a G in a certain location as being the norm, while a C is considered the SNP, while another lab could view this oppositely. So it's important to get back to the call letter that each lab is reporting for a particular person to be able to compare results.

    Additional confusion may come from the fact that a lab like 23andme does haplotype analyses, which amounts to analyzing for fairly long segments of DNA that tend to be inherited in whole pieces, while others, such as the one Yasko uses, analyze individual genes for their SNPs. 23andme infers the presence of SNPs from the presence of certain haplotypes, each of which can contain many individual genes on them. With the 23andme results, it would be important to find out how they are defining a particular SNP, i.e. what call letter they are viewing as the SNP.

    I hope this helps. I also hope that I will be able to spend more time studying this sometime soon, because I think it can be a powerful thing.

    Best regards,

    Rich
  18. drex13

    drex13 Senior Member

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    Columbus, Ohio
    Thanks, Rich. More info is always helpful. Below is info form 23andMe.

    Which DNA strand does 23andMe report for SNP genotypes?
    The SNP genotypes you are seeing in Browse Raw Data might not match what you learn about the SNP from other sources such as dbSNP. This is because every SNP can be represented using either of the two DNA strands and this representation will often differ from database to database or publication to publication.

    For example, 23andMe might report that a SNP has two versions, G and A. But other sources may report that the versions are C and T. Because of the double-stranded nature of DNA, both ways of reporting the SNP are correct: G pairs with C on the opposite DNA strand, while A pairs with T.

    All of the genotypes displayed in Browse Raw Data are oriented with respect to the positive strand on the reference assembly of the human genome (build 36). Note that this could be different from how the SNP is oriented in dbSNP or how it might be presented in a publication.
  19. richvank

    richvank Senior Member

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    Oh, O.K., drex. That explains it. Thanks.

    Rich
  20. LaurieL

    LaurieL Senior Member

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    Midwest
    I got my results back today.

    COMT Yasko-V156M Yasko Normal G(-) 23andme Normal G(+) 23andme- rs4680 GG +
    COMT Yasko-H62H Yasko Normal C(-) 23andme Normal C(+) 23andme- rs4633 CC +
    COMT Yasko-61 Yasko Normal G(-) 23andme Normal G(+) 23andme-rs769224 GG +

    VDR Yasko-Taq Yasko Normal T(+) 23andme Normal ~ 23andme- rs731236 AG-
    VDR Yasko-fok No data

    MAO-A Yasko-R297R Yasko Normal ~ 23andme Normal G(+) 23andme-rs6323 TT(+)

    ACAT No data

    ACE No data

    MTHFR
    Yasko-C677T Yasko Normal C(-),T(+) 23andme Normal G(-) 23andme-rs1801133 AA(-)
    Yasko-A1298C Yasko Normal A(-) 23andme Normal T(-) 23andme-rs1801131 TT(-)

    MTR
    Yasko-A2756G Yasko Normal A(-) 23andme Normal A(+) 23andme-rs1805087 AG(+)

    MTRR
    Yasko- A66G Yasko Normal A(-) 23andme Normal A(+) 23andme-rs1801394 GG(+)
    Yasko- H595Y Yasko Normal C(-) 23andme Normal C(+) 23andme-rs10380 CC(+)

    BHMT
    Yasko-1 Yasko Normal (-) 23andme Normal (-) 23andme-rs492842 CT (-)
    Yasko-2 Yasko Normal C(-) 23andme Normal C(+) 23andme-rs6894156 CT(+)
    Yasko-4 Yasko Normal (-) 23andme Normal (+) 23andme-rs6875201 AG(+)
    Yasko-8 Yasko Normal T(+) 23andme Normal (+) 23andme- rs3797546 TT(+)
    rs-567754 CC(+)

    AHCY
    Yasko-2 Yasko Normal T(-) 23andme Normal (+) 23andme-rs1205357 TT(+)

    CBS
    Yasko- C699T Yasko Normal C(-) 23andme Normal (+) 23andme-rs234706 GG(+)
    Yasko- A360A Yasko Normal C(-),T(+) 23andme Normal ~ 23andme-rs1801181 AG(-)

    SOUX No data

    SHMT
    Yasko-C1420T Yasko Normal G(-) 23andme Normal ~ 23andme-rs1979277 AG(+)

    NOS No data

    I flagged the ones in red in which I think may be variants. Others I just wasn't sure of so I did nothing to them. The code after Yasko is yasko speak for the rs 23andme speak. The Yasko number can also be read as an rs number usually from 23andme. Yasko Normals have been interpreted into 23andme normals. The last bit of info in the line is my own result in 23andme speak.

    I sure would appreciate Rich, rwac, and others familar with Yasko or 23andme speak to take a look at my interpetations. TIA!! I sure wish I had some data on NOS and Soux. I have been having awful problems with ammonia the last 30 days or so.

    I also have other interesting results such as selective IgA deficiency mutation variants, of which I believe this would be considered a primary immune deficiency as opposed to a secondary or acquired deficiency.

    Laurie

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