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TigerMW
10-30-2015, 08:11 PM
Great news. I've got a spreadsheet of the SNPs covered in Geno 2.0 Next Gen. Let's be clear, that this is a fixed SNP package, not a Next Generation Sequencing test. Therefore, knowing the SNP list is critical.

I haven't had time to analyze and I don't know if I can pass it on so don't ask yet. There are just under 15,000 Y SNPs if I'm looking at this correctly.

I am hopeful. I count almost 1500 BY named SNPs and almost 1800 FGC named SNPs so they must have used the Big Y results fairly extensively in creating this test. I even saw one of my own ZW SNPs... however, the wrong one. There are ZS named SNPs and even an ZZ type.

Okay.... I get it. This is the fixed SNP package based on Next Gen discovery.

TigerMW
11-02-2015, 11:54 PM
Please note that I'm looking at this from only one perspective, that is SNPs I'm familiar with and have data and discovery history on. National Geno may have looked at academic studies, included past learning from the old Geno 2 results, etc. that I don't know about. I'm just looking at what I see from have first hand experience.

This very good news for the early Big Y testers. This is a case of the early bird gets the worm with some kind of minimum criteria. I was aware back in 2013 that Big Y would be used for research and I was hopeful that would include a future "Geno 3". It happened but its called Geno 2 Next Gen, apparently because the SNP selection on the Y side was based on Next Gen results.

I don't know the minimum/threshold but it may have just been two individuals' Big Y results sharing a common SNP that passed some other testing criteria. I could be wrong, but there appears there are some SNPs that I think are specific to surname.

It appears that SNPs that were not known from the old Geno 2 AND were outside of Big Y covered regions were not as lucky but there may be exceptions.

I can not tell (nor see any evidence) that National Geno did any special work to evaluate tree branching and ensure selection of SNPs to cover tree branching.

L21 has hit Big Y pretty hard, but I'm counting 830 SNPs that I see in Big Y results for L21 people that I think are phylogenetically consistent and exclusive to L21. These would be the kind people see on the Big Tree. I'd like to see National Genographic promote this Geno 2 Next Gen more prolifically in the Old World. We might see a few more surprises and with this many SNPs, people may get lucky hits down at the true genetic genealogy level.

haleaton
11-03-2015, 01:14 AM
Please note that I'm looking at this from only one perspective, that is SNPs I'm familiar with and have data and discovery history on. National Geno may have looked at academic studies, included past learning from the old Geno 2 results, etc. that I don't know about. I'm just looking at what I see from have first hand experience.

This very good news for the early Big Y testers. This is a case of the early bird gets the worm with some kind of minimum criteria. I was aware back in 2013 that Big Y would be used for research and I was hopeful that would include a future "Geno 3". It happened but its called Geno 2 Next Gen, apparently because the SNP selection on the Y side was based on Next Gen results.

I don't know the minimum/threshold but it may have just been two individuals' Big Y results sharing a common SNP that passed some other testing criteria. I could be wrong, but there appears there are some SNPs that I think are specific to surname.

It appears that SNPs that were not known from the old Geno 2 AND were outside of Big Y covered regions were not as lucky but there may be exceptions.

I can not tell (nor see any evidence) that National Geno did any special work to evaluate tree branching and ensure selection of SNPs to cover tree branching.

L21 has hit Big Y pretty hard, but I'm counting 830 SNPs that I see in Big Y results for L21 people that I think are phylogenetically consistent and exclusive to L21. These would be the kind people see on the Big Tree. I'd like to see National Genographic promote this Geno 2 Next Gen more prolifically in the Old World. We might see a few more surprises and with this many SNPs, people may get lucky hits down at the true genetic genealogy level.

Cool! Though is this a list of designed SNPs or from somebody's test results? There will always be failed sites. Nice thing about SNP Packs is they do seem to be able to modify them.

TigerMW
11-03-2015, 02:17 AM
Cool! Though is this a list of designed SNPs or from somebody's test results? There will always be failed sites. Nice thing about SNP Packs is they do seem to be able to modify them.
For Y DNA, I don't think Geno 2 NG is a very good substitute for Packs and Panels, and of course, real Next Generation Sequencing, i.e. Big Y, is something completely different than a fixed SNP test.

However, Geno 2 NG is a multi-purpose test with other types of DNA beyond Y so for some there may be something there. More importantly, though, National Genographic has the ability to get media attention and bring in new people that we need. That's the good news part, in my book, getting more people in and they'll be tested on our Y SNPs (the early NGS testers that is.)

Huntergatherer1066
11-03-2015, 03:40 AM
Geno 2.0 is a good option if an NGS test isn't affordable for people in some haplogroups without SNP packs yet; I'm thinking in particular of Haplogroup O, which is covered pretty extensively.

haleaton
11-03-2015, 03:54 AM
For Y DNA, I don't think Geno 2 NG is a very good substitute for Packs and Panels, and of course, real Next Generation Sequencing, i.e. Big Y, is something completely different than a fixed SNP test.

