PDA

View Full Version : FTDNA R1b-L51 (xP312 xU106) SNP Pack



TigerMW
12-31-2016, 07:11 PM
I requested this a long time ago. I think several people have requested it. I'm not an expert in this branches and have had little input other than the initial request months ago.

We probably have a couple of business days to put together a request of last minute adds. However, I noticed this pack seems to have a high umber SNPs already, 146, so someone must have been busy.

Also, I see someone at FTDNA marketing listed me as a contact on this pack. I'm not the best contact. It would be the R1b Basal Subclades administrators and I will engage them if I get questions. They are probably the true sources for this set of SNPs anyway. I apologize that FTDNA lists my name. I think that is just the easy and safe out for them as I've requested they not use me unless it is a pack I'm actually driving. (L21 top-layer, L513, etc.)

R1b - L51xP312xU106 SNP Pack

Includes the following SNPs on the haplotree:
L51, P310, P311, P312, U106, CTS4528, PF7589, CTS6889, A8055, A8056, A8057, A8058, A8059, A8060, A8053, FGC37100, FGC37082, FGC37097, FGC37115, FGC37112, FGC37107, FGC37093, A8041, A8043, A8045, A8046, A8050, A8040, A8039, S1194, Y16484, Y16485, Y16742, Y16743, A8467, FGC23894, FGC23892, S23564, CTS1195, CTS7354, CTS8326, CTS10694, F4036, CTS7141, S17181, S18017, S23097, S6868, FGC23877, S15363, S24014, A8490, A8530, S1211, S1199, S1187, A8500, S1196, A8463, A8471, A8474, A8475, S14328, S11481, A8472, DF100, BY11990, Z2113, CTS5981, BY11998, FGC24107, A5922, BY11999, BY12000, BY12001, BY12004, BY12007, FGC24158, FGC24138, Y16631, Y16633, Y16634, Y16635, Y16636, Y16632, A605, A607, A610, A611, A614, A626, A636, CTS6192, CTS7416, CTS8679, BY11300, Y23483, Y23488, CTS11824, A613, P15, BY12053, BY12054, BY12055, BY12057, BY12058, A8051, A8052, FGC12521, BY11306, BY11307, BY11782

Includes the following SNPs that are NOT on the haplotree:
PF6714, CTS1276, PH1203, M10071, PF1806, Z3512, Z29844, Z29843, Z29841, Z29840, Z29839, Z29838, S8933, S819, S6863, PF7590, S1186, S1192, S1195, S1197, F1200, FGC31995, SK1562, FGC38687, CTS2484, CTS5940, Y5141, Y5142, Y5144, Y5145, Y5146, Y5149, Y5150, E207

lgmayka
12-31-2016, 08:28 PM
For someone who has already tested DF100+, is this really the best choice? Or will FTDNA soon release a more specific SNP pack for R1b-DF100?

I have attached a screenshot of what this L51 SNP Pack does and does not cover, within the DF100 clade.

Joe B
12-31-2016, 09:02 PM
Thanks Mike for the heads up. Have not had a chance to go over the new SNP pack in detail. Looks like it covers most of the clades. FTDNA has not highlighted all of the SNPs this pack covers on their tree. The SNPs will need to be cross referenced to the R1b-M269 (P312- U106-) tree at the R1b Basal Subclades project. Timing for this is not to good. Best bet will be to wait until next year so this new SNP pack can be evaluated. Should be fine for CTS4528, DF100 folks. Happy New Years everyone.
https://www.familytreedna.com/groups/r-1b-basal-subclades/about/results

TigerMW
01-01-2017, 01:48 AM
Thanks Mike for the heads up. Have not had a chance to go over the new SNP pack in detail. Looks like it covers most of the clades. FTDNA has not highlighted all of the SNPs this pack covers on their tree. The SNPs will need to be cross referenced to the R1b-M269 (P312- U106-) tree at the R1b Basal Subclades project. Timing for this is not to good. Best bet will be to wait until next year so this new SNP pack can be evaluated. Should be fine for CTS4528, DF100 folks. Happy New Years everyone.
https://www.familytreedna.com/groups/r-1b-basal-subclades/about/results

Yes, I think that S1194 (is that the one right above CTS4528?) gets the bulk of the SNPs in this pack.

