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Kwheaton
07-29-2015, 02:10 PM
FYI
This should be good news for those that are unwilling to test outside of FTDNA---and need a lower price point than the Big Y. I am ecstatic to see that FGC22501 is included.

Dear Group Administrators,



Exciting news! If you haven’t already heard, we’re offering members of Y-haplogroup R1b the opportunity to purchase the beta release of our new R1b Backbone Panel for only $79!


Starting today, Wednesday, July 29, we’re sending notices to customers who are eligible to get in on this great deal.



We created this panel of carefully curated Y-DNA SNPs with the assistance of Mike Walsh, who is administrator of several R1b groups, including the gateway R1b and All Subclades Project.



The 140-SNP panel includes R-M343, which is above the R-M269 SNP we use to designate the R1b branch, plus 139 downstream SNPs that come from a number of testing sources and which represent the upper portion of the R1b branch of the Y-DNA haplotree. Eighty of those 140 SNPs are being newly added to the FTDNA Y tree.



Keep in mind that the R1b Backbone Panel is not meant to provide your project members with a terminal SNP. Rather, it’s designed to help identify the branch of the enormous R1b haplogroup to which those members belong, and will hopefully encourage further exploration of their ancestral origins. Even if your project member has done some preliminary SNP testing, this panel can be valuable since it includes SNPs not previously found on the tree.



This special beta price of $79 is just $1 more than the cost of testing two individual SNPs! All they have to do to order is click on the banner ad on their myFTDNA dashboard.



For those group administrators who do not routinely deal with Y-DNA SNPs and who have questions about the panel, please direct your questions to [email protected] and put “R1b Backbone Panel” on the subject line. We'll be happy to help.



Here are the SNPs included in the R1b Backbone panel:


SNPs Already on Tree


A6454

BY2896

A1773

A2150

A274

A4670

A517

BY2823

BY2868

BY575

CTS10429

CTS11567

CTS11994

CTS1751

CTS3386

CTS4466

CTS4528

CTS5330

CTS5689

CTS6937

CTS7763

DF103

DF110

DF13

DF17

DF19

DF21

DF41

DF49

DF63

DF81

DF83

DF88

DF90

DF95

DF99

F2691

F2863

FGC10516

FGC11134

FGC13620

FGC13780

FGC20761

FGC22501

FGC396

FGC5301

FGC5336

FGC5338

FGC5344

FGC5345

FGC5351

FGC5354

FGC5356

FGC5367

FGC5373

FGC5494

FGC5798

L1335

L2

L21

L23

L238

L277

L278

L371

L389

L408

L47

L48

L51

L513

L584

L617

L881

M1994

M222

M269

M335

M343

M73

MC14

P297

P310

P311

P312

PF3252

PF331

PF6610

PF6658

PF6714

PF7562

PF7589

PF7600

S1026

S1051

S11493

S11601

S12025

S1567

S16264

S1688

S18632

S18827

S6317

S7721

SRY2627

U106

U152

V88

Y5058

Z156

Z16500

Z17

Z17300

Z18

Z1862

Z195

Z198

Z209

Z2103

Z2106

Z2109

Z225

Z251

Z253

Z2542

Z255

Z2573

Z262

Z295

Z296

Z301

Z302

Z36

Z367

Z381

Z49

Z56

Z8056

Z9

haleaton
07-31-2015, 11:58 PM
Here is table summarizing the U152 subclades in the $79 (current) test, unless I missed one, in the same order as the U152 & Subclades Group tree.

Two SNPs were not publicly defined and may or may not be in U152, though they were listed next to a L2 SNP. They would be from a Big Y test where the SNP never got named. I requested SNP definition from FTDNA. My selfish hope is they are the two L2 unamed SNPs, then all of known L2 subclades would be covered.

Interesting surprise was they included many of the currently equivalent SNPs for FGC5336 et cetera. found in one FTDNA sample which Rich matched with data from the Francalacci et al 2013 Sardinian study. Perhaps the thought is these may all be very old.

One thing I do not know is whether there will be nocalls with this type of testing which I guess is different than individual SNP testing, whereas in the old Deep Clade they would keep Sanger testing until they got a reliable result.



U152 & Subclades SNP R1b Backbone Test
U152 On FTDNA Tree
L2 On FTDNA Tree < U152
Z49 On FTDNA Tree < L2
Z367 On FTDNA Tree < L2
DF103 New < L2
FGC5336 New < L2
FGC5338 New ~FGC5336
FGC5344 New ~FGC5336
FGC5345 New ~FGC5336
FGC5351 New ~FGC5336
FGC5354 New ~FGC5336
FGC5356 New ~FGC5336
FGC5367 New ~FGC5336
FGC5373 New ~FGC5336
PF7600 New ~FGC5336
FGC10516 New < L2
CTS5689 On FTDNA Tree < L2
S1567 New < L2
S18827 On FTDNA Tree < L2
DF110 New < L2
DF90 New < L2
BY2823 New < L2
7426675 etc. MISSING < L2
FGC13620 New < L2
L199 etc. MISSING [L408] < L2
L408 New < L199 < L2
FGC22501 New < L2
6182427 etc. MISSING < L2
A6454 New < L2
FGC5301 New < L2
Z36 On FTDNA Tree < U152
Z56 On FTDNA Tree < U152
PF6658 New < U152
A517 New < U152
PF6610 On FTDNA Tree < U152
A1773 New < U152
A274 New < U152
23505791 MISSING < U152
NOT PUBLICLY DEFINED (yet)
BY2895 New ?
BY2896 New ?

abds
08-02-2015, 10:22 AM
they work really bad

Z56 On FTDNA Tree < U152
this is false their tree for U152 totaly miss it and many other sub brench

haleaton
08-02-2015, 11:57 AM
they work really bad

Z56 On FTDNA Tree < U152
this is false their tree for U152 totaly miss it and many other sub brench

In the e-mail FTDNA sent out it said was Z56 was "already on tree" which may not mean the tree they make public. I did not compare it with FTDNA's current online tree which I basically ignore at this point. Point here is to compare what in test with what is known and unknown in their e-mail list.

Thanks for pointing this out. Yes, this test is not really useful if someone has already tested positive for one these top level U152 or L2 SNPs.

Of course current public FTDNA tree, last time I checked, has several other U152 & subclades SNPs that are not on this list or on the U152 & Subclades Group Tree, that presumably came from widespread GENO testing--but there is no supporting data on matches.

haleaton
08-02-2015, 12:04 PM
The following quote is from Charles Moore, U106 Project administrator and ISOGG R1b-U106 and Subclades administrator:

This is just a U152 & Subclades thread. It would be good to see similar comparisons for other clades in other places, so I will look for them elsewhere.

Don't know if there any plans by FTDNA in work for U152 SNP pack testing. Don't know what it costs to put together this sort of "Pack" test which I read was different than that just running a bunch of Sanger tests at the same time. Look forward to seeing how efforts for U106 proceed.