However, Geno 2 NG is a multi-purpose test with other types of DNA beyond Y so for some there may be something there. More importantly, though, National Genographic has the ability to get media attention and bring in new people that we need. That's the good news part, in my book, getting more people in and they'll be tested on our Y SNPs (the early NGS testers that is.)

I agree, but Geno 2.0 NG may help feed in interested people with enough haplogroup definition to order appropriate SNP Pack. I still wonder if FTDNA will allow transfers to join group projects based on SNP pages without having STRs.

TigerMW
11-03-2015, 04:18 AM
I agree, but Geno 2.0 NG may help feed in interested people with enough haplogroup definition to order appropriate SNP Pack.
Yes, that's what I was trying to say, "More importantly... National Genographic has the ability to ... bring in new people that we need."

Also, I agree that it will help in directing to a pack and in some causes skip pack testing altogether. If you a Geno 2 NG tester hits upon an early Big Y tester (a subclade forming pair), then they may be able to skip pack testing altogether.

The problem is the tree coverage. It's going to be very deep in some places, not too deep in others. It just depends so it is hit or miss.


I still wonder if FTDNA will allow transfers to join group projects based on SNP pages without having STRs.
I don't see why any of this would cause them to change their policy on the STR requirement. I'd just like to see them make 37 STRs very cheap. I think part of the problem is their business model on this. It must be expensive to support the IT expenses of the project system and it appears they use the STRs as the "entry price" into the system. The alternative is they could charge us an annual fee to be in projects - not my favorite solution.

haleaton
11-03-2015, 04:46 AM
" ...
I don't see why any of this would cause them to change their policy on the STR requirement. I'd just like to see them make 37 STRs very cheap. I think part of the problem is their business model on this. It must be expensive to support the IT expenses of the project system and it appears they use the STRs as the "entry price" into the system. The alternative is they could charge us an annual fee to be in projects - not my favorite solution.

Good points. They will need additional new customers to avoid subscription fee, because once you get to the point where I am, with Full Genomes Corp testing, there is nothing more to test me for--unless there is new technology that increases Y coverage. They also do not seem interested in individual SNP tests much.

The nice thing about STR FTDNA pages is admins still can use SNP data from other sources to group, if grouping could be added to the SNP pages, then it might be a plus for them.

What will be interesting about GENO is how much it can be marketed in areas that are undersampled.

C.Goodell
11-06-2015, 02:24 PM
Have any of these made it to the Geno NG chip? In I1 Downstream of z74

7549521 Consensus allele: C Reference allele: G Named FGC12551 found in 4 big y kits

Downstream of Cts2208 (Not found in L287 )

6834008 Consensus allele: A Reference allele: G Named FGC12553 found in 2 Big Y Kits
8885613 Consensus allele: T Reference allele: C Named FGC12554 found in 2 Big Y Kits
8885761 Consensus allele: T Reference allele: C Named FGC12555 found in 2 Big Y Kits
15614381 Consensus allele: G Reference allele: T Named FGC12557 found in 2 Big Y Kits
16402552 Consensus allele: A Reference allele: G Named FGC12558 found in 2 Big Y Kits
16475648 Consensus allele: T Reference allele: C Named FGC12559 found in 2 Big Y Kits
17113406 Consensus allele: G Reference allele: C Named FGC12560 found in 2 Big Y Kits
18608123 Consensus allele: G Reference allele: A Named FGC12561 found in 2 Big Y kits
19318850 Consensus allele: C Reference allele: T Named FGC12562 found in 2 Big Y Kits
22302920 Consensus allele: A Reference allele: T Named FGC12563 found in 2 Big Y Kits
23613999 Consensus allele: C Reference allele: T Named FGC12564 found in 2 Big Y Kits

If you can , let me know if yes and if more then 1. It would be appreciated.

TigerMW
11-06-2015, 03:38 PM
Have any of these made it to the Geno NG chip? In I1 Downstream of z74...

If you can , let me know if yes and if more then 1. It would be appreciated.
I am not forwarding the spreadsheet on at this point. I'm not sure if it is official and I could easily see some SNPs drop out of it. National Geno should release it directly and I'm hopeful this will happen at the upcoming FTDNA conference where Dr. Spencer Wells will speak. If you know anyone going you should ask them to place the request if they don't volunteer it.

VinceT
11-06-2015, 04:16 PM
I am not forwarding the spreadsheet on at this point. I'm not sure if it is official and I could easily see some SNPs drop out of it. National Geno should release it directly and I'm hopeful this will happen at the upcoming FTDNA conference where Dr. Spencer Wells will speak. If you know anyone going you should ask them to place the request if they don't volunteer it.
Spencer Wells resigned as Director of the Genographic Project in mid-August. It's curious that FTDNA has scheduled him to talk about Geno 2 Next-Gen at the upcoming FTDNA conference!

https://twitter.com/spwells/status/632591995752587264
(https://twitter.com/spwells/status/632591995752587264)

But I wouldn't mind seeing a copy of that spreadsheet myself.