Joe B
01-01-2017, 10:52 PM
I agree that that CTS4528 folks should be very happy. Hopefully it's the same for the PF7589 and CTS6889. Should be. It's good that they included a number of SNPs not on the FTDNA haplotree.

The R1b-L51 (xP312 xU106) SNP Pack has a lot of interesting potential. With the increased testing and mapping, perhaps it'll help tell us something about R-L51. Interestingly, the first order is from an Armenian. We will have to take a little extra care on recommending this test. Many people who have not tested P312, from Nat Geno or whatever, will be labeled R-P311 or R-L51. The good thing is this test has SNPs P312 and U106.

FTDNA upgraded this area of the tree recently so something was in the works. They are starting to have a good working relationship with smal. They speak the same phylogenetic language. My guess is they took that information and built a SNP Pack. After all, this is something FTDNA should be able to do with their software. Thank you Mike for promoting the concept of SNP packs. They are good to have in the testing arsenal.

TigerMW
01-03-2017, 06:59 PM
I agree that that CTS4528 folks should be very happy. Hopefully it's the same for the PF7589 and CTS6889. Should be. It's good that they included a number of SNPs not on the FTDNA haplotree.

The R1b-L51 (xP312 xU106) SNP Pack has a lot of interesting potential. With the increased testing and mapping, perhaps it'll help tell us something about R-L51. Interestingly, the first order is from an Armenian. We will have to take a little extra care on recommending this test. Many people who have not tested P312, from Nat Geno or whatever, will be labeled R-P311 or R-L51. The good thing is this test has SNPs P312 and U106.

FTDNA upgraded this area of the tree recently so something was in the works. They are starting to have a good working relationship with smal. They speak the same phylogenetic language. My guess is they took that information and built a SNP Pack. After all, this is something FTDNA should be able to do with their software. Thank you Mike for promoting the concept of SNP packs. They are good to have in the testing arsenal.

There are some new BY SNPs that I've not seen before. My guess is that Smal is working with FTDNA. I wish they would use his name rather than mine on their marketing emails. It always causes hard feelings. Believe me, I don't want any more emails. The traffic redirector business is too much in the first place. I'd rather people go right to the right source. Actually, much of the reason for R1b-YDNA forum is so people can go there and ask and multiple project admins will get a crack at answering. I appreciate the project admins participating as they do.

Joe B
01-06-2017, 06:26 PM
SNP coverage of the new R1b-L51 (xP312 xu106) SNP pack is temporarily posted to the R1b Basal subclades "Goals" page until FTDNA updates their haplotree. As with all new SNP packs, the actual tested SNPs are subject to change by FTDNA. There are many significant changes to the L51+ xU106 xP312 subgroups too. https://www.familytreedna.com/groups/r-1b-basal-subclades/about/goals

lgmayka
01-06-2017, 09:44 PM
SNP coverage of the new R1b-L51 (xP312 xu106) SNP pack is temporarily posted to the R1b Basal subclades "Goals" page until FTDNA updates their haplotree. As with all new SNP packs, the actual tested SNPs are subject to change by FTDNA. There are many significant changes to the L51+ xU106 xP312 subgroups too. https://www.familytreedna.com/groups/r-1b-basal-subclades/about/goals
If I understand that tree correctly: If someone along the Meek branch orders the SNP pack, he will end up merely S14328*. A waste of $99. Darn. I wish that the SNP pack had been designed for maximum branch coverage--e.g., one SNP for each branch--rather than many SNPs for some branches and no SNPs for others.

My suspicion is that #119582 of Poland is somewhere along the Meek branch. Or does someone else have a better prediction?