GTC
08-02-2015, 01:05 PM
This is just a U152 & Subclades thread

Apologies, I meant to post in U106!

haleaton
08-02-2015, 02:26 PM
One thing we just found, and your results may vary, is that Big Y named SNPs in the FTDNA results page for SNPs on the R1b Backbone list seem to be updated if you are positive for that particular SNP. So for example it now shows I am positive for FGC5301 which was found in my FGC BGI test and named by them and the name, at that time, made public in YBrowse because I had it Sanger checked at YSEQ. Other FGC named SNPs at the same tree were not included, so perhaps this one was selected because of alphabetical order.

It also says FGC5301 is on the FTDNA tree in Big Y. Also side thing is does report Z56 negative in named SNPs, but has it listed as on their Tree. So there is clearly the public tree and a tree that is referenced in Big Y or it is a typo in Big Y.

EDIT: Also notice that in the pull Shared Novel Variants down menu on the Big Y matches page, by SNP FGC5301, now appears as the name rather than the location. So perhaps a user or admin (Rich) can check BY2895 & BY2896 for the samples that were used to define the numbered SNPs in the U152 & Subclades Group tree.

Kwheaton
08-02-2015, 05:24 PM
Hal,
I would be really interested in the process they are using. I am going to check into that. If anyone knows please post.
Kelly

haleaton
08-02-2015, 05:44 PM
Hal,
I would be really interested in the process they are using. I am going to check into that. If anyone knows please post.
Kelly

Kelly, you mean the process used to test SNP Packs? Such as equipment used and method? I would like to like to get a better idea on that. Also if the YSEQ panels are just several Sanger Sequence tests and how these are different.

Kwheaton
08-02-2015, 07:39 PM
Kelly, you mean the process used to test SNP Packs? Such as equipment used and method? I would like to like to get a better idea on that. Also if the YSEQ panels are just several Sanger Sequence tests and how these are different.

Precisely! I'll post here if I turn up a reply.

Kwheaton
08-02-2015, 08:52 PM
Hal Janine posted this

I don't know what the process is, other than it's "Next Gen." I have learned, though, that no matter what process you use, there will be SNPs won't work well with it. Some SNPs that work well on the panels don't amplify individually, some that don't do well with Big Y do fine on the panels or individually..I don't think there's any method that will amplify 100% of the SNPs submitted 100% of the time.

I posted some follow ups but I am guessing this is a 2X-10X run of NGS....so it may just pick up some good stuff.

haleaton
08-03-2015, 02:39 AM
Hal Janine posted this


I posted some follow ups but I am guessing this is a 2X-10X run of NGS....so it may just pick up some good stuff.

I bet they do use the same Illumina machines and lab infrastructure which maybe be idling as the Big Y wave has passed and gone. Interesting, if so, what the coverage might be and if they will report locations other than the specific SNP list. One of the nice things about YSEQ Sanger is they evaluate all the entire locations the primers cover--same idea as WTY. So there is actually a chance for SNP discovery, though they rarely test complete newbies.

I am also trying to get some illumination on this over on FB ISOGG.

FTDNA entry page says that GENO testing can also be entry to be allowed to order the R1b Backbone test. Need to see what the new Geno Test offers. For a complete newbie it would be great to have one cheaper test that gives you mtdna, autosomal equivalent to current, and then Y Haplogroup definition enough to interest them in spending on a like costing test to learn more about Y. At least until Full Genome NGS gets down to less than 200 bucks. Then of course, once a person is tested, there is no longer any market for them as customer except in recruiting others.

True experts please chime in an tell exactly what the FTDNA SNP Pack testing is, though what FTDNA provides to customer may be a subset. :)

haleaton
08-03-2015, 03:27 AM
According to (the great) Ann Turner over on FB ISOGG:

"This is third hand information, but apparently the SNP Packs use a custom SNP chip (microarray, like the Illumina chips used for autosomal DNA). It would contain probes to check for the presence or absence of a particular allele at a particular location on the Y chromosome. Read length would be irrelavant, and there would be no hidden raw data. No-calls or ambiguous results would be a possibility if the probes don't behave as expected. That happened with 23andMe's experimental Y SNPs. For instance, some probes designed to find locations on the Y chromosome might attach to somewhat similar locations on the X."

So we may be way off. Again this is third hand. Looks like it may be a cheap small Illumina bead chip instead of going for a large, more expensive, array for which testing is about the same cost but has a much greater market segment, hence reduce the cost of consumables.

This is all speculation.

Kwheaton
08-03-2015, 03:54 AM
Hal,


This is all speculation.
Since Janine said Bennet woukd be the only one to ask...not sure what's up.
Scenario one: probes designed to test X regions of the Y will ikely give ambiguous results....so why would they do that knowing this up front????
Scenario two: this is a pilot low run NGS type test -- doesn't seem to fit Ann's explanation
Scenario three: some unknown chip test that probes more accurately???? than Sanger????

So as usual as transparent as mud!
On the other hand if FGC does some Beta testing and finds that a low coverage Y test yields a good quantity of aleardy discoverd SNPS then were talking. I want a $79 or $99 for my project members and suspected L2's that probably will pick up the majority of downstream SNPs......wishful thinking????

VinceT
08-03-2015, 04:15 AM
The tech that is actually being used is a closely guarded secret, but all clues suggest that it is similar to bead-chips, although I have seen several denials that it is a bead-chip specifically.

haleaton
08-03-2015, 04:56 AM
The tech that is actually being used is a closely guarded secret, but all clues suggest that it is similar to bead-chips, although I have seen several denials that it is a bead-chip specifically.

Thanks. So it appears nobody really publicly knows. As before, it is probably an existing customized chip product or NGS machine.

What limits it to a around hundred SNPs intrigues me, unless they are going to guarantee a firm result for each stated SNP, with some leeway as it is a beta, as was done with deep clade and then it is a reasonable limit due to the cost of retesting. I think if they state that it has the same chance of providing data on each SNP as individual orders using Sanger then it would really enhance its selling point to new testers.

Kwheaton
08-03-2015, 05:58 PM
My issue is the big draw is FGC22501. This is on the 98% X region so they either need to have developed some new process for getting this info from a chip set or it will need to be a NGS (which it does not appear to be) for it to have any value for my particular research needs.
I am compiling a list of DYS438=13 for further SNP testing.

R.Rocca
08-05-2015, 12:28 PM
My issue is the big draw is FGC22501. This is on the 98% X region so they either need to have developed some new process for getting this info from a chip set or it will need to be a NGS (which it does not appear to be) for it to have any value for my particular research needs.
I am compiling a list of DYS438=13 for further SNP testing.

The reliability of some of the SNPs will reveal themselves during the beta phase, but certainly we should expect a couple here and there to be unreliable. The one I'm most keeping my fingers crossed for is PF6658, as it is possibly the second largest subclade after L2.