Heber
11-10-2015, 08:49 AM
I have received my Geno 2.0 Next Gen kit in the post this morning. Although I strictly do not need it as I have done NGS testing, I would like to benchmark it against Geno 2.0 and other products. I see it as a good test for new testers. They can transfer results to FTDNA and upgrade to panels or NGS at a later date if required.
I should get results ten weeks after mailing back the sample. I will post my results when I get them.
Genographic tested in Mayo and Asturias using what appeared to be a discovery chip so I would expect good coverage of M222 and DF27 which had high frequency in those projects.

MacUalraig
11-14-2015, 09:02 AM
TIA, TIA

paulgill
11-14-2015, 09:50 AM
I have received my Geno 2.0 Next Gen kit in the post this morning. Although I strictly do not need it as I have done NGS testing, I would like to benchmark it against Geno 2.0 and other products. I see it as a good test for new testers. They can transfer results to FTDNA and upgrade to panels or NGS at a later date if required.
I should get results ten weeks after mailing back the sample. I will post my results when I get them.,
Genographic tested in Mayo and Asturias using what appeared to be a discovery chip so I would expect good coverage of M222 and DF27 which had high frequency in those projects.

I think if you don't need it then you can donate it, your friend, a relative etc.

Cofgene
11-14-2015, 06:29 PM
Please note that I'm looking at this from only one perspective, that is SNPs I'm familiar with and have data and discovery history on. National Geno may have looked at academic studies, included past learning from the old Geno 2 results, etc. that I don't know about. I'm just looking at what I see from have first hand experience.

This very good news for the early Big Y testers. This is a case of the early bird gets the worm with some kind of minimum criteria. I was aware back in 2013 that Big Y would be used for research and I was hopeful that would include a future "Geno 3". It happened but its called Geno 2 Next Gen, apparently because the SNP selection on the Y side was based on Next Gen results.

I don't know the minimum/threshold but it may have just been two individuals' Big Y results sharing a common SNP that passed some other testing criteria. I could be wrong, but there appears there are some SNPs that I think are specific to surname.

It appears that SNPs that were not known from the old Geno 2 AND were outside of Big Y covered regions were not as lucky but there may be exceptions.

I can not tell (nor see any evidence) that National Geno did any special work to evaluate tree branching and ensure selection of SNPs to cover tree branching.

L21 has hit Big Y pretty hard, but I'm counting 830 SNPs that I see in Big Y results for L21 people that I think are phylogenetically consistent and exclusive to L21. These would be the kind people see on the Big Tree. I'd like to see National Genographic promote this Geno 2 Next Gen more prolifically in the Old World. We might see a few more surprises and with this many SNPs, people may get lucky hits down at the true genetic genealogy level.


Darn! I'm counting only 290 for U106.

Kwheaton
11-14-2015, 09:46 PM
FYI Debbie Kennett tweeted; "Heard from another source Geno 2.0 price reduced to $149. 17,000 Y SNPs and 750,000 atDNA SNP"
And several tweeters form the FTDNA conference gave they same info sans price.

TigerMW
11-15-2015, 01:13 AM
Darn! I'm counting only 290 for U106.
I think the reason why L21 has over 800 is that the L21 guys have been very aggressive at Big Y testing from the git-go. A key is that you have more than one person in your cluster doing Big Y testing. That is how new, pertinent public subclades are identified. As near as I can tell, National Genographic had some kind of minimum number of individuals found derived. In L21, we have quite a few surname groups that were very aggressive with multiple testers. It's paying off for them. I wasn't that successful as there is only one other guy (surname variant of mine) that have our SNP that is probably about 350 years old. However, we have a third guy with an SNP that only the three of share. I think it is about 500 or 600 years old. That SNP made the cut. I don't know what the Geno 2 NG SNP criteria is. They may be looking at other data too, well, certainly they would have looked at Geno 2 results.

How does 290 for U106 compare with the old Geno 2 or Chromo 2? I think Geno 2 NG is big step forward but it will always suffer the fate of fixed SNP panels.

Heber
11-15-2015, 02:52 PM
Darn! I'm counting only 290 for U106.

We are lucky to have Mike Walsh and Alex Williamson and all the hard working L21 Admins in our corner.:).

VinceT
11-15-2015, 03:20 PM
I think the reason why L21 has over 800 is that the L21 guys have been very aggressive at Big Y testing from the git-go. A key is that you have more than one person in your cluster doing Big Y testing. That is how new, pertinent public subclades are identified. As near as I can tell, National Genographic had some kind of minimum number of individuals found derived. In L21, we have quite a few surname groups that were very aggressive with multiple testers. It's paying off for them. I wasn't that successful as there is only one other guy (surname variant of mine) that have our SNP that is probably about 350 years old. However, we have a third guy with an SNP that only the three of share. I think it is about 500 or 600 years old. That SNP made the cut. I don't know what the Geno 2 NG SNP criteria is. They may be looking at other data too, well, certainly they would have looked at Geno 2 results.

