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Thread: further testing for mutations

  1. #1
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    further testing for mutations

    I had my DNA done through 23&me.
    I opted for the basic pkg.
    My doctor asked me if I might have the MTHFR mutation that is common among Ashkenazi Jews.
    I have all my raw data. How and where do I find out about this. I dont want to spend much money and dont need to know about anything else. Thank you!

  2. #2
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    This might help. Open your raw data text file and Press ctrl + F, and see if you can find the SNPs listed.

    https://www.snpedia.com/index.php/MTHFR

    You could alternatively upload your raw data into codegen (free) and see if they give you any clues.
    Last edited by Kulin; 04-19-2019 at 12:57 AM.

  3. #3
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    thank you!

  4. #4
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    23andMe offers "Raw Data Browser" even with the ancestry service, which is lot better than the text file, so you can just check the SNP's online. The most discussed MTHFR mutation for example can be found at https://you.23andme.com/tools/data/?query=rs1801133 while logged on in 23andMe account. The other one that could be covered by "common among Ashkenazi Jews" is rs1801131. (https://www.ncbi.nlm.nih.gov/pubmed/10494095)

    Pay attention to the disclaimer "This data has undergone a general quality review; however, only a subset of markers have been individually validated for accuracy. As such, the data from 23andMe's Browse Raw Data feature is suitable only for research, educational, and informational use and not for medical, diagnostic or other use." on that page.

    The SNPedia page is useful though, providing links to much of the criticism that's been levied at the MTHFR "panic". Also see https://ghr.nlm.nih.gov/gene/MTHFR

    Note, also, that there's a thing known as "orientation". DNA consists of complementary nucleotides bound to each other, forming two "mirror" strands. Unfortunately, there's no obvious distinction over which strand you should read, and so different conventions exists. 23andMe for example lists above SNP as "A or G" but SNPedia gives it as C or T.

    The nucleotide A pairs with T, and C with G. In this case you can therefor easily tell which is which. GG on 23andMe is CC on SNPedia, AA on 23andMe is TT on SNPedia, and AG on 23andMe is TC on SNPedia (In this case, as one can see from the available alleles).

    I also recommend checking OpenSNP in this case https://opensnp.org/snps/rs1801133 (For some reason it's reallly slow right now). This gives a quick check on the plausibility and orientation of the SNP. In this case we see that the "bad" variant has baout 35% frequency in microarray DTC genetic testing, and since we get one copy from both parents, over half people have at least one "bad" copy. SNPedia has similar values, with GMAF = 0.3246 = 32%, so it looks likely that this SNP is identified correctly by the test, and this allele alone can't cause a meaningful decrease in fitness/survivability when most people have at least one copy.

    MTHFR has many known pathogenic variants https://www.ncbi.nlm.nih.gov/clinvar...%5D+pathogenic however microarray SNP tests don't generally test for very rare variants.

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