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Celtarion
03-23-2014, 12:32 PM
I have created this new thread to avoid to interfere with FGC results, I think it's better to discuss in the correct thread when it is about specific SNP.


Joss, I'm using each mutation's position (rather than name) when I cross-check the results, so different names for the same SNP should not be a problem.

Here is how I see the Z2534 branches at present:
1. Z2534>Z2185 (I'm using Z2184 in the Big Y results, as it is currently phylogenetically equivalent to Z2185, which is not covered by Big Y).
2. Z2534>L226.
3. Z2534>DF73 (so far only derived in people of Iberian ancestry, and there are no known DF73+ testers in FG, Big Y or Chromo 2).
4. Z2534> four new SNPs and four new indels shared by two Big Y testers, one of whom (MacKenzie) is L643+ and the other (Whitehead) L643-; the SNPs are 6103210 A>T, 7654538 C>T, 9101775 A>G and 14049507 T>G.
5. Your own new SNPs; you are of course Z2534+.
6. New SNPs from Penaloza (Big Y), who is also Z2534+.

Since I can't see any shared new SNPs among branches 4, 5 and 6, the new SNPs should all be downstream of Z2534. However I'd prefer to confirm this with more results.

Greg H

I'm afraid that I would not have any other reference to compare with or I didn't see it. I'm still waiting for BIG Y, it might help to identify with a bit more of accuracy in general the new SNPs and might help to cross-check with other results at some stage.

Among these 50+ new SNPs, how can we determine which ones are immediately below Z2534 in a specific order? I think that I partially have the answer, by cross-checking with other results I'd say, the more people we have the more it is accurate. I suppose that the most difficult exercise is to know which ones are the most recent and which ones are the core underneath Z2534.

Joss.

hoxgi
03-27-2014, 12:35 PM
Among these 50+ new SNPs, how can we determine which ones are immediately below Z2534 in a specific order? I think that I partially have the answer, by cross-checking with other results I'd say, the more people we have the more it is accurate. I suppose that the most difficult exercise is to know which ones are the most recent and which ones are the core underneath Z2534.

Joss.

Joss, thanks for moving the thread.

I suspect that we will discover that there are groups of phylogenetically equivalent SNPs which we won't be able to separate. All we can do is compare results, using such tools as are available, like the spreadsheets maintained by Mike W, Dennis W, Alex W and others, and then recheck the raw data if something shows up.

Re the Z2534 branches in my previous post, Penaloza, who is apparently of Iberian origin, is derived for the following SNPs: Z2189, Z2190, Z2191, Z2195, Z2197, Z2198, Z2199, Z2201 and Z2202.

These are part of a larger group of SNPs, numbered consecutively from Z2187 to Z2206, found in 1000 Genomes data in two or three persons who were Z253+ DF73+. DF73 is downstream from Z2534. Penaloza is Z2534+ but DF73-.

So the above nine SNPs are positioned above DF73, and very probably between Z2534 and DF73, as they have not shown up in the results of other Z2534+ persons so far. DF73 remains a terminal SNP at this stage.

Seven of the above nine SNPs are available for a la carte testing from FTDNA. Other Z2534+ DF73- people, especially those of of Iberian ancestry, should consider testing for one or more of these SNPs.

Greg H

IrishTypeIII
04-02-2014, 07:09 AM
Perhaps the Big-Y Novel Variants (https://dl.dropboxusercontent.com/u/14028750/Z253%20BigY%20Novel.xlsx) trial tree that I have constructed for the Big-Y data is relevant.

Dennis W

Celtarion
04-14-2014, 11:36 PM
Big Y has finally arrived this evening, would be interesting to compare both Big Y and FGC.

Joss.

Dubhthach
04-15-2014, 08:26 AM
Big Y has finally arrived this evening, would be interesting to compare both Big Y and FGC.

Joss.

Make sure to give permission to Mike to share it on L21 group. Regarding comparing the two. I have a basic command script that takes the "positions" of novel SNP's in BigY and see if they show up in BigY variants.vcf file.

-Paul
(DF41+)

Celtarion
04-15-2014, 11:27 PM
Yep, it's done last night, uploaded this morning!