So, it's safe to say that Geno2 Next-Gen inherited the affluent/UK/Irish/American bias in FTDNA's customer base? ;)

lgmayka
11-15-2015, 07:21 PM
According to Jennifer Zinck's blog post (http://www.ancestorcentral.com/11th-international-conference-on-genetic-genealogy/):
---
They took off some Y markers that were repetitive and added new ones, to bring the total to about 17,000.
...
The price is $149.95 with free shipping and handling, which they believe to be competitive.
...
The Y-chromosome DNA has about 8,000 new SNPs, many of which we are still placing on the tree.
...
The list of new Y-SNPs can be made available but they are still testing some. They are about 90% done.
...
They attempted to put all Big Y SNPs that didnít appear to be singleton, that appear to be cladistically significant. onto the chip.
...
The Big Y SNPs that were harvested and put on the chip are available only through Big Y or this new product.
...
Is the $149 permanent or is it a sale price for Geno 2.0 Next Gen? He is not sure but it will likely be there through the holidays.
...
Of the 17,000 Y-SNPs on the Geno 2.0, does that represent some kind of 80/20 compromise vs. the Big Y at 4x the price? The best of the SNPs that were known at the time were put on the chip. You have about 80 or 85% conversion rate. Some of the SNPs donít work and they didnít intentionally fill up the geographic chip with singleton, which are what youíre going to use to say that youíre most derived on a branch and give you the predictions that you are related in 250 years or 400 years. The Big Y is a discovery project.
---

VinceT
11-15-2015, 07:43 PM
Is there some place where these new Y-SNPs are posted so we can see what haplogroups are represented and how well they are represented? If not, why does Mikewww have exclusive and private access?

Clinton P
11-15-2015, 10:28 PM
Jennifer Zinck on her blog on the 11th International Conference on Genetic Genealogy reports.... "The list of new Y-SNPs can be made available but they [the Geographic Project] are still testing some. They are about 90% done."

Clinton P

Giosta
12-13-2015, 09:24 PM
Just a reminder. If someone already have Geno 2 NG results and raw data,
Please extract all Y-SNP lines, remove your alleles (those A C G T) and put
the SNP list somewhere Dropbox. Thank You!

I think ordering Geno 2 NG without knowing what SNPs you will get is not ok.

TigerMW
12-13-2015, 09:55 PM
.. I think ordering Geno 2 NG without knowing what SNPs you will get is not ok.
Has anyone went on the National Genographic blog and asked what SNPs are included?

I've got a list from FTDNA of what's in it, but the official list should come from the National Genographic Project. They are the ones who have to stand behind it.

However, I do disagree somewhat with who should get Geno 2 NG. The key is if you want the autosomal DNA in Geno 2 NG to go with the Y DNA. It's a good deal for those who want a combination test or don't know what they want.

If your only or primary interest is in Y DNA you should go to specialized Y SNP and Y STR testing from FTDNA, FGC or YSEQ.

paulgill
12-14-2015, 03:40 AM
Has anyone went on the National Genographic blog and asked what SNPs are included?

I've got a list from FTDNA of what's in it, but the official list should come from the National Genographic Project. They are the ones who have to stand behind it.

However, I do disagree somewhat with who should get Geno 2 NG. The key is if you want the autosomal DNA in Geno 2 NG to go with the Y DNA. It's a good deal for those who want a combination test or don't know what they want.

If your only or primary interest is in Y DNA you should go to specialized Y SNP and Y STR testing from FTDNA, FGC or YSEQ.

Where is that list from FTDNA, anyways, can we have access to it?
,

vettor
12-14-2015, 04:55 AM
Has anyone went on the National Genographic blog and asked what SNPs are included?

I've got a list from FTDNA of what's in it, but the official list should come from the National Genographic Project. They are the ones who have to stand behind it.

However, I do disagree somewhat with who should get Geno 2 NG. The key is if you want the autosomal DNA in Geno 2 NG to go with the Y DNA. It's a good deal for those who want a combination test or don't know what they want.

If your only or primary interest is in Y DNA you should go to specialized Y SNP and Y STR testing from FTDNA, FGC or YSEQ.

Nat geno only told me where to find it........but did say , ........................any transfer of your natgeno data to ftdna, they ftdna, will only accept the positive SNP even though Natgeno present both positive and negative SNP in the transfer.

razyn
01-09-2016, 04:21 PM
One of the R1b-DF27 and Subclades project members' Geno2v2 result posted this morning, and is problematic. His terminal SNP has been changed to Z270, which is several steps below Z195 -- for which he has previously tested (I believe, correctly) negative. Scrolling through his Haplotree display, one can see quite a few positive (green) SNPs scattered throughout, that are mutually exclusive. Several of those others are correct, but I believe they were separately confirmed by his prior BigY and/or his M-343 "backbone" SNP pack, and an individual DF27 test that came as an add-on after the latter. To me, this looks like bugs in the new Geno2 NextGen product. Or possibly the transfer process.