Cofgene
01-07-2017, 04:53 PM
On a side topic for this SNP pack we are wondering if anyone has collected the VCF/BED files for this region and upstream under R1b. Iain McDonald is looking for them to add to the broader R1b haplogroup age estimation project he is working on.

smal
01-08-2017, 08:22 PM
If I understand that tree correctly: If someone along the Meek branch orders the SNP pack, he will end up merely S14328*. A waste of $99. Darn. I wish that the SNP pack had been designed for maximum branch coverage--e.g., one SNP for each branch--rather than many SNPs for some branches and no SNPs for others.

My suspicion is that #119582 of Poland is somewhere along the Meek branch. Or does someone else have a better prediction?

I've asked FTDNA to include some additional markers. I hope they will realise the corrected version of the L51xP312xU106 Pack.

lgmayka
02-08-2017, 04:09 PM
My project member's order for this pack is not yet marked complete, but I think it's already gone as far as it's going to go. Kit 119582 of Poland has tested
CTS4528+
S14328+
A8467+
Y16484- Y16485- Y16742- Y16743-
S1196-
A8463- A8471- A8474- A8475-

On YFull's haplotree (https://yfull.com/tree/R-S14328/), he would end up at R-S14328*, because YFull has not yet encountered an R-A8467*.

He also has a (false?) positive for S6863.

Joe B
02-08-2017, 04:31 PM
He'll probably end up being R1b-S14328* with negative results for the downstream SNPs. A8467 and S6863 are giving false positive results says smal.

lgmayka
02-08-2017, 05:37 PM
He'll probably end up being R1b-S14328* with negative results for the downstream SNPs. A8467 and S6863 are giving false positive results says smal.
Frankly, that is the worst possible outcome--it makes the entire $99 look like a waste. :(

Joe B
02-08-2017, 08:05 PM
Frankly, that is the worst possible outcome--it makes the entire $99 look like a waste. :(On the bright side, there's potentially a new branch of R1b-CTS4528>S14328. One of the limitations to a SNP pack is the dependence on previous Big Y tests. So when there is a haplotype that diverges from the STR modal of the tests that created the FTDNA R1b-L51 (xP312 xU106) SNP Pack, it probably won't advance very far. That's what happened to the Armenian R1b-CTS4528* and the French R1b-L51>P310,P311*. That's why we have been so dependent on NGS testing for the FTDNA R1b Basal Subclades project or YFull group R1b-M343 (xP312 xU106). Let's hope the funds can be found to do a NGS for the Polish R1b-CTS4528>S14328.

lgmayka
03-07-2017, 01:42 AM
He'll probably end up being R1b-S14328* with negative results for the downstream SNPs. A8467 and S6863 are giving false positive results says smal.
FTDNA has declared his result final: A8467+ . Any administrator who disagrees would have to take up the matter with FTDNA.

smal
03-07-2017, 08:02 AM
FTDNA has declared his result final: A8467+ . Any administrator who disagrees would have to take up the matter with FTDNA.

from my letter to FTDNA, 23.02.2017

"R-S14328 subclade in FTDNA tree that is based on NGS data is divided into two subclades, R-A8469 (main) and R-A8467 (small). An analysis of bam files shows that all S14328+ kits, that are negative for A8469 (7197554 C to T), are really positive for A8467 (6444859 T to C).

However, the problem is that A8467 is not really SNP but STR, or at least SNP flanked by STR stretches. The 6444828..6444881 region has the following structure:

for S14328+ A8469+ samples
(AAACT)2(AT)8-11 AT (AC)5(AT)6

for S14328+ A8469- samples
(AAACT)2(AT)8-11 A(T-> C) (AC)5(AT)6

It looks like the NGS technique allows us to read this region correctly but I think it is not possible to create a probe for MassARRAY System that will correctly anneal near the target T/C.

Thus, if it is possible, please, remove A8467 from an interpretation of R-L51xP312xU106 Pack."

Cofgene
03-07-2017, 10:38 PM
... One of the limitations to a SNP pack is the dependence on previous Big Y tests. .....