Solothurn
08-12-2015, 10:46 AM
If PF6658 proves unreliable could they test the next level downstream markers instead?

Or are there too many?

R.Rocca
08-12-2015, 01:58 PM
If PF6658 proves unreliable could they test the next level downstream markers instead?

Or are there too many?

Remember that the backbone test was designed primarily for people in the R-M269 state. I think we will wind up with an additional U152+ backbone test or two U152+ tests, one for L2+ and the other for L2-. The L2- test would need to have markers downstream of PF6658/Z193.

Kwheaton
08-12-2015, 02:04 PM
Remember that the backbone test was designed primarily for people in the R-M269 state. I think we will wind up with an additional U152+ backbone test or two U152+ tests, one for L2+ and the other for L2-. The L2- test would need to have markers downstream of PF6658/Z193.

Is anyone in discussion with either or both FTDNA and/or YSEQ about developing such panels?

R.Rocca
08-12-2015, 02:08 PM
Is anyone in discussion with either or both FTDNA and/or YSEQ about developing such panels?

The admins have discussed what would make sense in the past, but want to see some results from the R1b panel tests before submitting anything to FTDNA.

Kwheaton
08-12-2015, 02:47 PM
The admins have discussed what would make sense in the past, but want to see some results from the R1b panel tests before submitting anything to FTDNA.

Thanks Rich.

R.Rocca
08-21-2015, 02:43 AM
As I feared, it looks like PF6658 was not stable enough as it is not reported on in any of the backbone test results.

haleaton
08-21-2015, 03:08 AM
As I feared, it looks like PF6658 was not stable enough as it is not reported on in any of the backbone test results.

Looks like A6454, BY2895, DF90, FGC5338, PF6658, & Z56 did not make it as reported as negatives.

The others < U152 seemed to have all been there from the list, though L2 may have come from other testing.

Overall looks like less than 10% failure rate of the 142 on list.

Kwheaton
08-22-2015, 01:21 AM
Rich,
Any word on FGC22501?
Kelly

R.Rocca
08-22-2015, 01:41 AM
Rich,
Any word on FGC22501?
Kelly

It seems to have been kept in the panel and nine of nine were FGC22501-. It would be good to verify with a known positive member of the project.

Cofgene
08-22-2015, 09:15 AM
The admins have discussed what would make sense in the past, but want to see some results from the R1b panel tests before submitting anything to FTDNA.

When creating a submission definitely look at the SNPs from publications or the Z-series SNPs within your region that are not covered by Big-Y. The panels provide an opportunity to figure out where they layer in. Testing a lot of the equivalent SNPs for some of the haplogroup blocks will provide an opportunity to layer them. Use panels to supplement results coming from Big-Y not just as a tool to place an individual onto a barebone tree.

haleaton
08-22-2015, 09:32 AM
It seems to have been kept in the panel and nine of nine were FGC22501-. It would be good to verify with a known positive member of the project.

If you go to the R1b Gateway FTDNA project SNP pages there are 128 FGC22501- results mostly outside of L2, so it is good there are no false positives. I checked the other U152 ones and it was the same. Sad that PF6658 & Z56 in particular seem not to be working.

Nobody seems to know if these SNP Packs will be modified or if it is set chip and would take money to change. If it can't be changed then there are different strategies for any proposed U152 SNP Pack as far as redundancy goes assuming some failures. Also since FGC22501 cannot be easily Sangered, and if working would be fantastic, should there be preference for SNPs that can only be NGS sequenced when they are established to be old?

[EDIT: Also I noticed DF103 & DF110 now appear on the FTDNA Y Haplotree]

Kwheaton
08-22-2015, 10:18 PM
It seems to have been kept in the panel and nine of nine were FGC22501-. It would be good to verify with a known positive member of the project.

I agree. But there are few and far between of us and not sure the $99 is worth it to prove what I suspect that everyone will be negative because it is in an unreliable region of the Y for SANGER type---we shall see...
The only two positive are 210621 WHIFFING Surrey, UK and 7Z8F5 WHEATON ENG WALES. The rest are anonymous from 1000 genomes etc. Maybe we will eventually get more.

Interestingly FGC22500 may be a better choice as it is SANGER sequenceable it is positive in HG01431 Columbia Anonymous HG02253 Peru Anonymous 7Z8F5 WHEATON ENG WALES and 45421 TRIPP Lincolnshire ENG. Rich, It might be worth checking to see if 210621 WHIFFING Surrey, UK was negative or untested.



I am holding out for the feedback on the FGC 2X and 4X Betas which is likely to give us lots more bang for the buck.

MitchellSince1893
11-14-2015, 11:53 AM
Anything new to report on a U152 backbone test for U152? Is something in the works?

Just looking through Richard's tree I counted ~130 SNPs at 1-4 levels below U152....e.g. U152>L2>Z49>Z142>Z150. If you did a L2+ test and an L2- test you might be able to get 5 levels down.

TigerMW
11-15-2015, 02:02 AM
... Nobody seems to know if these SNP Packs will be modified or if it is set chip and would take money to change...
I don't know if this was addressed but it is no longer a question mark. FTDNA Packs can be modified. Some of these packs have had multiple iterations upon their introduction, in fact, it could be almost all do. The M222 Pack just had a major refresh and is now labeled "v2". The Z255 pack had a new release to "v1.1" within the first couple of months.

haleaton
11-15-2015, 02:07 AM
This is not a question. FTDNA Packs can be modified. Some of these packs have had multiple iterations upon their introduction, in fact, it could be almost all do. The M222 Pack just had a major refresh and is now labeled "v2". The Z255 pack had a new release to "v1.1" within the first couple of months.

That was posted a long time ago when there was no info being provided. I was happy to see they are being modified! Maybe somebody will fess up and say if the technology is really programmable microarray chip-based genotyping or something else.

MitchellSince1893
11-15-2015, 04:18 AM
So what are we waiting for on the U152 side?

haleaton
11-15-2015, 06:26 AM
So what are we waiting for on the U152 side?

Anybody hear from Rocca? We can work to propose something if he is busy. I thought the Mikewww spreadsheet had some good features. Need to classify all the SNPs by combBED and ISOGG Criteria. Also get their names instead of numbers, if possible. Rich usually has the best handle on distribution from the bulk testing.

I think problem is how to choose width versus depth to maximize the most usefulness and not repeat the Backbone test. Just some random thoughts.

MitchellSince1893
11-15-2015, 11:55 AM
Anybody hear from Rocca? We can work to propose something if he is busy. I thought the Mikewww spreadsheet had some good features. Need to classify all the SNPs by combBED and ISOGG Criteria. Also get their names instead of numbers, if possible. Rich usually has the best handle on distribution from the bulk testing.

I think problem is how to choose width versus depth to maximize the most usefulness and not repeat the Backbone test. Just some random thoughts.