It is kit #359222, in case Mike W or others with access want to have a look.

vettor
01-09-2016, 06:01 PM
One of the R1b-DF27 and Subclades project members' Geno2v2 result posted this morning, and is problematic. His terminal SNP has been changed to Z270, which is several steps below Z195 -- for which he has previously tested (I believe, correctly) negative. Scrolling through his Haplotree display, one can see quite a few positive (green) SNPs scattered throughout, that are mutually exclusive. Several of those others are correct, but I believe they were separately confirmed by his prior BigY and/or his M-343 "backbone" SNP pack, and an individual DF27 test that came as an add-on after the latter. To me, this looks like bugs in the new Geno2 NextGen product. Or possibly the transfer process.

It is kit #359222, in case Mike W or others with access want to have a look.

same thing happened to me, so I rang ftdna and ask them to transfer my natgeno manually as natgeno was ahead of SNP tested than ftdna. I also got them to transfer 2 negatives ( there was more , but they would not do it ) as well

they did this but they had to get an advanced person to do it

GoldenHind
01-09-2016, 09:16 PM
I am informed that the new Geno 2 test does not include R1b-DF99. This is directly below P312, was discovered more than two years ago, and while not as numerous as the major P312 subclades, it is not a rare SNP. It would probably be even more numerous if it was included in tests like this. So much for the claim it is based on the latest advances in genetics.

The previous version did not include R1b-P312, which is probably the largest subclade in Europe.

I don't know who is in charge of determining what SNPs are included in these tests, but they to replace him or her with someone who has a better understanding of the subject.

I simply cannot recommend this test.

Ann Turner
01-10-2016, 09:51 AM
It's not always a matter of understanding the tree. Sometimes a SNP test simply doesn't perform well with chip technology. It may even work OK with one version of a chip but not another, depending on the whole assembly. That is probably why Geno did not provide the whole list of SNPs from the beginning. They needed to see enough results to evaluate how many of the SNPs they submitted worked in practice.

Cofgene
01-10-2016, 12:52 PM
Some Geno 2 NG imports over the last couple of days have problems with calls. Not sure how they can call a haplogroup under U106 when there are positive results at various places under all of the branches. A real mess of "positive" results.

ArmandoR1b
01-10-2016, 03:40 PM
The worst part of the Geno 2.0 NextGen is that the negative results aren't reported at the Geno 2.0 NextGen Y-DNA page. Geno 2.0 NextGen customers aren't getting good value for their money.

TigerMW
01-10-2016, 03:46 PM
I double checked to make sure I'm not recommending Geno 2 on the R1b project screens.... I thought I added it as we just had a discussion about it between P312 project admins. I did have a reference to Geno 2 on the background page but I deleted it.

It appears that Geno 2 NG is a reasonable "starter" for many people, particularly L21ers since we have so many SNPs; but that's it. As it was before, anyone who is serious in researching their paternal lineages will need specific Y DNA tests.

Essentially, that means if you are reading this or in an project you should probably not buy Geno 2 NG. However, a lot of people will buy it anyway. A lot of newbies and that's not a bad thing as we need more newbies.

From everything I can see National Geno does not leverage FTDNA for their view of what the tree is. I personally think National Geno has some kind of automated system to identify SNPs to add. That accounts for things like DF99 missing. Their data is probably based on old Geno 2 only and I think some period of Big Y results. Hence, FGC results, FTDNA Sancer Sequencing and YSEQ are left out as sources.

ArmandoR1b
01-10-2016, 04:09 PM
It appears that Geno 2 NG is a reasonable "starter" for many people, particularly L21ers since we have so many SNPs; but that's it. As it was before, anyone who is serious in researching their paternal lineages will need specific Y DNA tests. The improper placement of some people and the lack of information of negative results and what isn't tested makes me see this as a bad "starter" since many people will have a false belief or lack of understanding of where they truly sit in the phylogenetic tree.


From everything I can see National Geno does not leverage FTDNA for their view of what the tree is. I personally think National Geno has some kind of automated system to identify SNPs to add. That accounts for things like DF99 missing. Their data is probably based on old Geno 2 only and I think some period of Big Y results. Hence, FGC results, FTDNA Sancer Sequencing and YSEQ are left out as sources.

Not good at all. The money spent towards the Geno 2.0 NextGen test would be better spent at FTDNA, FGC, or Yseq.net if they want the best results for their money.

ph.
01-10-2016, 04:19 PM
I naively assume that National Geographic hires the appropriate scientific competence, but my reason for using their services is that they claim to sample various groups from around the globe. If this data is collected and analyzed in a proper statistical manner, it will provide kowledge that no commercial testing outfit can match.