I got an email from Britains DNA this afternoon, I noticed that they have changed from S218 (Z253) to S868 (Z2534) which makes sense. However, I have noticed a possible mistake in the ISOGG tree as S868 has been recorded as S686, I suspect a typo...

With the change, BritainsDNA advised the following, there is not a big change in the narrative, I have highlighted what's new.

Subtype
Your subtype is R1b-S868
Your S868 subtype was recently discovered using Chromo2, so its distribution is not yet understood. It belongs to the larger S218 cluster, which - without the downstream S168 marker - includes Scottish and English representatives and, intriguingly, more Spanish than any other S145 subtype. It is too early to be certain what this means, but might indicate an Iberian connection at some point. You may carry markers that further define your subtype, but do not yet appear on our tree. You will find these in your genetic signature.

I had a look at the RAW Data, there is a good number of SNP who became "No Call", I haven't checked in details.

Regarding the maps and other features, there is no change, and their phylogenetic tree remains the same without including S868/Z2534, there may be some change at some stage during the weeks/months.

In addition, my mtDNA has been displayed this afternoon for the first time since I placed the order las october, then removed for some reason. However, I had the time to see that they have named M30 as Gange.

Joss.

hoxgi
04-17-2014, 02:12 PM
Perhaps the Big-Y Novel Variants (https://dl.dropboxusercontent.com/u/14028750/Z253%20BigY%20Novel.xlsx) trial tree that I have constructed for the Big-Y data is relevant.
Dennis W

Dennis, your spreadsheet is very helpful, as it includes FGC and Chromo 2 results as well as Big Y. Mike's Tree Discovery spreadsheet is also extremely useful. I have used these spreadsheets, your Z253 Research Tree and the Chromo 2000 public results to further review the branches of Z2534 and have re-checked the raw data and Big Y coverage where relevant.

So here is the current state of play for Z2534, based only on SNPs. My intention was to develop an SNP testing approach for people who are found to be Z2534+, which means that we need one reliable SNP per branch which is available for a la carte testing. I think the branches are as follows:

1. Z2185, which is numerically the largest branch. Z2185 appears to be phylogenetically equivalent to Z2184 and Z2182 at present. Z2185 should be the first SNP for which a Z2534+ person tests, unless he has a good STR match to one of the other branches. Z2185 is included in Big Y, but as its alias of CTS9975.

2. L226, sometimes referred to as Irish Type 3, which as far as I am aware remains a well-recognised clade on STR results at present.

3. Z2189, which leads to DF73. There are a number of SNPs which at present are phylogenetically equivalent to Z2189, but I have selected Z2189 as the marker for this branch because there are already a couple of a la carte Z2189 tests under way, one in a DF73+ person and one in a Z253+ Z2534+ DF73- person of Iberian ancestry. We already have a Big Y result which is Z2189+ DF73- in another person of Iberian ancestry, and the two DF73+ persons in the 1000 Genomes Project were Z2189+ as well. So DF73 will drop down a level if the Z2189 results are confirmed.

4. This branch is defined by four unnamed SNPs: 6103210 A>T, 7654538 C>T, 9101775 A>G and 14049507 T>G. These SNPs are shared by two Big Y kits, both of which are Z2534+ and one of which is L643+, thus dropping the position of L643 down a level.

5. Joss' branch, which I think should be defined by FGC8244+. This was found in his Full Genomes results and is also derived in one of the FGC references, HGO2771 (I'm not sure of the source of this reference, as the name doesn't fit for either the 1000 Genomes Project or the Personal Genomes Project as far as I am aware). We don't know which of his novel SNPs are private at this stage, but FGC8244 should turn out to be public in due course.

6. Kiely has his own branch at present, with over 30 novel SNPs in his Big Y results, as well as being Z2534+ and negative for the SNPs which define the other Z2534 branches. Again, there is no way to tell at present which of these SNPs are private SNPs.