That is only the case if the individual doing the design did not evaluate existing Genographic, Chromo2, and public genome results and include relevant ones as investigational equivalents. Inclusion of unpositioned relevant variants from those tests into the SNP as equivalents does wonders for identifying levels not accessible via BigY results. 2 weeks ago the node within a previous set of equivalent variants was confirmed at FTDNA via SNP pack. Without a proper SNP pack design we would not have identified all of those intermediate levels. 3 of the 10 levels above my results come from SNP pack and Elite/WGS/Public genome results where BigY does not have the coverage.

TigerMW
03-07-2017, 10:55 PM
That is only the case if the individual doing the design did not evaluate existing Genographic, Chromo2, and public genome results and include relevant ones as investigational equivalents. Inclusion of unpositioned relevant variants from those tests into the SNP as equivalents does wonders for identifying levels not accessible via BigY results. 2 weeks ago the node within a previous set of equivalent variants was confirmed at FTDNA via SNP pack. Without a proper SNP pack design we would not have identified all of those intermediate levels. 3 of the 10 levels above my results come from SNP pack and Elite/WGS/Public genome results where BigY does not have the coverage.
I made the original request to FTDNA for this L51 xP312 xU106 Pack. I tried to pull together information from multiple sources so it is true this pack was not just Big Y derived SNPs.
FTDNA looked at their own database and may have made updates/additions from it.
I think Smal kindly made some late requests too, and I think some of those were accommodated.

I'm pretty sure the Basal (old ht35) projects were reviewed closely. In that sense, this is really a derivative of their work with some lag time.

It's probably due for an update request to be submitted. What needs to be added? What isn't working? What hasn't added any value?

Joe B
03-08-2017, 05:55 PM
That is only the case if the individual doing the design did not evaluate existing Genographic, Chromo2, and public genome results and include relevant ones as investigational equivalents. Inclusion of unpositioned relevant variants from those tests into the SNP as equivalents does wonders for identifying levels not accessible via BigY results. 2 weeks ago the node within a previous set of equivalent variants was confirmed at FTDNA via SNP pack. Without a proper SNP pack design we would not have identified all of those intermediate levels. 3 of the 10 levels above my results come from SNP pack and Elite/WGS/Public genome results where BigY does not have the coverage.That's a good example of overcoming one of the coverage problems of Big Y with a SNP pack. After taking another look at the R1b-L51 (xP312 xU106) SNP Pack coverage on the R1b Basal Subclades haplotree, it does look like SNPs from Francalacci's Sardinian haplotypes were used at the R1b-PF7589>BY11990>PH1214/Z29840 level. My bad. The BDNA test has provided a lot of the SNPs that were BIG Y confirmed and made the SNP pack. CTS4528/S2100 for example. The major problem with the R1b-L51 (xP312 xU106) SNP Pack coverage is that is doesn't have undiscovered SNPs from Eastern Europe, the Caucasus or other regions. The R1b-L51 (xP312 xU106) clades are really rare and still ripe for SNP discovery. It's still a pretty good test for haplotypes from Western Europe.

I made the original request to FTDNA for this L51 xP312 xU106 Pack. I tried to pull together information from multiple sources so it is true this pack was not just Big Y derived SNPs.
FTDNA looked at their own database and may have made updates/additions from it.
I think Smal kindly made some late requests too, and I think some of those were accommodated.

I'm pretty sure the Basal (old ht35) projects were reviewed closely. In that sense, this is really a derivative of their work with some lag time.

It's probably due for an update request to be submitted. What needs to be added? What isn't working? What hasn't added any value? We've got an outstanding Big Y test for the Armenian R1b-CTS4528 haplotype, R1b-L51 (xP312 xU106) SNP Pack tested, that might produce a few new SNPs.

ajc347
07-01-2017, 11:03 AM
My results for this pack have shown me as being:

U106-, A8039-, CTS4528-, S1194-, FGC37100-, E207+, P312+ & S6863+

I can't find any information on E207 and YFull list S6863 as being downstream of CTS4528 / S1194.

I can't work out how this could be the case given that the results showed me as being negative for both CTS4528 & S1194, whilst being positive for P312.

