PDA

View Full Version : What major L21 subclade SNPs are included in Geno 2.0?



Mikewww
07-31-2013, 12:27 PM
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?

David
07-31-2013, 02:09 PM
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

RobertCasey
07-31-2013, 03:32 PM
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 ?

David
07-31-2013, 03:47 PM
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

Mikewww
07-31-2013, 10:42 PM
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?

David
07-31-2013, 11:15 PM
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

Mikewww
08-01-2013, 01:07 PM
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.

Dubhthach
08-01-2013, 01:25 PM
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+)

rms2
08-01-2013, 01:34 PM
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.

RobertCasey
08-01-2013, 03:22 PM
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.

Mikewww
08-01-2013, 04:09 PM
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.

Per Paul and David... DF41 is probably not really a hole in Geno 2 and the holes should be considered:
DF63
DF49xDF23
Z253xL226xL1066(CTS1202)
L144.1
L1335xL1065(CTS11722)
Z251xL555xL583

I do still have concerns about missing Z251x, DF49x and Z253x as those subclades could be wider spread than we know. Z253 has been around for a while and has aggressive advocates so it is probably not as problematic of a hole as Z251x and DF49x are.

Are Z253 subclades Z2185 or Z2534 in Geno 2?

All in all, Geno 2 is not a bad thing at all, especially if you consider autosomal and mt DNA thrown in. It's price point doesn't fit every one's budget but this is similar to many things in life. One at a time acquisitions can lead to total higher costs in the long run.

jdean
08-01-2013, 05:27 PM
Per Paul and David... DF41 is probably not really a hole in Geno 2 and the holes should be considered:
DF63
DF49xDF23
Z253xL226xL1066(CTS1202)
L144.1
L1335xL1065(CTS11722)
Z251xL555xL583

I do still have concerns about missing Z251x, DF49x and Z253x as those subclades could be wider spread than we know. Z253 has been around for a while and has aggressive advocates so it is probably not as problematic of a hole as Z251x and DF49x are.

Are Z253 subclades Z2185 or Z2534 in Geno 2?

All in all, Geno 2 is not a bad thing at all, especially if you consider autosomal and mt DNA thrown in. It's price point doesn't fit every one's budget but this is similar to many things in life. One at a time acquisitions can lead to total higher costs in the long run.


Apparently FTDNA are working on Geno2.1 (or whatever they decide to call it) which is supposed to be including DF49 and the entire Z29xx series.

Quite what sort of take up we can expect after the rush for Geno2 is another matter.

WRT Rich's comment, the R-DF49 project has only picked up a couple of members via Geno2 results (which they've still failed to download). I get the impression there are a lot of people more than a little bemused with their results and the lack of an up to date haplotree at FTDNA can't be helping matters.

MJost
08-01-2013, 05:31 PM
Most have only predicted HGs or even to a major R1b SNP discovered via old testing and those guys still do NOT match a known variety that has a subclade, then Geno 2 is the only way to go as an initial SNP test for the price. Remember the old Deep Clade test and its price and what you really only got tested for? When one is found negative via either products, additional individual SNP tests will have to be suggested. The Full Y results may help refine SNP choices but Geno2 or its next generation will be on most people's radar as the next step in the discovery process to find one's Terminal SNP.

MJost