7. S27687 is derived in two Z2534+ results in the Chromo 2000 speadsheet of results and negative in all other Chromo 2 results which are accessible. These two kits are negative for the other SNPs downstream from Z2534 which are included in Chromo 2. Unfortunately S27687 is not included in the Big Y coverage of the Y-chromosome.

8. CTS6458 is derived in one Z2534+ Chromo 2 result. However it appears to be a recurrent SNP, as there are four more derived results in Chromo 2 distributed across 4 other haplogroups. Despite this, it may still be useful in sorting out the branches of Z2534.

I have omitted S1984 (aka PF810) from the above analysis. It is causing confusion, as FTDNA report some results as positive (T>A), while in Chromo 2 all the Z253+ results but one are derived, leading to the conclusion that the one ancestral result represents a back-mutation (which may therefore be genealogically useful). However, S1984 has a mix of ancestral and derived results in Chromo 2 across 23 other haplogroups, including four other L21 clades. So I think this SNP is best disregarded.

Comments, criticisms and corrections are very welcome.

Greg H

hoxgi
04-17-2014, 11:11 PM
6. Kiely has his own branch at present, with over 30 novel SNPs in his Big Y results, as well as being Z2534+ and negative for the SNPs which define the other Z2534 branches. Again, there is no way to tell at present which of these SNPs are private SNPs. Greg H

Sorry, Kiely is Z2534- on checking his raw data and previous Sanger results, so branch #6 above can be deleted.

I also count five other STR spreadsheet varieties or unassigned individuals who are Z2534+ and have not fully tested for downstream SNPs yet, so there are probably more Z2534 branches out there. In terms of age, Z2534 is at least three SNP levels above L1066.1, so I would expect considerable genetic diversity in this clade.

Greg H

Celtarion
06-06-2014, 11:58 PM
Just got some results from YSEQ for my brother, hope this helps.

CTS10274 ChrY 19364376 19364376 T-
CTS10466 ChrY 19470901 19470901 A-
CTS11203 ChrY 23008875 23008875 G-
CTS11275 ChrY 23046520 23046520 C-
CTS11276 ChrY 23046558 23046558 A-
CTS11277 ChrY 23046565 23046565 G-
F2450 ChrY 17345004 17345004 C-
F2451 ChrY 17345105 17345105 T-
FGC176 ChrY 19470788 19470788 ins-
FGC4783 ChrY 21991029 21991029 A-
FGC8271 ChrY 15920155 15920155 C+
FGC8274 ChrY 17345113 17345113 T+
FGC8275 ChrY 17405431 17405431 C+
FGC8277 ChrY 18027313 18027313 C+
FGC8278 ChrY 19364222 19364222 C+
FGC8279 ChrY 19470695 19470695 G+
FGC8280 ChrY 21427307 21427307 A+
FGC8281 ChrY 21594698 21594698 A+
FGC8282 ChrY 21787055 21787055 G+
FGC8283 ChrY 21969780 21969780 T+
FGC8284 ChrY 21990905 21990905 G+
FGC8285 ChrY 22188835 22188835 T+
FGC8291 ChrY 22778392 22778392 T+
FGC8292 ChrY 23008607 23008607 A+
FGC8293 ChrY 23046478 23046478 A+
FGC8295 ChrY 23956188 23956188 A+
M10263 ChrY 21969900 21969900 G-
M2914 ChrY 17405475 17405475 C-
M3063 ChrY 23046363 23046363 G-
M6028 ChrY 22778408 22778408 C-
PF3818 ChrY 21969746 21969746 C-
S4385 ChrY 21969892 21969892 C-
S5096 ChrY 17405520 17405520 G-
S6203 ChrY 21594733 21594733 A-
Y1251 ChrY 21969940 21969940 C-
Z4382 ChrY 17405475 17405475 C-
Z5898 ChrY 21594932 21594932 G-
Z960 ChrY 23046558 23046558 A-

Huntergatherer1066
10-07-2015, 10:17 PM
I ordered BigY for my brother today, we're the other Godfreys (167477 and 304969) in the Z253 project. The third Godfrey and currect Z2534* on the Big Tree (106724) is a 60/67 match with us and disappears as a match at 111 (I think he was something like 99/111). Our paper trails going back to the 1600s do not cross and our lines are from separate parts of the USA and England so our common ancestor is far enough back that I think the comparison of our results will break up 106724's currently private SNPs. i believe that GD is also great enough to potentially qualify common SNPs as public SNPs at ISOGG. I'll make sure to get the raw data to Alex once it is available. My current Z2534* status comes from Geno 2.0 and the Z253 pack.

