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Gestalt's Genova, 23andMe & Yasko Methylation genetic results

Discussion in 'Genetic Testing and SNPs' started by Gestalt, Jul 3, 2012.

  1. greenshots

    greenshots Senior Member

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    Now thats a big difference for treatment! That combo of both MTHFRs, CBS, and SHMT, a complete SHMT no less! Do you have leaky gut or digestive problems? I'd have to think you would with all of those! I know the glutamine helped some of that but I'd have to figure you'd be a big risk for bacteria and gut stuff.

    So, unless your VDRs are normal, it looks like the difference might be 7 or 8 snps from yasko to 23&me? I guess it could be worth it as long as you have normal SHMT and ACAT snps. I say that about the ACAT cuz my girlfriend had 23's done in March and her ACAT was read as normal but when they came back from Yasko last month, it was heterozygous. So 23's ACAT might not be reliable or its a different ACAT snp? Or maybe it was the saliva test vs. blood results, I don't know. But it made a huge difference in her treatment plan since ACAT and SHMT are more important then the others.
    Gestalt likes this.
  2. caledonia

    caledonia

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    What is 23andme's coverage of the detox SNPs like? In other words, is it necessary to have the Detoxigenomics testing?
  3. Gestalt

    Gestalt Senior Member

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    Good question. And yes, 23andMe does test some of the Genova Detoxigenomic SNPs. It get's most of them but not all. Whether it's necessary depends on what your results are, and what overall impact/significance they have as well in relation to your other genes.

    You can convert your 23and Me results to the Detoxigenomic profile using Calico13's spreadsheet .Just click on the bottom tabs.
  4. caledonia

    caledonia

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    I've seen that spreadsheet, but missed the other tabs - thank you!
  5. Calico13

    Calico13

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    Hey Gestalt, I just saw this thread now. I'm glad the spreadsheet has been helpful and most importantly the results matched up when you got the Yasko test done. Thanks for posting all of this.

    Edit: I had been accused on here by someone will I will not name but has posted in this thread, that my spreadsheet was inaccurate and obsolete, so I hope this clears that up for good.
    Gestalt likes this.
  6. Gestalt

    Gestalt Senior Member

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    One thing, supposedly in terms of VDR, the Bsm and Taq are two different things, and don't correlate. So I am unsure if rs1544410 can be considered Taq but perhaps it is the Bsm? Yasko has recently changed things up a bit and apparently VDR Taq "TT" is the equivalent of +/+ which would contradict the rs1544410 result I got, so this makes sense in those terms.

    I was also going to ask how you figured out which SNP allele letters in the 23andme format correlate to '+' and '-' status? You used "Plus strand"? Where can I access this?
  7. Calico13

    Calico13

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    Hey! I did see she had changed the way she was reporting the VDR, but I did not look into it more tbh. She used to test 3 different VDR; Bsm/Taq, Taq and Fok I. She stopped testing for VDR taq and when she dropped it, I removed it from the spreadsheet keeping the original VDR "Bsm/Taq" SNP on there.On that SNP I was using the RS Id for Bsm.

    If you want to know the VDR Taq RS ID, it is rs731236. G would be the risk allele. When she stopped reporting this one I just removed it from the spreadsheet and kept the other. If she is just reporting on Taq, then yes I need to update the spreadsheet and remove the SNP listed for Bsm/Taq now because it is not the right SNP. I'll probably end up keeping Bsm and adding Taq just in case.

    All of the results on my spreadsheet were converted specifically for 23andme data and the alleles reported there. 23andme results are always reported on the plus strand as opposed to the minus strand of DNA. Some SNP's like the MTHFR ones are known as their values on the minus strand, so that's why the letters for A1298C and C677T don't match up on 23andme. For A1298C they are G or T and C677T they are AG. Is this is one of the things you are wondering about? The thing to remember is that A=T C=G. If something on the minus strand is reported as A, then in 23andme data it would be listed as a T instead.

    The + and - for risk alleles were determined by google, dbSNP and what I found in studies. I also looked at their frequency within the population. Typically (but not always) the "bad" + allele would be the more rare one in a population.

    Did I answer all of your questions? If not, let me know!! :)

    Edit: Here's a thread on 23andme that explains what the plus and minus strand means. https://www.23andme.com/you/community/thread/7106/
    roxie60 and Gestalt like this.
  8. caledonia

    caledonia

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    I have a question regarding Calico's spreadsheet and the Detoxigenomics CYP genes.

