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Thread: A Genuine Geno 2 Mess and Mystery

  1. #1
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    A Genuine Geno 2 Mess and Mystery

    Recently I had occasion to look at someone's Geno 2 results. Full disclosure: I am not a fan of Geno 2. However I have never seen anything quite like this. The person is classified as R-Z2970, which appears to be either equivalent or below M222. However M222 itself is only shown as presumed positive, not tested positive. Z2983 and Z976, which appear above Z2970, are also shown as tested positive. Also listed as tested positive is MC14, which is parallel to DF49 rather than under it, so inconsistent with the above. DF49, DF13 and L21 are all shown as presumed positive. I know for a fact that L21 is tested in Geno 2, so why is it only presumed as opposed to tested positive? I believe M222 and at least some of the others are also tested.

    This is only the beginning. His results show he tested positive for the folllowing, all of which are below U152: CTS57193, L552, Z148 and CTS278. Yet U152 is shown as presumed negative. Again, I know U152 is tested. so why presumed negative rather than tested negative?

    There is more. He is also shown as testing positive for Z274, which is below DF27.

    More yet: he is also listed as positive for Z306, Z319 and four more SNPs under U106, which is also shown as presumed rather tested negative.

    Now I am fully aware that FTDNA's R haplotree is on life support and that some SNPs occur in more than R-1b subclade, but I've never seen anything like this before. Has anyone else?

    Does anyone know if it is possible to get a list of the SNPs which tested negative (none are listed in his results)? If so. how does one go about getting them?

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  3. #2
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    Is this Geno 2.0 Next Generation? My impression is that the test has a lot of false positives which have not yet been weeded out of the results. In consequence, perhaps, the latest transfer from Geno 2+ (as FTDNA calls it) goes in the other direction of extreme conservatism--as if rolling back to the original Geno 2.0.

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  5. #3
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    I do not believe it is the Next Generation test. However the results were only very recently tranferred to FTDNA.

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  7. #4
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    Some possibilities:
    a) significant DNA contamination (no intimate relations with other men before swabbing!)
    b) insufficient DNA (high noise-to-signal ratio)
    c) bad chip
    d) instrumentation failure
    e) data corruption

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  9. #5
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    When a transfer to FTDNA is fully successful a CSV file is included with around 13,000 SNPs. It has the allele value from the test result. So if negative it has the ancestral value and if positive it has the derived allele. I can explain this better tomorrow.

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  11. #6
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    This happend to me. I am d27 y16018 but initially nat geo had me as u152 cts278.
    This matter was just resolved but now I don't know if my regional info is wrong too?

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  13. #7
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    It is stories like this, which have cropped up from time to time over the years, albeit rarely, that make me glad I have tested with more than one company and have had my FTDNA results confirmed by BritainsDNA's Chromo2 test.

    Good to have a second opinion.
     


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    Y-DNA: R1b-FGC36981 (L21> DF13> Z39589> CTS2501> Z43690> Y8426> BY160> FGC36974>FGC36982 >FGC36981)

    Additional Data:
    Lactase Persistent:
    rs4988235 AA (13910 TT)
    rs182549 TT (22018 AA)

    Red Hair Carrier:
    Arg160Trp+ (rs1805008 T) aka R160W

    Dad's mtDNA: K1a1

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  15. #8
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    Quote Originally Posted by GoldenHind View Post
    I do not believe it is the Next Generation test. However the results were only very recently tranferred to FTDNA.
    You can tell the difference between a Geno 2.0 and a Geno 2.0 NextGen test by looking at the order history -

    Genographic 2.0 Transfer is for the regular Geno 2.0

    Genographic 2+ Transfer is for the Geno 2.0 NextGen

    I can tell by the SNPs that you have listed in the first post that the results are for Geno 2.0 NextGen. A lot of people are getting false positive results and people don't know how to find and use the CSV sheet with the test results that include ancestral alleles which are negative test results. M222 was tested and it will show what the allele result was in the CSV file.

    The Geno 2.0 NextGen CSV file can be downloaded from the myDashboard, which is the initial page when logging into an account, and below the other tests that have been performed there will be a section that says Genographic Transfer and below it the Download mtDNA SNPs as CSV | Download Y-DNA SNPs as CSV links. That is where the CSV file is with the more than 13,000 NextGen SNPs and alleles. The file in the Haplotree & SNPs page is completely different and does not include the alleles from the Geno 2.0 NextGen test. The CSV file cannot be downloaded from the Geno 2.0 NextGen site.

    The original Geno 2.0 didn't transfer the CSV file but it could be downloaded from the Geno 2.0 site.

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  17. #9
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    Does anyone here know how to create programs like the one's Felix created at http://www.y-str.org/p/tools-utilities.html or work with spreadsheets in order to convert the SNPs and alleles from the Geno 2.0 NextGen CSV file into a list of positive and negative SNPs and maybe even place them into a tree like structure?

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  19. #10
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    I'm not sure if this answers your question but when I analysed Chromo2 results for the M222 group I loaded them all into an Access database and had a table from the already known tree with a column for 'tree level' from 1 down to 8 or whatever. Then I did a join to that table and ordered it by descending tree level,and hey presto the terminal SNP comes out at the bottom.

    Mind you, C2 had the actual positive/negative call at the end. If G2+ doesn't have that you can add a compare against the reference SNP table to the query.
    Last edited by MacUalraig; 01-30-2016 at 02:55 PM.
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