Huntergatherer1066
10-27-2015, 11:01 PM
My brother's BigY results came back today, still waiting on the matching and VCF components though. I've requested the BAM file and once I have all that I'll send to the Big Tree. In the meantime I'll manually compare novel variants with the other Godfrey and see what we share.

Huntergatherer1066
10-27-2015, 11:36 PM
I took a look at the unique mutations listed for 106724 on the Big Tree rated as a pass, these are the SNPs my brother shares:

6696255
6708044
7622894
8038161
8327180
9024586
9115634
14394319
14969296
15715180
16243264
16567589
17282934
17843848
17907568
18670446
18900315
19184307
20823807
21253044
21530416
21882306
21936733
22140561
22212486
22475672
22513513

My brother is negative for:

13657862
15964028
16504528
19439264
22239378
23145061

hoxgi
10-28-2015, 01:06 PM
Congratulations. We now have a new branch of Z2534. We will need to select one of the novel SNPs shared by the two Godfreys to be the lead SNP for this branch. To assist with this, perhaps you might send your BAM link to Dennis Wright (as well as Alex) for review of the raw data; Dennis has already checked the other Godfrey's BAM file and included his SNPs in his Z253 Big Y spreadsheet. There is a separate thread on the L21 section of this forum regarding having your BAM file re-analysed by Full Genomes Corp, which you might also consider.

The GD between the two Big Y Godfrey kits is enough to add this branch to the ISOGG Y-tree once we have a technically reliable, named, lead SNP. In Mike's L21+ spreadsheet, Horwill 168477 looks as though he will be on this branch as well, although he has only tested as far as L21 so far.

Huntergatherer1066
10-28-2015, 10:22 PM
Congratulations. We now have a new branch of Z2534. We will need to select one of the novel SNPs shared by the two Godfreys to be the lead SNP for this branch. To assist with this, perhaps you might send your BAM link to Dennis Wright (as well as Alex) for review of the raw data; Dennis has already checked the other Godfrey's BAM file and included his SNPs in his Z253 Big Y spreadsheet. There is a separate thread on the L21 section of this forum regarding having your BAM file re-analysed by Full Genomes Corp, which you might also consider.

The GD between the two Big Y Godfrey kits is enough to add this branch to the ISOGG Y-tree once we have a technically reliable, named, lead SNP. In Mike's L21+ spreadsheet, Horwill 168477 looks as though he will be on this branch as well, although he has only tested as far as L21 so far.

I have uploaded the zipped VCF file to the L21 Yahoo group, once the BAM file link is available I'll send that to Dennis and Alex. It would be nice to get some non-Godfreys that would branch off earlier to take BigY and break up that first block of SNPs a bit. I should note that this cluster of Godfreys is largest group in the Godfrey project, so odds are in favor of most Godfreys falling in this subclade as this one seems to have been the most prolific of the various unrelated Godfrey lines.

Celtarion
10-28-2015, 10:28 PM
This is good news! Well done :-)

Huntergatherer1066
11-16-2015, 11:18 PM
Just a quick update, I submitted my brother's BAM file to FGC, I'll keep the relevant interested parties in the loop with those results when they're ready.

Huntergatherer1066
11-28-2015, 03:09 PM
Got the FGC interpretation results back today and shared them with l21yresearch at gmail.com; my brother/167477 is QK7WM at FGC. Looking through the results I didn't see any major surprises but it will be nice to have them in the FGC database as well for comparative purposes.