I would be happy to work on a proposal. We might as well do a L2+ and L2- to maximize the benefit. Do we know the true max of how many SNPs can be on a backbone test?

lgmayka
11-15-2015, 12:27 PM
Do we know the true max of how many SNPs can be on a backbone test?
The new J1-M267 v2.0 pack has 167 SNPs. Does any other SNP pack have more?

mafe
11-15-2015, 02:31 PM
Personally, I think "Big-Y" and other sequencing tests are the only way forward for the U152 group. "Geno 2.0" had a couple of important no-calls, and it seems that the "R1b Backbone Panel" also has a couple of important and unfortunate no-calls. It isn't unthinkable that other specific FTDNA panels and the new "Geno 2.0 Next Gen" test will also have the same issues. In the end, a sequencing test will turn out to be more cost effective for U152.

lgmayka
11-15-2015, 10:41 PM
Do we know the true max of how many SNPs can be on a backbone test?
The R1b-L21 SNP Pack has 178 SNPs.

MitchellSince1893
11-15-2015, 11:27 PM
Personally, I think "Big-Y" and other sequencing tests are the only way forward for the U152 group. "Geno 2.0" had a couple of important no-calls, and it seems that the "R1b Backbone Panel" also has a couple of important and unfortunate no-calls. It isn't unthinkable that other specific FTDNA panels and the new "Geno 2.0 Next Gen" test will also have the same issues. In the end, a sequencing test will turn out to be more cost effective for U152.

Ideally everyone in the U152 project would do FGC Elite 2.0, but in reality most folks aren't going to pay/can't afford to pay over $700 for a single test. In those situations a U152 backbone test would be better than nothing.

Just to get the ball rolling, for a single test one could do the following SNPs that would cover every branch on Richard Rocca's last tree going down 4 levels from U152...roughly 130 SNPs

1 Level down: L2, Z36, Z56, PF6658, A517, PF6603, 8968256(G/A), A274, 23505791(C/T)
2 levels down: Z49, Z367, FGC4183, FGC5336, FGC10516, CTS5689, S1555, S18827, DF110, DF90, BY2823, 7426675(A/C), FGC13620, L199, FGC22501, BY2895, A6454, FGC5301, PF7609, CTS5531, 13672823(C/T), FGC6411, FGC6511, S8024, 7268704(G/A), PF6634, 22087296(C/CT), 7959751(G/C), Z192, 6087904(A/T), 13407674(G/A), CTS2617, 7717741(T/C), S20550, CTS7193, 7065025(C/T), 15797586(A/G), A520, A1773, 13668489(T/C), 7162203(A/C)
3 levels down: Z142, 3251629(T/C), S8183, L20, Z33, FGC8158, FGC4166, PF7599, FGC10530, 9810615(G/A), 17983816(G/T), FGC29430, 6711888(G/A), 7283648(T/C), 2783738(A/C), FGC13616, 6812286(A/G), L408, FGC22538, 7866684(A/G), 21391079(C/T), 8203243(C/G), Z54, 17178479(G/T), 7649448(G/A), S8034, 9496327(G/A), 7950732(G/A), PF6633, CTS10851, S47, S1523, PF6652, CTS617, 8246899(G/A), 8681571(C/T), CTS11993, FGC5033, 14109630(C/A), Y6354
4 levels down: L562, Z150, FGC22963, S22778, FGC31474, Z291, Z1910, CTS9733(T/C), 3214090(A/C), 14210841(G/A), 23615856(T/A), Z35, FGC8154, S16930, BY1020, FGC10525, CTS10009, 17508781(T/C), 17651518(G/C), 6643898(A/G), FGC22516, 2889012(G/C), 7411270(T/C), CTS115, CTS8149, 5426448(G/C), 14066779(C/T), S8010, 6141128(G/T), PF6582, CTS6389, Z48, 9029206(G/A), Z194, PF6654, CTS7688, CTS36, 8816972(G/T), FGC5029, 6995659(G/A), Z10676
EDIT: 5 levels down would add ~37 more SNPs for a total of 178.

If one of the SNPs above won't work then when available, replace it with an equivalent substitute that would work with backbone technology.

MitchellSince1893
11-15-2015, 11:58 PM
The R1b-L21 SNP Pack has 178 SNPs.

EDIT my comment here was redundant..already discussed in post above and below

MitchellSince1893
11-16-2015, 12:03 AM
Anybody hear from Rocca? We can work to propose something if he is busy. I thought the Mikewww spreadsheet had some good features. Need to classify all the SNPs by combBED and ISOGG Criteria. Also get their names instead of numbers, if possible. Rich usually has the best handle on distribution from the bulk testing.

I think problem is how to choose width versus depth to maximize the most usefulness and not repeat the Backbone test. Just some random thoughts.

I didn't check the R1b backbone test to see what was repeated in my list or which ones were in the combBED area, but regardless, 5 levels down from U152 appears to be quite doable based on the comments here.

Kwheaton
11-16-2015, 12:49 AM
Ideally everyone in the U152 would do FGC Elite 2.0, but in reality most folks aren't going to pay/can't afford to pay over $700 for a single test. In those situations a U152 backbone test would be better than nothing.

Just to get the ball rolling, for a single test one could do the following SNPs that would cover every branch on Richard Rocca's last tree going down 4 levels from U152...roughly 130 SNPs

1 Level down: L2, Z36, Z56, PF6658, A517, PF6603, 8968256(G/A), A274, 23505791(C/T)
2 levels down: Z49, Z367, FGC4183, FGC5336, FGC10516, CTS5689, S1555, S18827, DF110, DF90, BY2823, 7426675(A/C), FGC13620, L199, FGC22501, BY2895, A6454, FGC5301, PF7609, CTS5531, 13672823(C/T), FGC6411, FGC6511, S8024, 7268704(G/A), PF6634, 22087296(C/CT), 7959751(G/C), Z192, 6087904(A/T), 13407674(G/A), CTS2617, 7717741(T/C), S20550, CTS7193, 7065025(C/T), 15797586(A/G), A520, A1773, 13668489(T/C), 7162203(A/C)
3 levels down: Z142, 3251629(T/C), S8183, L20, Z33, FGC8158, FGC4166, PF7599, FGC10530, 9810615(G/A), 17983816(G/T), FGC29430, 6711888(G/A), 7283648(T/C), 2783738(A/C), FGC13616, 6812286(A/G), L408, FGC22538, 7866684(A/G), 21391079(C/T), 8203243(C/G), Z54, 17178479(G/T), 7649448(G/A), S8034, 9496327(G/A), 7950732(G/A), PF6633, CTS10851, S47, S1523, PF6652, CTS617, 8246899(G/A), 8681571(C/T), CTS11993, FGC5033, 14109630(C/A), Y6354
4 levels down: L562, Z150, FGC22963, S22778, FGC31474, Z291, Z1910, CTS9733(T/C), 3214090(A/C), 14210841(G/A), 23615856(T/A), Z35, FGC8154, S16930, BY1020, FGC10525, CTS10009, 17508781(T/C), 17651518(G/C), 6643898(A/G), FGC22516, 2889012(G/C), 7411270(T/C), CTS115, CTS8149, 5426448(G/C), 14066779(C/T), S8010, 6141128(G/T), PF6582, CTS6389, Z48, 9029206(G/A), Z194, PF6654, CTS7688, CTS36, 8816972(G/T), FGC5029, 6995659(G/A), Z10676
EDIT: 5 levels down would add ~37 more SNPs for a total of 178.