I am, therefore, a tad confused as to how I should interpret the S6863+ result?

Any thoughts or advice will, as always, be gratefully received. :)

TigerMW
07-01-2017, 12:07 PM
My results for this pack have shown me as being:

U106-, A8039-, CTS4528-, S1194-, FGC37100-, E207+, P312+ & S6863+

I can't find any information on E207 and YFull list S6863 as being downstream of CTS4528 / S1194.

I can't work out how this could be the case given that the results showed me as being negative for both CTS4528 & S1194, whilst being positive for P312.

I am, therefore, a tad confused as to how I should interpret the S6863+ result?

Any thoughts or advice will, as always, be greatefully received. :)
What is your kit number? Let's have FTDNA look at it.They will rerun the test if needed.

ajc347
07-01-2017, 12:16 PM
What is your kit number? Let's have FTDNA look at it.They will rerun the test if needed.

Thanks Mike. My kit is #679121. :)

Joe B
07-01-2017, 04:22 PM
E207/Y410/GG528 is on the L51 level. The R1b Basal Subclades project haplotree has a question mark next to S6863 so I wouldn't put much stock in that SNP. Did you get any results for S14328, S1196, S6868, FGC23877, FGC23892 or FGC23894? They are the relevant SNPs downstream to CTS4528. My guess is P312+ is good. Mike can confirm the results.

ajc347
07-01-2017, 10:38 PM
Thanks Joe.

FGC23877, FGC23892, FGC23894, S1196, S14328 & S6868 were all negative.

AOK
11-13-2017, 04:45 AM
Now that's funny, nothing in that pack for me and I am my own branch 2 steps below L51. And ISOGG still has the tree wrong (pays to look beyond FTD folks).

TigerMW
11-13-2017, 05:58 AM
AOK. What SNPs are missing? We need to update the Pack. I will check with the R1b Basal project admins.

AOK
11-13-2017, 02:56 PM
Sorry, didn't mean to imply missing as in you left something out, but more like not yet discovered or not yet placed on the tree. Based on the number of SNPs in the major parallel branches downstream there should be dozens (maybe hundreds?) of SNPs that don't show up yet. Some are just private so far but may be meaningful later if more people ever test. TK found one private one for me but I'm waiting to see if it is old enough before going public. (I don't have any cousins who are interested in this stuff, but our surname project found 3 unrelated-in genealogy-timeframe lines that appeared to have a common ancestor ~3000 years ago so may be on the same as yet unidentified branch.) I'm not a FTDNA customer so this pack is only of interest to me for whatever may be learned from the results of others but so far the best it could do is identify more P311/S128* people so ISOGG will finally get the placement right.

TigerMW
11-13-2017, 03:35 PM
AOK. What SNPs are missing? We need to update the Pack. I will check with the R1b Basal project admins.


Sorry, didn't mean to imply missing as in you left something out, but more like not yet discovered or not yet placed on the tree. Based on the number of SNPs in the major parallel branches downstream there should be dozens (maybe hundreds?) of SNPs that don't show up yet. Some are just private so far but may be meaningful later if more people ever test. TK found one private one for me but I'm waiting to see if it is old enough before going public. (I don't have any cousins who are interested in this stuff, but our surname project found 3 unrelated-in genealogy-timeframe lines that appeared to have a common ancestor ~3000 years ago so may be on the same as yet unidentified branch.) I'm not a FTDNA customer so this pack is only of interest to me for whatever may be learned from the results of others but so far the best it could do is identify more P311/S128* people so ISOGG will finally get the placement right.

No problem, AOK, and no need to be sorry. I just thought there might be some new branches not covered by SNPs. We would want to submit those to FTDNA so they will make it into the pack. If so, or more like - when so, please email or post here.

By the way, this is a good reason to consider Big Y. If you were in their database you could go on-line with your Big Y Chromosome Browser and see if any one was out there that had some of your personal SNPs. You never know, and unfortunately everyone does not join a project. Big Y has about an estimated 95% share of the consumer market place so who knows what's out there?