Huntergatherer1066
01-19-2016, 11:47 PM
I noticed the SNPs below Z2534 identified by the Godfrey BigYs are now listed in Ybrowse, series FGC41890-FGC41919 (FGC41919 is an INDEL), plus the three recurrent but otherwise stable SNPs, YP4465 and F3590. F3590 is actually in both iterations of the Geno 2.0 chip (I'm positive for it through Geno 2.0), so I'll keep an eye out for any occurrences in Z253 members. I'm guessing it is on the newer end of the block though given that it has only turned up in the three Godfreys so far in Z253. The other location is in Haplogroup O, also very rare.

Huntergatherer1066
01-21-2016, 03:11 AM
Using the analyses done by Alex Williamson/Ytree, Dennis Wright/Z253, and FGC BAM file analysis, I created the below haplotree for my branch of Z2534. I also created a detailed comprehensive SNP list with the haplotree for this branch in an Excel file if anyone is interested in that.

http://i.imgur.com/OVVF8r0.png

Huntergatherer1066
05-06-2016, 04:36 PM
I keep forgetting to post but several SNPs from my subclade of Z2534 have been added to the new version of the FTDNA Z253 SNP Pack, hopefully we'll get a few more people besides us Godfreys. I am willing to help sponsor if need be some NGS testing when they are found. FGC41891, FGC41892, FGC41893, FGC41894, FGC41895, FGC41896, FGC41890, FGC41897, FGC41898, FGC41905, YP4465, F3590 are all included, I'm not sure if maybe a few of the newer BY SNPs added may be some of the previously unnamed ones. I'm hoping the subclade as seen Alex's Ytree will eventually be updated with the SNP names rather than just positions, they have been in Ybrowse since January. I have updated my own personal spreadsheet of the subclade adding what SNPs are available for testing where as well, if anyone wants me to send them a copy. I have also been tracking which SNPs are recurrent and where, none of the recurrent ones seem to be recurrent in a problematic way though.

TigerMW
05-06-2016, 05:28 PM
I keep forgetting to post but several SNPs from my subclade of Z2534 have been added to the new version of the FTDNA Z253 SNP Pack...
I haven't had time to check. Is version 2 of this available now?

Huntergatherer1066
05-06-2016, 05:43 PM
I haven't had time to check. Is version 2 of this available now?

Yep, here are the full details:

Includes the following SNPs on the haplotree:
Z253, Z2201, L226, FGC8244, A14, Z2185, Z2534, FGC17449, S15280, BY157, Z18132, S7898, A494, FGC3251, FGC3221, PF825.2, FGC3222, L554, FGC3268, BY312, FGC20561, FGC20562, Z17685, S846, S845, FGC20563, L1308, S856, S844, S847, BY279, DF73, BY325, FGC20566, Z17688, FGC3249, FGC3236, S7897, BY410, A16, FGC5618, FGC5626, FGC5641, FGC5642, FGC5655, FGC5656, CTS2646, Z2184

Includes the following SNPs that are NOT on the haplotree:
BY127, S933, BY4221, A1002, A1040, A1041, A1046, A1048, A1054, A17, A20, A22, A277, A4661, A4662, A4664, A495, A499, A503, BY10, BY357, BY4063, BY4064, BY4065, BY4066, BY4067, BY4068, BY4069, BY4070, BY4071, BY4072, BY4073, BY4074, BY4075, BY4076, BY4077, BY4078, BY4079, BY4080, BY4081, BY4083, BY4084, BY4085, BY4086, BY4087, BY4089, BY4090, BY4220, F3590, FGC13897, FGC17434, FGC17436, FGC17448, FGC17450, FGC20559, FGC20565, FGC20567, FGC20568, FGC20571, FGC3238, FGC3244, FGC3245, FGC3247, FGC3250, FGC3252, FGC3258, FGC3263, FGC3265, FGC41890, FGC41891, FGC41892, FGC41893, FGC41894, FGC41895, FGC41896, FGC41897, FGC41898, FGC41905, FGC8533, FGC8537, FGC8539, FGC8561, PH1119, S7879, S841, S849, S850, S853, S854, S928, S932, YP4465, Z17259, Z17692, Z18133, Z2188, Z2189, Z2190, Z2191, Z2195, Z2197, Z2204, Z252, Z29748, Z29757, ZZ5_1, ZZ6_1, BY4302, BY4303, BY4304, A1057, BY4306, BY4307, BY4308