I also assume that as with all scientifically serious ouitfits, the results will in due course be published and open to peer review.

p.

gotten
01-10-2016, 04:27 PM
I must say that without Geno 2.0 I probably wouldn't have made the plunge into the world of DNA testing. National Geographic is more of a household name than FTDNA, FGC, YSEQ etc (even though FTDNA does all the testing for the Genographic Project). In retrospect I would have been cheaper off otherwise but for newbies without any connection with other genetic genealogists it is a great entry point.

If people only have a casual/passing interest in DNA I show them the Geno 2.0 Next Gen as an easy and cheap solution. Hopefully some of them will stick around/transfer to FTDNA and if they are interested in more testing I'll happily point them towards a Full Genome test.

That being said, the reported false positives of the NG test worry me a bit, but hopefully they will be ironed out by the team.

ArmandoR1b
01-10-2016, 04:50 PM
I naively assume that National Geographic hires the appropriate scientific competence, but my reason for using their services is that they claim to sample various groups from around the globe. If this data is collected and analyzed in a proper statistical manner, it will provide kowledge that no commercial testing outfit can match.
The samples from around the globe can be helpful if you are from a location that isn't well represented at FTDNA or for better autosomal results but not so much for Y-DNA that has been heavily tested elsewhere.


I also assume that as with all scientifically serious ouitfits, the results will in due course be published and open to peer review.

p.

I think that they don't publish the data for peer-review due to a confidentiality agreements with the parties they tested.

ArmandoR1b
01-10-2016, 04:55 PM
That being said, the reported false positives of the NG test worry me a bit, but hopefully they will be ironed out by the team.

There aren't many false positives. The problem is with recurrent SNPs that happen in various subclades and a lack of testing of specific SNPs and a lack of negative SNPs being reported on the Y-DNA page. Geno 2.0 NextGen isn't providing a simple way for customers to evaluate their placement. FTDNA, FGC, and Yseq all provide negative results and a list of which SNPs have been tested on the main site.

MJost
01-10-2016, 04:58 PM
I have a FGC5494+ member, from a FtDNA R1b-M343 Backbone SNP Pack, who just got his results back from Genographic 2+ and transferred to FtDNA. Interestingly, FtDNA now shows L625 as his SNP badge. I wish FtDNA would show a Tree for only just Genographic 2+ data.

MJost

TigerMW
01-10-2016, 05:18 PM
..
Not good at all. The money spent towards the Geno 2.0 NextGen test would be better spent at FTDNA, FGC, or Yseq.net if they want the best results for their money.
I get what you are saying and agree with you. I also think it would be better if people would not spend their money on Geno 2 NG, 23andMe, etc. and instead spend it on your preferred vendor list.

However, Geno 2.0 NG is a different kind of package and includes other things, as does 23andMe. It's a moot point, except for existing customers of the vendor list you are noting.... the kind that are following us here.

Organizations like the National Geographic Magazine and 23andMe are doing marketing that hobbyists and some of our favorite vendors aren't doing and are reaching people we don't reach... and a lot of them. That's a good thing.

VinceT
01-10-2016, 05:44 PM
Geno 2.0 (original and NG) uses a SNP-chip based on discoveries found through >5 year old research, 1KGP data, and FTDNA's WTY. Geno 2.0 NG added a few more variants found though Big-Y. The chip itself is completely impracticable for making new discoveries. It is essentially a survey tool.

SNP-chip tech easily throws out about 40% of those discoveries because probes for those SNPs can't be implemented accurately within the limitations of the chip. The ONLY reason the Nat. Geo. Soc. use it is because it's cheaper than borscht, which in combination with their market penetration, makes it an easy sell for uninformed neophytes.

The box looks good on the shelf, but that's about as far as it goes.

ArmandoR1b
01-10-2016, 06:26 PM
I get what you are saying and agree with you. I also think it would be better if people would not spend their money on Geno 2 NG, 23andMe, etc. and instead spend it on your preferred vendor list.

However, Geno 2.0 NG is a different kind of package and includes other things, as does 23andMe. It's a moot point, except for existing customers of the vendor list you are noting.... the kind that are following us here.

Organizations like the National Geographic Magazine and 23andMe are doing marketing that hobbyists and some of our favorite vendors aren't doing and are reaching people we don't reach... and a lot of them. That's a good thing.

Some people do research before purchasing or even after getting the test results back but want to know more. There are also people that want to know if they should recommend the test to friends and they have no idea which haplogroup they belong to and they want them to get the best bang for their buck without spending $425 or more. Some of the existing customers of the vendor list I noted also recommend tests to people and they also try to keep up with what's out there. This test just isn't very good for most people even if they are neophytes.

GoldenHind
01-10-2016, 08:10 PM
The ONLY reason the Nat. Geo. Soc. use it is because it's cheaper than borscht, which in combination with their market penetration, makes it an easy sell for uninformed neophytes.