If one of the SNPs above won't work then when available, replace it with an equivalent substitute that would work with backbone technology.

Mitchell how about pitching this to MikeWW? It sure would work great for my group! :)

MitchellSince1893
11-16-2015, 12:56 AM
Mitchell how about pitching this to MikeWW? It sure would work great for my group! :)

I would really like Richard to chime in on this but if he's unwilling I will.

mafe
11-16-2015, 10:05 AM
Ideally everyone in the U152 project would do FGC Elite 2.0, but in reality most folks aren't going to pay/can't afford to pay over $700 for a single test. In those situations a U152 backbone test would be better than nothing.

Just to get the ball rolling, for a single test one could do the following SNPs that would cover every branch on Richard Rocca's last tree going down 4 levels from U152...roughly 130 SNPs

1 Level down: L2, Z36, Z56, PF6658, A517, PF6603, 8968256(G/A), A274, 23505791(C/T)
2 levels down: Z49, Z367, FGC4183, FGC5336, FGC10516, CTS5689, S1555, S18827, DF110, DF90, BY2823, 7426675(A/C), FGC13620, L199, FGC22501, BY2895, A6454, FGC5301, PF7609, CTS5531, 13672823(C/T), FGC6411, FGC6511, S8024, 7268704(G/A), PF6634, 22087296(C/CT), 7959751(G/C), Z192, 6087904(A/T), 13407674(G/A), CTS2617, 7717741(T/C), S20550, CTS7193, 7065025(C/T), 15797586(A/G), A520, A1773, 13668489(T/C), 7162203(A/C)
3 levels down: Z142, 3251629(T/C), S8183, L20, Z33, FGC8158, FGC4166, PF7599, FGC10530, 9810615(G/A), 17983816(G/T), FGC29430, 6711888(G/A), 7283648(T/C), 2783738(A/C), FGC13616, 6812286(A/G), L408, FGC22538, 7866684(A/G), 21391079(C/T), 8203243(C/G), Z54, 17178479(G/T), 7649448(G/A), S8034, 9496327(G/A), 7950732(G/A), PF6633, CTS10851, S47, S1523, PF6652, CTS617, 8246899(G/A), 8681571(C/T), CTS11993, FGC5033, 14109630(C/A), Y6354
4 levels down: L562, Z150, FGC22963, S22778, FGC31474, Z291, Z1910, CTS9733(T/C), 3214090(A/C), 14210841(G/A), 23615856(T/A), Z35, FGC8154, S16930, BY1020, FGC10525, CTS10009, 17508781(T/C), 17651518(G/C), 6643898(A/G), FGC22516, 2889012(G/C), 7411270(T/C), CTS115, CTS8149, 5426448(G/C), 14066779(C/T), S8010, 6141128(G/T), PF6582, CTS6389, Z48, 9029206(G/A), Z194, PF6654, CTS7688, CTS36, 8816972(G/T), FGC5029, 6995659(G/A), Z10676
EDIT: 5 levels down would add ~37 more SNPs for a total of 178.

If one of the SNPs above won't work then when available, replace it with an equivalent substitute that would work with backbone technology.

Do we know which SNPs failed on the R1b Backbone Panel? PF6658/Z193 is definitely one of them, and if I look at the U152 project there might be some issues with L2, Z36 and Z56 aswell.

MitchellSince1893
11-16-2015, 10:49 PM
Do we know which SNPs failed on the R1b Backbone Panel? PF6658/Z193 is definitely one of them, and if I look at the U152 project there might be some issues with L2, Z36 and Z56 aswell.

I sent Richard a PM yesterday asking for his assistance and pointing him to this thread. I'm still waiting for him to respond.

R.Rocca
11-17-2015, 08:42 PM
I sent Richard a PM yesterday asking for his assistance and pointing him to this thread. I'm still waiting for him to respond.

My big issue with a U152 specific test is that, unlike some other sublades of P312, U152 is very "bushy". So, I think it may be more prudent to have U152 specific backbone tests for L2, Z36, Z56, PF6658 and "other" separately. Thoughts on this approach?

Petr
11-17-2015, 09:21 PM
Maybe I missed something, but based on Y-DNA 37 STR test, are you able to determine which of L2, Z36, Z56, PF6658 and "other" backbone tests to use?

razyn
11-17-2015, 09:44 PM
I think the question posed much earlier in this thread (2-3 months ago) has been answered, about what technology is being used for the new SNP packs. Some explanation of it was given on Sunday afternoon at the Administrators' Conference in Houston. The report on that by Jennifer Zinck has been cited elsewhere. If you scroll through her report to the paragraph beginning "Max introduced Connie Bormans, PhD and Arjan Bormans, PhD," that and the next few paragraphs describe an entirely new testing method. The url is abbreviated, as posted here -- so rather than copying it and hoping it all works, I'll just link to the Anthrogenica thread that contains the right url: http://www.anthrogenica.com/showthread.php?5827-FTDNA-Annual-Conference-2015&p=120797&viewfull=1#post120797

haleaton
11-17-2015, 11:15 PM
My big issue with a U152 specific test is that, unlike some other sublades of P312, U152 is very "bushy". So, I think it may be more prudent to have U152 specific backbone tests for L2, Z36, Z56, PF6658 and "other" separately. Thoughts on this approach?

I would agree with this, going deep one level down from U152. Only I think I might consider is including one SNP from those shallow branches that was not in or working the R1b Backbone test so that there would be an FTDNA test as a backup since they may not ever be available on individual orders or cannot be Sanger sequenced or can be tested cheaper that way.

I think this is a small number to add. However, another issue is that some branches have many many SNPs so how many to pick just one that could actually be very recent.

Other issue is there may be many more branches coming, but without NGS sequencing there is no info.

I also have not had access to GENO 2.0 Next Generation SNP listings but I read it includes a lot of SNPs found in Big Y. So maybe the thing is to wait until results come in. If a lot of new U152 > SNPs are present and working in GENO 2.0 and they keep the price reduced to $150 dollars it may be an alternative for those who want to stick within FTDNA and also pick up autosomal data if they do not have it. I forget if there is going to be transfer fee.

Rich, I understand your hesitations. Also you and Steve G. have always given the best bang for the buck advice as admins.

