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Thread: What major L21 subclade SNPs are included in Geno 2.0?

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    What major L21 subclade SNPs are included in Geno 2.0?

    or their equivalents?

    DF13 people have a long list of SNPs to test for so Geno 2.0 might make a lot of sense for them.

    I don't think Z251 is included, though. Which ones are?

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     rms2 (08-01-2013)

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    Quote Originally Posted by Mikewww View Post
    or their equivalents?

    DF13 people have a long list of SNPs to test for so Geno 2.0 might make a lot of sense for them.

    I don't think Z251 is included, though. Which ones are?
    Tested: L21, CTS2457 (pending), CTS2501, CTS4466, DF21, L96, L371, L513, L679 (pending), Z253, Z255
    Not Tested: DF13, DF63, DF41, DF49, L144, L195, L1335, Z251

    Note that while DF41 is not tested, CTS2501 is, and is now recognized as phylogenetically equivalent to DF41 by both the DF41 project team and ISOGG.

    Note that while L1335 is not tested, unofficially, CTS6838 is a reasonable proxy for it.

    --david
    Last edited by David; 07-31-2013 at 02:12 PM.

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    Even though, many of the sons of DF13 are not tested, major descendant SNPs are tested as well:

    L1335 has CTS11722 (equivalent of L1065) which is 90 % of L1335.
    DF49 has DF23 which is around 80 to 90 % of DF49.
    Z253 has L226 and CTS1202 (equivalent of L1066) which is over 50 % of Z253.
    Z251 has L555 & L583 which is over 50 % of Z251.

    So we have pretty good coverage of these other DF13 sons via their descendants.

    Does pending for CTS2457 and L679 mean that these are just pending new sons of DF13 that need to
    qualify via ISOGG as sons of the DF13 ?

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     rms2 (08-01-2013)

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    Quote Originally Posted by RobertCasey View Post
    Even though, many of the sons of DF13 are not tested, major descendant SNPs are tested as well:

    L1335 has CTS11722 (equivalent of L1065) which is 90 % of L1335.
    DF49 has DF23 which is around 80 to 90 % of DF49.
    Z253 has L226 and CTS1202 (equivalent of L1066) which is over 50 % of Z253.
    Z251 has L555 & L583 which is over 50 % of Z251.

    So we have pretty good coverage of these other DF13 sons via their descendants.

    Does pending for CTS2457 and L679 mean that these are just pending new sons of DF13 that need to
    qualify via ISOGG as sons of the DF13 ?
    Good point on the coverage, Robert.

    CTS2457 and L679 are very close to being added to the ISOGG tree under R-DF13. We are waiting for two individual SNP tests for CTS2457 and a Geno 2.0 test for L679. A serious DF13 tester should definitely take both into account.

    --david

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    Quote Originally Posted by David View Post
    Not Tested: DF13, DF63, DF41, DF49, L144, L195, L1335, Z251
    What about the positioning of CTS241 and Z2542 vis a vis DF13? Are they proxies?

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    Quote Originally Posted by Mikewww View Post
    What about the positioning of CTS241 and Z2542 vis a vis DF13? Are they proxies?
    CTS241 is an alternate name (synonym) for DF13.

    I just reviewed the data for Z2542. Ymap shows 29/46 positive results. Testing focus has primarily been by the DF13* folks, so we do not have data points for all the DF13 subclades (and given that all those results are expected to be positive, I've been reluctant to ask people to spend $39 in the name of "dotting the 'i' and crossing the 't'"). So no, I would not feel comfortable using Z2542 as a proxy for DF13--29 positive results for such a large group is still just a little too light on the coverage.

    --david

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    Quote Originally Posted by David View Post
    CTS241 is an alternate name (synonym) for DF13.

    I just reviewed the data for Z2542. Ymap shows 29/46 positive results. Testing focus has primarily been by the DF13* folks, so we do not have data points for all the DF13 subclades (and given that all those results are expected to be positive, I've been reluctant to ask people to spend $39 in the name of "dotting the 'i' and crossing the 't'"). So no, I would not feel comfortable using Z2542 as a proxy for DF13--29 positive results for such a large group is still just a little too light on the coverage.
    Thanks, David.

    I want to be sure to note that I would never say Geno 2.0 is the only SNP testing an L21 person will ever need.

    However, if Z2542 holds as providing good coverage (or complete coverage) for DF13, Geno 2.0 looks like a pretty good start for people who can't find strong GD & STR pattern matches* with existing subclades and haven't done much testing.

    The remaining holes in Geno 2 are:

    DF63
    DF41
    DF49xDF23
    Z253xL226xL1066(CTS1202)
    L144.1
    L1335xL1065(CTS11722)
    Z251xL555xL583

    The worst of the above are probably Z253x, DF41 and Z251x. Those are important. On the other hand, Geno 2 covers the majority of circumstances, perhaps a strong majority.

    The economics are fairly straight forward. Five a la carte advanced order SNPs at $39 each reaches the breakeven point with the cost of Geno 2. Particularly for a true DF13* person, you could burn through the cost of a Geno 2 test twice. Hence, I think a good, safe starting point is Geno 2.

    Right or wrong?

    I'm in agreement we need to push for more testing of several SNPs. I agree that Z251 is one, but I also still think DF49 in particular is undertested as well as DF13 itself.

    * Please note this whole conversation from my perspective is about people who do NOT match well with existing terminal SNPs and are kind of hanging out in "I don't know what to do" land.
    Last edited by TigerMW; 08-01-2013 at 06:25 PM.

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    Quote Originally Posted by Mikewww View Post
    The worst of the above are probably Z253x, DF41 and Z251x. Those are important. On the other hand, Geno 2 covers the majority of circumstances, perhaps a strong majority.
    As David pointed out though CTS2501 is included in the test. Obviously at the moment it's regarded as equivalent to DF41 though this may change in the future. In general we'd recommend that anyone who tests CTS2501+ (from Gen 2.0) and who doesn't belong to a known DF41+ cluster should also test for DF41.

    In sense we have been lucky in that it acts as a "proxy" for DF41 within the Geno 2.0 test.

    -Paul
    (DF41+)

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    Quote Originally Posted by Dubhthach View Post
    As David pointed out though CTS2501 is included in the test. Obviously at the moment it's regarded as equivalent to DF41 though this may change in the future. In general we'd recommend that anyone who tests CTS2501+ (from Gen 2.0) and who doesn't belong to a known DF41+ cluster should also test for DF41.

    In sense we have been lucky in that it acts as a "proxy" for DF41 within the Geno 2.0 test.

    -Paul
    (DF41+)
    I am frankly surprised at how few hits we've gotten with CTS2501 thus far . . . unless there is a silent army out there of guys who have done the Geno 2.0 thing, have a CTS2501+ result, and are just not involved, enthusiastic, or knowledgeable enough to do anything about it.

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    Quote Originally Posted by rms2 View Post
    I am frankly surprised at how few hits we've gotten with CTS2501 thus far . . . unless there is a silent army out there of guys who have done the Geno 2.0 thing, have a CTS2501+ result, and are just not involved, enthusiastic, or knowledgeable enough to do anything about it.
    We not only need to DF41+ submissions to test for CTS2501 but we also need DF13** submissions to also test occasionally as well. There always seems to be a bias for testing below the equivalent SNP (in this case DF41, only DF41+ submissions) where in reality CTS2501 has an equal chance of just being before DF41 in creation (somewhere between DF13 and DF41). Of course, that gives the DF13* submissions a lot of equivalents to test for.

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