    How do you know that the ones you have listed on the spreadsheet are the correct ones that correlate to the Detoxigenomics Panel?

    23andme lists like 100 SNPs for each one. In the sample report, I saw info that would pin down the correct NATs and so forth, but not for the CYPs.
  9. kday

    kday Senior Member

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    Here is a tool that one can use to convert their 23andME results to Yasko-like presentation.

    Go here to test it out: http://71.252.248.35/

    There is more I could add to it (such as a personalized interpretation like on the Yasko analysis). And I could also save genetic data anonymously in a repository so researchers and amateur researchers could play with it.

    Note: I am not saving any genetic data on the server right now.

    Please let me know if there is any problems. I want to see if people would be interested in something like this. I will be taking it offline within the next few days probably. Just want to make sure it works. About 5 will show up blank since 23andME doesn't have the SNPs.

    I was a web developer and designer at one point in my life, but my brain has a lot of trouble these days. The version you see is barebones.
  10. caledonia

    caledonia

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    OMG you are my hero. The web based converter works great on my clunky old Mac. Too bad I already hand converted my results, but I do have another to convert. That will save me tons of time and possible errors. Love the pretty colored chart output.

    Please consider doing the Detoxigenomics SNPs too.

    Adding an analysis section would be even more awesome.

    I understand this is a lot of work, especially with brain probs, so no pressure.
  11. caledonia

    caledonia

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    Hmmm, one problem has cropped up. When I printed it, it shows up in black and white only, no colors. I just got a new color printer and it's not set to grayscale, so the problem appears to be online?
  12. kday

    kday Senior Member

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    When you print in Safari or Firefox, you have to select "print background colors" from the print dialogue. I don't think you can do this in Chrome. I am not sure about Internet Explorer as I don't have it on this system.
  13. caledonia

    caledonia

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    Kday,
    Thank you, that worked. I'm using Firefox.
  14. caledonia

    caledonia

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    A couple other things - COMT V158M rs4680 show the Alleles, but not the Result. ACAT1-02 rs 3741049 is missing. Everything else looks ok - matches my hand done results.
  15. kday

    kday Senior Member

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    Both issues should be fixed.
  16. greenshots

    greenshots Senior Member

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    please don't take this down. I have family who've done 23&me and this might be a good way for them to convert the findings. I spent hours and hours trying to do it for them a year ago and finally gave up since so many were wrong. I know people have been happy with Calico's sheet and last I heard, my doc said anyone who didn't have alotta gut issues could do 23&me and use that sheet but if this is easier, it'd really help my less then up to date relatives.
  17. caledonia

    caledonia

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    ACAT is in there now, but the COMT V158M is still not showing in the Results column.
  18. kday

    kday Senior Member

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    I think I found the problem this time Caledonia.

    And I am willing to leave this up. I just need to pay for a domain and a proper server (I don't have one). I don't have much money, so I guess I'll have to put some donate buttons or something. If donations are enough, I will be able to keep it running and perhaps have incentive to do detoxigenomics SNPs and customized reports - and of course make it look like a real website. Any other ideas are welcome.

    A tool like this could save an individual a lot of money in the long term, and avoid the technical headaches and challenge of converting things yourself.
  19. greenshots

    greenshots Senior Member

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    I had naively not even thought about the fact that it would cost you to keep it up. But I would be willing to donate and could get those relatives to do so. Even if you could keep it up for a year, it'd be great. Could you maintain something like this on a website that's already functioning? I say this because my doctor told my sister that if someone had a good conversion method, she would host it. I'm not sure what that would entail or if she really meant it but I could ask her again? I know she has other patients who can't afford the Yasko set and was interested in having something like this available. I think its really more of a liability thing so she can't stand by it but wants to have it all the same. Let me know and I'll talk to her asst, Renee.
  20. kday

    kday Senior Member

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    I am actively working on the project. I would prefer to have it on my own server. Here is what I am actively working on. I can't make it live because it's not fully functional yet, and I can not make it live from my home. I might be able to put it on my friends server who I trust with my data. I would prefer donations, but I am not sure if it's against forum rules.

    Here is what the site looks like so far. I know there are errors in text.

    You can still use the 23andMe methylation panel analysis here: http://71.252.248.35/


    [​IMG]
    Jarod likes this.

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