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23andme genetic testing

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

  1. LaurieL

    LaurieL Senior Member

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    Thank you for answering all of my questions. I am also hoping this will be a great value for the money. I have two tests coming. One for me, and one for my son.

    It is my understanding they also have this sale periodically throughout the year. I believe the last one was four months ago. So they should be having another say in August sometime?

    Also, reading the fine print, it basically says that whatever saliva is left over from the testing becomes their property to do what they determine. Anybody know what that may be? Had they of just come out and said what they will do with it would have made me feel a whole lot better than a vague blanket statement. Anybody else have any concerns there?

    Laurie
     
  2. LaurieL

    LaurieL Senior Member

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    For others interested in more information.

    The V2 and V3 are microarrays used in genetic testing and are what has been referred to in this thread as a chip. It is actually a microarray unit on a slide. You can see the process here.

    [video=youtube;ePFE7yg7LvM]http://www.youtube.com/watch?v=ePFE7yg7LvM[/video]

    If you are interested in more videos, http://www.youtube.com/watch?v=ePFE7yg7LvM

    Microarray as defined by Wiki:

    A microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate (usually a glass slide or silicon thin-film cell) that assays large amounts of biological material using high-throughput screening methods.

    A DNA microarray is a multiplex technology used in molecular biology. It consists of an arrayed series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing a specific DNA sequence, known as probes (or reporters).

    These can be a short section of a gene or other DNA element. These short section genes or DNA elements are detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target.

    Since an array can contain tens of thousands of probes, a microarray experiment can accomplish many genetic tests in parallel. Therefore arrays have dramatically accelerated many types of investigation.

    For more in depth information, see this link.

    http://en.wikipedia.org/wiki/DNA_microarray

    The difference between a V2 and V3 chips are in the number of SNP's that can be measured with a aparticular microarray used. Some older chips only measure 500,000 where as some newer ones can measure more.

    Laurie
     
  3. LaurieL

    LaurieL Senior Member

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  4. camas

    camas Senior Member

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    Thanks for all the links, LaurieL.

    I read everything too before deciding to fill out any of the surveys. There were a few I didn't proceed with, but I was pleased to see that the very first survey asked about CFS and FM. It's clear to me that they are trying to find a genetic link, so I am happy to participate.

    After decades with this illness I'm pleased that anyone is interested in studying us even if they are hoping a discovery will lead to a financial reward down the line.
     
    SickOfSickness likes this.
  5. drex13

    drex13 Senior Member

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    I got my 23andMe results last night. Is there a way to view all of the genetic and SMP results at once, instead of having to click on each disease or carrier trait and viewing the information seperately ?
     
  6. searcher

    searcher

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    hi drex13- if you go to "account"->"raw data" you can download all of your SNPs at the top right.
     
  7. rwac

    rwac Senior Member

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  8. drex13

    drex13 Senior Member

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    Hi searcher and rwac,
    Thanks for the help. I actually stumbled into it last night by accident, but wasn't sure how I got there as it linked from another site. But, I'm all good now. Now, I just have to figure out how to interpret the findings. It looks as though I am heterozygous on MTHFR, so I am only making methylfolate on 1/2 of the sites (?) and homozygous on MTRR , so there is a problem converting to mb12 (?). Looks like I have alot of reading to do.
     
  9. penny

    penny Senior Member

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    I got my results as well but am struggling to interpret them. I've been looking at the links rwac provided re: yasko and the links to dbsnp - hoping some pattern will emerge that will help me understand - but with little success.

    For example for the MTHFR gene, snp C677T(yasko)/rs1801133(23andme) my genotype is GG. I understand that probably means I'm homozygous but how does one know if that's homozygous in a good way or bad?

    Does anyone know how to untangle these or have any recommended reading that might help?
     
  10. penny

    penny Senior Member

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    I still don't understand this stuff but found a site which has been useful: http://www.snpedia.com/index.php/SNPedia

    It doesn't have all the snp's but for some it has a little to a lot of info, for example the one I mentioned before:
    http://www.snpedia.com/index.php/Rs1801133
    If you scroll down, there's a box on the right hand side of the window that shows a graph of the distribution of different genotypes.
    (the difference in G's versus C's seems to be related to the orientation - I don't suppose I understand this but in your 23andme page for a specific snp, if you click on the + sign next to the gene name, it will show your "dbsnp genotype" which seems to be the letters used more commonly online and in snpedia - so for this one my 23andme genotype is GG but my dbsnp genotype is CC)


    For some there are even individual pages which address a specific genotype:
    http://www.snpedia.com/index.php/Rs1801394(A;G)
    or
    http://www.snpedia.com/index.php/Rs4633(C;T)

    Sharing here in case it helps anyone else.
     
