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Question: How can I tell if new SNP is downstream or upstream?

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  • pyromatic
    replied
    Originally posted by hishy View Post
    Hi pyromatic, excellent so my understanding of this is right so far.



    How can I found out if this is false-negative or false-positive if FTDNA officially posted the results for SNP to me?

    If I test BIG-Y , and 30 novel SNPs are found, and somebody else who is 101/111 Match with me also test BIG-Y 3 months or 1 month after me, will FTDNA test him for my novel SNPs?

    In other words, will my novel SNPs be automatically registered in FTDNA to be tested for those who test BIG-Y after me?


    Regards.
    FTDNA will sequence a portion of his Y chromosome, just as they did yours. The sequence will most likely include the region containing your novel SNPs, since they've said they're targeting the most informative region of the Y. The only variable will be whether his sample has enough reads over the particular locations to give reliable calls for those SNPs.

    So if his sample has those same SNPs read as reliably as necessary, FTDNA should report them out. Now I don't know what kind of IT infrastructure will be in place for you two to sort through them. You may just have to do it by hand. Right now, joining an appropriate group with good administrators is important.

    Leave a comment:


  • Brunetmj
    replied
    In other words, will my novel SNPs be automatically registered in FTDNA to be tested for those who test BIG-Y after me?
    I cannot answer this question directly , but perhaps this indirect reply will be helpful in understanding what must be done with these novel SNP 's.

    I am part of newly discovered subclade ( discovered elsewhere). I am fortunate enough to have an extremely knowledgable subclade guru. My Big Y novel SNP's were presented to a testing company , with whom this guru has a relationship. My 52 novel SNP's were evaluated by them and it was determined that 28 of them were testable . They in turn will develop a panel for testing them and my small group has offered assistance with fees. This testing expands knowledge of this new subclade.
    So I stress joining projects and immersing yourself in your subclade blogs and groups. All of this is so very new and may take years to sort out

    Leave a comment:


  • hishy
    replied
    Hi pyromatic, excellent so my understanding of this is right so far.

    So under your scenario, we have three individuals who are V88* of which two test positive and one negative for a new SNP, which would then be downstream of V88 provided these results are reliable, i.e., no false-negatives, false-positive, unstable site prone to recurrent mutations, etc.
    How can I found out if this is false-negative or false-positive if FTDNA officially posted the results for SNP to me?

    If I test BIG-Y , and 30 novel SNPs are found, and somebody else who is 101/111 Match with me also test BIG-Y 3 months or 1 month after me, will FTDNA test him for my novel SNPs?

    In other words, will my novel SNPs be automatically registered in FTDNA to be tested for those who test BIG-Y after me?


    Regards.

    Leave a comment:


  • pyromatic
    replied
    M18 would be downstream of V88 if you can find members of the haplogroup who are V88+ M18-, others who are V88+ M18+, and none who are reliably V88- M18+.

    So under your scenario, we have three individuals who are V88* of which two test positive and one negative for a new SNP, which would then be downstream of V88 provided these results are reliable, i.e., no false-negatives, false-positive, unstable site prone to recurrent mutations, etc.

    Leave a comment:


  • Question: How can I tell if new SNP is downstream or upstream?

    Hi everyone,


    I have a question regarding Big Y results , Geno 2.0 , and any other company that provides SNP testing.

    Question 1:
    ------------
    Let's say my Haplogroup is R1 (for example), and I've tested "V88" SNP, results came positive, now I am confirmed to be R1b1c.

    After that, I tested M18, results came positive too, so the haplogroup is R1b1c1.

    So this means that V88 is upper than M18 (if we draw both SNPs as a tree).

    My question is, "Big Y" can discover lots of SNPs which are upper than V88 , lower than V88 (between V88 and M18), also lower than M18 , right? How can we tell which one is higher and which is lower?


    Question 2:
    ----------

    Let's say Person A , Person B, and Person C all tested positive for M18 .

    A new SNP , let's call it X2.

    Person A, B , C tested X2. Only person A, B were positive for X2, while C is negative.

    Does this mean that X2 is downstream SNP (under M18 on a haplotree?)

    -------


    So please somebody explain to me the way of how to know the links between SNPs and also place new discovered SNPs on the haplotree.

    Regards
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