Kwheaton
11-17-2015, 11:39 PM
Maybe I missed something, but based on Y-DNA 37 STR test, are you able to determine which of L2, Z36, Z56, PF6658 and "other" backbone tests to use?

Rich I am all for an L2 specific Panel. Limited to L2 would allow quite deep coverage and give most everyone smoething they could be happy with. My requests for such a panel would include. * being most important
FGC22501
FGC22500
FGC22516
FGC22530
FGC22538
FGC22528
FGC22533
FGC22547
FGC22548
17278274 G/A
22319065 T/C
17914294 A/T

Thanks for considering this.
Kelly

haleaton
11-17-2015, 11:54 PM
I think the question posed much earlier in this thread (2-3 months ago) has been answered, about what technology is being used for the new SNP packs. Some explanation of it was given on Sunday afternoon at the Administrators' Conference in Houston. The report on that by Jennifer Zinck has been cited elsewhere. If you scroll through her report to the paragraph beginning "Max introduced Connie Bormans, PhD and Arjan Bormans, PhD," that and the next few paragraphs describe an entirely new testing method. The url is abbreviated, as posted here -- so rather than copying it and hoping it all works, I'll just link to the Anthrogenica thread that contains the right url: http://www.anthrogenica.com/showthread.php?5827-FTDNA-Annual-Conference-2015&p=120797&viewfull=1#post120797

Fascinating! Three primers. I wonder if this will open up SNPs that can be sequenced above two primers in Sanger. May explain why some SNPs in the Pack are working when it was said they could not be Sanger Sequenced (with two primers).

We need to give some props (kudos to my generation) to FTDNA! Also for advancing the IT department.

I did not read anything though, about potential changes to Big Y like a drop in price or expansion in coverage. It would be nice to cover all the combBED regions.

MitchellSince1893
11-18-2015, 02:06 AM
I think the question posed much earlier in this thread (2-3 months ago) has been answered, about what technology is being used for the new SNP packs. Some explanation of it was given on Sunday afternoon at the Administrators' Conference in Houston. The report on that by Jennifer Zinck has been cited elsewhere. If you scroll through her report to the paragraph beginning "Max introduced Connie Bormans, PhD and Arjan Bormans, PhD," that and the next few paragraphs describe an entirely new testing method. The url is abbreviated, as posted here -- so rather than copying it and hoping it all works, I'll just link to the Anthrogenica thread that contains the right url: http://www.anthrogenica.com/showthread.php?5827-FTDNA-Annual-Conference-2015&p=120797&viewfull=1#post120797
Here is that section

Arjans introduced the Agena MassARRAY. There are now three primers. There are the forward and reverse primer and a third primer sits very close by the SNP, right in front of it. They’re doing a single base extension so that it gets a C, G, A, or T. Basically you feed in a small single base extension product, it shoots it with a laser and small fragments come off first and larger fragments second. Each has a weight. Each single base extension has a different mass and this machine can determine the difference. The data looks like a bunch of peaks, starting at 4,500 and going all the way up to 9,000. The limitation is that you have to separate the primers by molecular weight and not cross over into another section.
So far they have created about 40 panels, which takes a large amount of vetting. All of the primers have to be able to work together to create single base reactions. They pull out the weaker ones. Once they have the whole mapping down they can’t remove one and add another. They are now trying to develop a system to help them with redesigning all of the panels.
The 40 panels are primarily for the largest haplogroups. They are created by information provided by administrators. The more information they have, the more comfortable they are moving forward. Other haplogroups covered are G, J1, J2, N, and I. Additional panels are slated for release in December. 80-100 panels to cover the existing Y-Tree.

MitchellSince1893
11-18-2015, 02:11 AM
Here is a January version of Rich's tree that may help visualize what we are talking about here

https://s-media-cache-ak0.pinimg.com/originals/a6/85/2c/a6852cd1e6e603444691643abe4f22bc.jpg

MitchellSince1893
11-18-2015, 02:14 AM
My big issue with a U152 specific test is that, unlike some other sublades of P312, U152 is very "bushy". So, I think it may be more prudent to have U152 specific backbone tests for L2, Z36, Z56, PF6658 and "other" separately. Thoughts on this approach?

So the "other" test would be the yellow, orange, red, and dark red branches on the graph above.

As mentioned before, is the objective to go wide or deep? If you go for wide, then on the L2 branch you would fill up the SNP backbone test only 1 level down from L2 (based on the number of SNPs one level down from L2 on the graph above).

My preference (based on what I currently know) would be to go deep. Get one or two reliable SNPs per branch and you could get 5 levels down.

But I'm open to others' ideas on this. I'm just throwing it out there for discussion.

MitchellSince1893
11-18-2015, 02:58 AM
Maybe I missed something, but based on Y-DNA 37 STR test, are you able to determine which of L2, Z36, Z56, PF6658 and "other" backbone tests to use?

Someone correct me if I'm wrong, but I think these proposed U152 tests (I.e. L2, Z36, Z56, PF6658, and "other") are the next step after some one has done the R1b backbone test and finds out they are U152+; or through some other source. E.g. you are L2+ from 23andme test, or you took an individual YSEQ or FTDNA SNP test.

haleaton
11-18-2015, 03:27 AM
Someone correct me if I'm wrong, but I think these proposed U152 tests (I.e. L2, Z36, Z56, PF6658, and "other") are the next step after some one has done the R1b backbone test and finds out they are U152+; or through some other source. E.g. you are L2+ from 23andme test, or you took an individual YSEQ or FTDNA SNP test.

Yes, though in some cases STR values may indicate a probability to go for a downstream test based on probability. I would think the next SNP Pack under U152 would be for those those that that think they are a downstream SNP or want to gamble and stay within FTDNA. Somebody could go one by one at YSEQ based on probabilities.

My hunch is SNP packs are for the loyal FTDNA folks willing to spend a little but not a lot. I would guess that FTDNA wants SNP packs that will attract over one hundred customers a year or more.

mafe
11-18-2015, 09:07 AM
My big issue with a U152 specific test is that, unlike some other sublades of P312, U152 is very "bushy". So, I think it may be more prudent to have U152 specific backbone tests for L2, Z36, Z56, PF6658 and "other" separately. Thoughts on this approach?

I'm not sure this is going to work for the subclades in the "other"-group. Some of these subclades can be determined by the R1b Panel, what other SNPs are there to test unless you put every novel variant known on the "Other-panel"? I can't imagine anyone ordering the "Other-panel" anyway, so FTDNA might even refuse it because of the low number of candidates.