I say let them eat borscht!

GoldenHind
01-10-2016, 08:10 PM
Double post deleted

TigerMW
01-10-2016, 10:57 PM
What I mean by "moot point" is that our discussion characterizing Geno 2 NG as good or bad is irrelevant except for our own edification. It's like saying Coke is bad for you. Probably so and I quit drinking pop a long time ago, but a lot of people will still drink it and there is not much we are going to be about it unless we are going solicit donations from Tom Brady (multi-millionaire) and mount an advertising campaign.

I'm not actually not unhappy with Geno 2 NG at all. Part of this is I foresaw that the National Genographic Project would use the early Big Y results and therefore encouraged a lot of people in my subclade to order early. That may be why L21 is nicely represented in Geno 2 NG and I have about a 600-800 year old SNP in my lineage in it and about 3 or 4 from 900-1200 years. I'm likely to take a few arrows for that comment, but this does not mean I'd recommend anyone in my immediate projects order Geno 2 NG. Given the possibility for likely conflicts and knowing the Packs and Panels are better targeted on the discovered tree, the Packs and Panels are clearly better for Y dedicated testing as far as fixed SNP packages go.

The really good news is there will be people who have no inkling of us and not much of genetic genealogy that will buy Geno 2 NG and 23andMe. I hope the ones who notice R1b something or another in their paternal lineage results will do some google searchers and find us.

razyn
03-24-2016, 03:27 PM
There aren't many false positives.

There are enough. Is anybody making a list, and checking it twice? To me, it's very annoying that FTDNA prioritizes the result (as they perceive it, sometimes incorrectly) from the flawed Geno2+ test. So, a few of my project members get (e.g.) "Your confirmed haplogroup is M222" from a false positive call of Z2970+, though they are in fact DF27+ and ZZ12+ (and almost certainly something below that, as yet untested, that's being called "Presumed negative").

Unaccustomed as I am to dark suspicions and paranoia -- of which I get a lot, recurrently, from specific project members -- I have a dark suspicion that some agreement about which results to prioritize was reached, perhaps between David Mittelman (no longer of FTDNA) and Spencer Wells (no longer of the Genographic team); and that 2013-ish agreement is still rather mindlessly being followed, in spite of our having (and our project members knowing) a much more accurate phylogeny that's been built up more recently from BigY, FGC, Chromo2, 1000 Genomes, and elsewhere.

I think almost everybody is getting a false positive call of Z270+. That's easy enough to ignore, if a level just above has been correctly called as ancestral, but sometimes it looks almost real.

Another weird possibility, when looking at a member's FTDNA Haplotree display, is that his correct terminal SNP is hiding behind the little word "More..." and one has to click that for the most specific green, correctly tested, positive call (from the Geno2+ transfer) to be visible. I don't believe the computer program that decides what terminal SNP to display for the member has been told to look there.

ArmandoR1b
03-24-2016, 03:57 PM
There aren't many false positives. The problem is with recurrent SNPs that happen in various subclades and a lack of testing of specific SNPs and a lack of negative SNPs being reported on the Y-DNA page. Geno 2.0 NextGen isn't providing a simple way for customers to evaluate their placement. FTDNA, FGC, and Yseq all provide negative results and a list of which SNPs have been tested on the main site.


There are enough. Is anybody making a list, and checking it twice?
My statement about not many false positives was based on the first version of Geno 2.0 and not seeing people put into a completely wrong haplogroup or subclade with that test and assuming that Geno 2.0 NextGen would be similar. Since that statement I have seen several people with too many false positives and people put into the wrong haplogroup or subclade. This is evident in the other threads in this same subforum and because of those threads and posts I hadn't updated this specific thread although the large amount of false positives, and the other problems that I outlined, reinforces my previous statements that "The money spent towards the Geno 2.0 NextGen test would be better spent at FTDNA, FGC, or Yseq.net if they want the best results for their money." and "This test just isn't very good for most people even if they are neophytes"

TigerMW
03-24-2016, 04:25 PM
There are enough. Is anybody making a list, and checking it twice? To me, it's very annoying that FTDNA prioritizes the result (as they perceive it, sometimes incorrectly) from the flawed Geno2+ test. So, a few of my project members get (e.g.) "Your confirmed haplogroup is M222" from a false positive call of Z2970+, though they are in fact DF27+ and ZZ12+ (and almost certainly something below that, as yet untested, that's being called "Presumed negative").