TigerMW
05-06-2016, 08:11 PM
Yep, here are the full details:

Includes the following SNPs on the haplotree:
Z253, Z2201, L226, FGC8244, A14, Z2185, Z2534, FGC17449, S15280, BY157, Z18132, S7898, A494, FGC3251, FGC3221, PF825.2, FGC3222, L554, FGC3268, BY312, FGC20561, FGC20562, Z17685, S846, S845, FGC20563, L1308, S856, S844, S847, BY279, DF73, BY325, FGC20566, Z17688, FGC3249, FGC3236, S7897, BY410, A16, FGC5618, FGC5626, FGC5641, FGC5642, FGC5655, FGC5656, CTS2646, Z2184

Includes the following SNPs that are NOT on the haplotree:
BY127, S933, BY4221, A1002, A1040, A1041, A1046, A1048, A1054, A17, A20, A22, A277, A4661, A4662, A4664, A495, A499, A503, BY10, BY357, BY4063, BY4064, BY4065, BY4066, BY4067, BY4068, BY4069, BY4070, BY4071, BY4072, BY4073, BY4074, BY4075, BY4076, BY4077, BY4078, BY4079, BY4080, BY4081, BY4083, BY4084, BY4085, BY4086, BY4087, BY4089, BY4090, BY4220, F3590, FGC13897, FGC17434, FGC17436, FGC17448, FGC17450, FGC20559, FGC20565, FGC20567, FGC20568, FGC20571, FGC3238, FGC3244, FGC3245, FGC3247, FGC3250, FGC3252, FGC3258, FGC3263, FGC3265, FGC41890, FGC41891, FGC41892, FGC41893, FGC41894, FGC41895, FGC41896, FGC41897, FGC41898, FGC41905, FGC8533, FGC8537, FGC8539, FGC8561, PH1119, S7879, S841, S849, S850, S853, S854, S928, S932, YP4465, Z17259, Z17692, Z18133, Z2188, Z2189, Z2190, Z2191, Z2195, Z2197, Z2204, Z252, Z29748, Z29757, ZZ5_1, ZZ6_1, BY4302, BY4303, BY4304, A1057, BY4306, BY4307, BY4308

I need to double check this but I believe this version (2) is a different cut of he Z253 tree than the original. The original was intended to cover all of Z253 as it was known at the time.

For version 2, I think two major pieces were pulled out for separate packs but I have to double check. FTDNA did have a plan to do this but I told them if they did they needed to have all of the packs come out at the same time or there could be confusion.

hoxgi
05-11-2016, 06:44 AM
I need to double check this but I believe this version (2) is a different cut of he Z253 tree than the original. The original was intended to cover all of Z253 as it was known at the time.

For version 2, I think two major pieces were pulled out for separate packs but I have to double check. FTDNA did have a plan to do this but I told them if they did they needed to have all of the packs come out at the same time or there could be confusion.

Mike is correct. There will be three new SNP Pack tests covering Z253, with the current plan being to release all three at the end of the month. SNP selection has just been finalized, subject to technical considerations. One test will cover all of Z2185 and downstream SNPs, particularly L1066 and its various branches (160 SNPs). Another will cover L226. The third will cover the rest of Z253 (also 160 SNPs). FTDNA selected most of the SNPs, but some of the Z253 Project admins have been able to nominate additional SNPs; I chose 13 for the Z2185/L1066 panel, which have been added to the final list.

A few of the SNPs chosen by FTDNA are not present in the results of any members of the Z253 Project. Presumably FTDNA discovered them in the results of some Z253+ people who have not joined the Z253 Project. Therefore we do not have any idea of their positioning on the Y-tree. However FTDNA have already started adding the SNPs in these new SNP Pack tests to the FTDNA Y-tree. Some of the SNPs included are equivalent in position to other SNPs; presumably FTDNA expect that they might not remain equivalent, but may split existing branches once more people have tested.

I don't know what the price of each of these tests will be, but the concept is very good and should result in more branches and more accurate positioning of those who test.