I had good hopes for these panels but in my opinion the only way forward for U152+L2-Z36-Z56- is a sequencing test, and I'm sure it would make life much easier for the admins aswell.

smal
11-18-2015, 11:27 AM
Here is that section

Arjans introduced the Agena MassARRAY. There are now three primers. There are the forward and reverse primer and a third primer sits very close by the SNP, right in front of it. They’re doing a single base extension so that it gets a C, G, A, or T. Basically you feed in a small single base extension product, it shoots it with a laser and small fragments come off first and larger fragments second. Each has a weight. Each single base extension has a different mass and this machine can determine the difference. The data looks like a bunch of peaks, starting at 4,500 and going all the way up to 9,000. The limitation is that you have to separate the primers by molecular weight and not cross over into another section.
So far they have created about 40 panels, which takes a large amount of vetting. All of the primers have to be able to work together to create single base reactions. They pull out the weaker ones. Once they have the whole mapping down they can’t remove one and add another. They are now trying to develop a system to help them with redesigning all of the panels.

I think this is the iPLEX® Assay (http://agenabio.com/wp-content/uploads/2015/05/51-20048R2.0-iPLEX-Reagents-Brochure_WEB.pdf)

lamahorse
11-18-2015, 02:30 PM
Seems I'm still hanging out in that glorious U152* realm. :P

mafe
11-18-2015, 04:03 PM
Seems I'm still hanging out in that glorious U152* realm. :P

I thought you were in the U152>23505791 "group"?

TigerMW
11-18-2015, 04:47 PM
I've got a couple of obligations out of the way and started looking at the U152 tree this week (plus my wife is out of town so I have some time.)

I have a spreadsheet format that FTDNA is used to so I'm trying load the U152 tree (including equivalents) into the spreadsheet format.

I just started looking, but there is no doubt that L2 has to have its own pack. Keep in mind that FTDNA can have a lot of SNPs in an SNP Pack. It costs almost no extra to have a 130 SNPs in a pack versus 110, for example. On the other hand the costs of an additional product are something they want to avoid so they want to minimize the number of packs while providing good coverage. They also look at things like STR patterns. I think this is part of the reason they picked R1b-M222 as the first pack over a year ago. Besides being a large group (about a 1300 in the project) it also has a strong signature, the NW Irish Haplotype. This gives individuals multiple entry methods to decide on what pack to get.

I should point out that any of the U152 packs would not likely be called "backbone" packs. The word "backbone" is something FTDNA uses to indicate testing for the "main trunk" of the tree. I think they other more descriptive terms but they haven't listened to what I've recommended on naming things. Probably, the only "backbone" pack is the R1b-M343 Backbone SNP Pack. I think most of the rest should be called "terminal subclade" packs with some being called "top-layer and misc. subclade" packs.

haleaton
11-18-2015, 05:13 PM
I've got a couple of obligations out of the way and started looking at the U152 tree this week (plus my wife is out of town so I have some time.)

I have a spreadsheet format that FTDNA is used to so I'm trying load the U152 tree (including equivalents) into the spreadsheet format.

I just started looking, but there is no doubt that L2 has to have its own pack. Keep in mind that FTDNA can have a lot of SNPs in an SNP Pack. It costs almost no extra to have a 130 SNPs in a pack versus 110, for example. On the other hand the costs of an additional product are something they want to avoid so they want to minimize the number of packs while providing good coverage. They also look at things like STR patterns. I think this is part of the reason they picked R1b-M222 as the first pack over a year ago. Besides being a large group (about a 1300 in the project) it also has a strong signature, the NW Irish Haplotype. This gives individuals multiple entry methods to decide on what pack to get.

I should point out that any of the U152 packs would not likely be called "backbone" packs. The word "backbone" is something FTDNA uses to indicate testing for the "main trunk" of the tree. I think they other more descriptive terms but they haven't listened to what I've recommended on naming things. Probably, the only "backbone" pack is the R1b-M343 Backbone SNP Pack. I think most of the rest should be called "terminal subclade" packs with some being called "top-layer and misc. subclade" packs.

Great! I was impressed by your spreadsheet methodology including combBED. I think ISOGG guidelines can also be a consideration such as no non-Sangerable MNPs or INDELs. However Now that FTNDA has revealed the 3 primer technology using Agena MassARRAY it will be interesting to see what it can do.

Many of the numbered SNPs in the U152 & Subclades Project tree are in YBrowse with letter names. Since you have a preliminary list of GENO 2.0 SNPs hopefully with definitions many others may have names. I do wish FTDNA would publish their BY names even for singletons. It is their lab that should have the honor.

Kwheaton
11-18-2015, 08:46 PM
I tend to believe that we could get 100 L2 Tests if the cost is low. It is easier to do this in two stages M343 Backbone then a L2 backbone. Most folks like the small bites even at $99 each still a lot cheaper than the Big Y which frankly even on sale is more than lots of folks will EVER go for. So I would be for pursuing the L2 and loading it up with whatever we can---test driving it and going from there. Just look at all those L2's ripe for the picking :hungry:

Kwheaton
11-18-2015, 08:51 PM
I've got a couple of obligations out of the way and started looking at the U152 tree this week (plus my wife is out of town so I have some time.)

I have a spreadsheet format that FTDNA is used to so I'm trying load the U152 tree (including equivalents) into the spreadsheet format.

I just started looking, but there is no doubt that L2 has to have its own pack. Keep in mind that FTDNA can have a lot of SNPs in an SNP Pack. It costs almost no extra to have a 130 SNPs in a pack versus 110, for example. On the other hand the costs of an additional product are something they want to avoid so they want to minimize the number of packs while providing good coverage. They also look at things like STR patterns. I think this is part of the reason they picked R1b-M222 as the first pack over a year ago. Besides being a large group (about a 1300 in the project) it also has a strong signature, the NW Irish Haplotype. This gives individuals multiple entry methods to decide on what pack to get.

I should point out that any of the U152 packs would not likely be called "backbone" packs. The word "backbone" is something FTDNA uses to indicate testing for the "main trunk" of the tree. I think they other more descriptive terms but they haven't listened to what I've recommended on naming things. Probably, the only "backbone" pack is the R1b-M343 Backbone SNP Pack. I think most of the rest should be called "terminal subclade" packs with some being called "top-layer and misc. subclade" packs.
Mikewww
I sent some info to the [email protected] but I wonder if perhaps I can send to you or Rich directly. We have many of the Big Y novel SNPS that are already named by FGC and it would be great to get these labeled properly and moved into a SNP L2 "Explorer's" Pack. I hate the word terminal so thus my word "explorer" ;)

lamahorse
11-18-2015, 11:04 PM
I thought you were in the U152>23505791 "group"?

What is the procedure to having "23505791" made into a more catchy three alphanumeric subclade?

Huntergatherer1066
11-19-2015, 12:25 AM
What is the procedure to having "23505791" made into a more catchy three alphanumeric subclade?

If a BAM file with the relevant positive SNP is submitted to YFull or FGC, they will name it (YFS or FGC). Alternatively if it is requested to be created as an individually tested SNP at YSEQ or FTDNA it would get a A or BY name. It could also get a Z name, but I'm not as familiar with that procedure.

haleaton
11-19-2015, 01:08 AM
What is the procedure to having "23505791" made into a more catchy three alphanumeric subclade?