  11. camas

    camas Senior Member

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    It is complicated! I ended up downloading my raw data from 23andMe and running it through the Promethease program at SNPedia which gives you more detailed health information. It was this program that pointed out my folate issues, so I decided to continue with Rich's protocol. I was going to look into the various snps more thoroughly then got side-tracked doing genealogy since I have 650 cousin matches. :D

    ETA: Promethease does the translation for you. At 23andMe I'm AG for 1801133. The program translated it to CT and gave me this report.

    rs1801133 (C;T), Magnitude: 2, References:43 Multiple, incl 1.17x for gastric cancer, also lung cancer.

    rs1801133 is a SNP that has been studied for a relatively long time. It encodes a variant in the MTHFR gene, which encodes an enzyme involved in folate metabolism. Homozygous rs1801133(T;T) individuals have ~30% of the expected MTHFR enzyme activity, and rs1801133(C;T) heterozygotes have ~65% activity, compared to the most common genotype, rs1801133(C;C). This reduced activity has been linked at least once to each of the following disorders (though not necessarily reproducibly): coronary artery disease, migraine, autism, depression.
     
  12. penny

    penny Senior Member

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    Ah Camas! You're the best! Totally made my day, my eyes were getting seriously crosed :)

    So far mine hasn't revealed anything that I could act on but I've only given it a quick read.

    Though one thing that seemed potentially interesting (but is probably meaningless) - I have the variant for increased risk of the "aggressive form of prostate cancer"
    http://www.snpedia.com/index.php/Rs4054823 . Of course being a female, I don't have a prostate, but since xmrv in prostate cancer is also associated with the aggressive variety, maybe there's a wee bit of xmrv sensitivity here?

    Total unbridled speculation.
     
  13. camas

    camas Senior Member

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    Thanks, penny. Glad you found that helpful! I also showed an increased risk for prostate cancer although not on that particular snp. Obviously not an issue for me either, but my dad did have aggressive prostate cancer that they caught early through PSA. I wondered about an XMRV connection too.

    I think it might have been earlier in the thread (too lazy to look) that someone mentioned another cool tool which is the snptips extension you can download if your browser is Firefox. It saves you from having to constantly cross reference with 23andMe to see what your results were on any particular snp. Here's the link to that extension: http://snptips.5amsolutions.com/
     
    geesiddiqui likes this.
  14. drex13

    drex13 Senior Member

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    Apparently, SNPTips doesn't work with the latest version of Firefox 4.0.1. The site says it's coming soon, so I am unable to download it at the moment.
     
  15. drex13

    drex13 Senior Member

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    camas,
    Is there a way to enter specific specific SNP's into the Promethease program to get its' interpretation ? I'm interested in the SNP's related to methylation. I loaded my raw data from 23andMe into it. It also showed variations at MTHFR (hetero for both rs1801133 and rs1801131) for folate, but in the 23andME, I also showed +/+ (GG) on MTRR (A66G , rs1801394), which would indicate a problem making mb12 (I think), but this isn't listed on Promethease as one of the "most interesting SNP's". I just wondered if I could enter and view that particular SNP.

    I wonder if there is someone who could look this info over and do a better job of interpreting the results than me. I would like to figure out what supplements I need to take based on the results. I seem to be heterozygous for many of the methylation related genes/SNP's like COMT, MTHFR, BHMT, MTR, CBS, .
     
  16. rwac

    rwac Senior Member

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    drex13,

    you can hit "Show Everything" and then search for the SNP you want.
     
  17. camas

    camas Senior Member

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    Were you able to find the SNPs you were looking for in the report? I think there's some standardization issues in the way SNPs are reported and even Promethease doesn't know how to translate everything from 23andMe.

    I haven't been able to figure it most of it out either. I wish someone more scientifically inclined would give us a hand with this!
    :Sign Help:
     
  18. determined

    determined Senior Member

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    Can someone help me get started with Promethease? I don't understand where to click to start the wizard. I watched the videos but the wizard was already on the screen when he started.

    I apologize if this question is as silly as it seems!
     
  19. rwac

    rwac Senior Member

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    what happens when you run promethease after downloading it ?
     
  20. determined

    determined Senior Member

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    download it....?....hmmmm. I'll go back and look for something to download. Thanks!
     

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