From U152 & Subclades tree: 23505791(C/T)

From YBrowse
Name: Z5805
Type: snp
Source: point
Position: ChrY:23505791..23505791 (+ strand)
Length: 1
allele_anc: C
allele_der: A
comment: New clade parallel to B1 & B2
count_derived: 0
count_tested: 1
isogg_haplogroup: B (not listed)
load_id: Z5805
mutation: C to A
primer_f: A7110_F
primer_r: A7110_R
ref: Ray Banks (2015)
ycc_haplogroup: B (not listed)
primary_id: 54395
gbrowse_dbid: chrY:database

Same location but different mutation. Z5805 is available from YSEQ, however it is not 23505791(C/T), though the test should be good for it. But it should have its own name which can be created by requesting it at YSEQ, though they already have primers defined.

TigerMW
11-19-2015, 05:36 PM
Mikewww
I sent some info to the [email protected] but I wonder if perhaps I can send to you or Rich directly. We have many of the Big Y novel SNPS that are already named by FGC and it would be great to get these labeled properly and moved into a SNP L2 "Explorer's" Pack. I hate the word terminal so thus my word "explorer" ;)
I've tried to indicate this elsewhere, but maybe the best thing about an SNP pack is getting the SNPs on their scoreboard which ultimately means their haplotree/haplogroup labeling and even stand-alone testing. They've stated their intentions on this but I won't repeat them because I'm still from Missouri (almost:)). Everything is always two steps forward then one back, then repeat.

What I'm saying is I can get this in front of their "Y team" and get real work done. I have a spreadsheet format they are used to and some feeling for their process steps.

Here is my look at the L2 SNPs in the experimental and draft trees. I started with Big Tree and then pulled in YFull's tree (which is tedious BTW) and then reviewed your project page tree chart. I think your project admins have encompassed everything within their work. Richard and Steve and/or whoever is helping them have been very thorough. I have YBrowse downloaded too so I populated SNP names where I found them. Don't get too hung SNP synonym usage. Where there are multiple, FTDNA will pick the one they say is first named but I've never figured out their process for that. I can't replicate it.

If I'm missing something let me know. The most likely things to miss would be some minor things from Geno 2 or Chromo 2.

https://dl.dropboxusercontent.com/u/17907527/R1b-L2-Tree-SNPs.pdf

How large are the populations of Z49 subclade and of Z367 subclade people? The general question is where do the bulk of L2 testers reside, subclade-wise?

I counted 20 major branches descending directly from L2 and just over 860 SNPs overall in L2. I included a column that shows what is found in CombBed regions. It is not always so, but coincidentally SNPs in CombBed regions are mostly likely to be accepted by FTDNA in their SNP selection process.

MitchellSince1893
11-19-2015, 05:54 PM
...How large are the populations of Z49 subclade and of Z367 subclade people? I guess general question is where do the bulk of L2 testers reside, subclade wise?

I counted 20 major branches descending directly from L2 and just over 860 SNPs overall in L2. I included a column that shows what is found in CombBed regions. It is not always so, but coincidentally SNPs in CombBed regions are mostly likely to be accepted by FTDNA in their SNP selection process.

Rich was saying back in late September the majority of R1b backbone results end up being Z49. http://www.anthrogenica.com/showthread.php?5212-R1b-SNP-Pack-did-its-job-Polish-DF110-and-DF103&p=110950#post110950


Also thank you for the work you are doing on this.

lamahorse
11-27-2015, 12:08 AM
I've requested this SNP at YSEQ. The wait begins. :)

MitchellSince1893
11-27-2015, 12:10 AM
I've requested this SNP at YSEQ. The wait begins. :)

It won't be a long wait. Mine appeared within 24 hours of my request...but today is a Holiday in the US and many folks have tomorrow off too.

MitchellSince1893
01-22-2016, 09:50 PM
I've tried to indicate this elsewhere, but maybe the best thing about an SNP pack is getting the SNPs on their scoreboard which ultimately means their haplotree/haplogroup labeling and even stand-alone testing. They've stated their intentions on this but I won't repeat them because I'm still from Missouri (almost:)). Everything is always two steps forward then one back, then repeat.

What I'm saying is I can get this in front of their "Y team" and get real work done. I have a spreadsheet format they are used to and some feeling for their process steps.

Here is my look at the L2 SNPs in the experimental and draft trees. I started with Big Tree and then pulled in YFull's tree (which is tedious BTW) and then reviewed your project page tree chart. I think your project admins have encompassed everything within their work. Richard and Steve and/or whoever is helping them have been very thorough. I have YBrowse downloaded too so I populated SNP names where I found them. Don't get too hung SNP synonym usage. Where there are multiple, FTDNA will pick the one they say is first named but I've never figured out their process for that. I can't replicate it.

If I'm missing something let me know. The most likely things to miss would be some minor things from Geno 2 or Chromo 2.

https://dl.dropboxusercontent.com/u/17907527/R1b-L2-Tree-SNPs.pdf

How large are the populations of Z49 subclade and of Z367 subclade people? The general question is where do the bulk of L2 testers reside, subclade-wise?

I counted 20 major branches descending directly from L2 and just over 860 SNPs overall in L2. I included a column that shows what is found in CombBed regions. It is not always so, but coincidentally SNPs in CombBed regions are mostly likely to be accepted by FTDNA in their SNP selection process.

Anything new to report on when SNP packs for U152 and/or L2 will be ready? I've got a couple of potential customers for this product if/when it comes out.

MitchellSince1893
03-23-2016, 05:17 PM
Anything new to report on when SNP packs for U152 and/or L2 will be ready? I've got a couple of potential customers for this product if/when it comes out.


2 months later...Anybody know the status of this?

MitchellSince1893
04-15-2016, 04:56 PM
Just got this email via R-U152 yahoo group.

I was told today that FTDNA would start releasing the first of several SNP Packs for U152.

It is a very important period once we see what the packs are and they are posted in the Advanced Tests menu (select SNP Pack and click on the name of the pack for SNP details). The reason there is some urgency now is that FTDNA has been able to do last minute adds of SNPs in the past. Once they submit the first run of orders to their lab for processing, the late adds are closed off and we are left waiting until a V2/update (months from now).

Please keep an eye on the Advanced Tests. I think this will be a series of packs and it will be obvious what's coming in the future as there will be holes or lack of coverage of some big branches in the first pack(s) of the series.

Mike W

Kwheaton
04-15-2016, 05:55 PM
Well I hope they include FGC22501, FGC22538, BY3459 and A7496:)

felipesc25
01-20-2018, 05:01 AM
Its is really interessing, i tested my grandma's brother and he is u152, it is interessing cause if i test this snp pack i could see more about her linage