Unaccustomed as I am to dark suspicions and paranoia -- of which I get a lot, recurrently, from specific project members -- I have a dark suspicion that some agreement about which results to prioritize was reached, perhaps between David Mittelman (no longer of FTDNA) and Spencer Wells (no longer of the Genographic team); and that 2013-ish agreement is still rather mindlessly being followed, in spite of our having (and our project members knowing) a much more accurate phylogeny that's been built up more recently from BigY, FGC, Chromo2, 1000 Genomes, and elsewhere.
I don't think there is any intentional priority given to a Geno 2 result versus an Advance Test, SNP Pack or Big Y result. I think this is just general ineptitude. They should have a priority system with Advanced Tests results being highest priority, IMO. You might disagree with me, but I also think an SNP in questionable region should receive lower priority. ZZ12 might fall into that category but I just don't think FTDNA has any kind of intelligence built into their programming of terminal haplogroup selection. My guess is they have to assume there are not conflicts in the tree. We can ask FTDNA's Y tree team. They seem more responsive to project administrators in the past.

I've long made the case that trees should be built on patterns of mutations, not just a single variant no matter how much of a "UEP" eternal event we may think a particular SNP is.

GoldenHind
03-24-2016, 05:18 PM
There are enough. Is anybody making a list, and checking it twice? To me, it's very annoying that FTDNA prioritizes the result (as they perceive it, sometimes incorrectly) from the flawed Geno2+ test. So, a few of my project members get (e.g.) "Your confirmed haplogroup is M222" from a false positive call of Z2970+, though they are in fact DF27+ and ZZ12+ (and almost certainly something below that, as yet untested, that's being called "Presumed negative").



Here is another example of a false positive Z2970 from someone in the R-P312 Project. He took the new and "Ômproved" Geno 2 test, and got a Z2970+ result. I suspected something was fishy because 1) the markers above Z2970 (L21, DF13, DF21) are listed only as "presumed" positive rather than tested positive, and 2) he has some matches at 67 markers who have tested DF99+. Incidentally the new Geno 2 test does not include DF99. I persuaded him to order an a la carte test for DF99, and sure enough, he got a positive result. He nonetheless remains classified as Z2970 by FTDNA. For some reason they never classified him as M222. His Geno 2 test was worse then a waste of money, as it gave him an erroneous rather than just a useless result.

I wouldn't recommend this test to anyone.

VinceT
03-25-2016, 03:38 AM
There are a significant number of false negatives as well. Overall, about 10% of the just-over 12,000 Y-SNPs being returned are not as expected. If you consider that the original allotment was for 18,000 Y-SNPs (implying that almost 6,000 were eliminated from post-production reports), that is a significant error rate for the Geno2 platform in general.

ChrisR
03-25-2016, 01:53 PM
There are a significant number of false negatives as well. Overall, about 10% of the just-over 12,000 Y-SNPs being returned are not as expected. If you consider that the original allotment was for 18,000 Y-SNPs (implying that almost 6,000 were eliminated from post-production reports), that is a significant error rate for the Geno2 platform in general.
Well it just confirms my impression that Geno2NG has a low value for Y-DNA research. I did not research on results so far, because I have no motivation to clear this mess up (at least for part of the tree) if it is even possible when 10% of the SNPs are unreliable. Based on the previous Geno 2 experience (which was a useful test at the time) and what came out in the last years they could have done much better.

vettor
03-25-2016, 05:09 PM
Well it just confirms my impression that Geno2NG has a low value for Y-DNA research. I did not research on results so far, because I have no motivation to clear this mess up (at least for part of the tree) if it is even possible when 10% of the SNPs are unreliable. Based on the previous Geno 2 experience (which was a useful test at the time) and what came out in the last years they could have done much better.

Having done the old NG2.0 test, I found both my positive and negative SNP's to not have any errors with any other researchers , ..............It still represents for myself, a test ahead of all the other tests I have done, that is , Ftdna 67 FMS and 23andme v3
I still use these SNP's ( 14 and half thousand ) as reference.

As for the new NG test , ...............I might test my younger son on it as he has been pushing me for a while on who to test with.

ArmandoR1b
03-26-2016, 12:48 AM
Having done the old NG2.0 test, I found both my positive and negative SNP's to not have any errors with any other researchers , ..............It still represents for myself, a test ahead of all the other tests I have done, that is , Ftdna 67 FMS and 23andme v3
I still use these SNP's ( 14 and half thousand ) as reference.
The problem is that there is a significant number of people that get incorrect Y-DNA results with NG.


As for the new NG test , ...............I might test my younger son on it as he has been pushing me for a while on who to test with.
The new NG test did not add any SNPs that are downstream from CTS8862, that are in the ISOGG list, so you won't see a difference in Y-DNA results other than maybe false positives.

vettor
03-26-2016, 06:25 AM
The problem is that there is a significant number of people that get incorrect Y-DNA results with NG.


The new NG test did not add any SNPs that are downstream from CTS8862, that are in the ISOGG list, so you won't see a difference in Y-DNA results other than maybe false positives.

thanks

They had CTS8862 for over 18 months

What do you suggest then?

ArmandoR1b
03-26-2016, 03:49 PM
thanks

They had CTS8862 for over 18 months

What do you suggest then?

Your only options for possibly finding downstream SNPs from CTS8862 are BigY and FGC but even then you might end up in that same group without a new branch. https://www.yfull.com/tree/T-CTS8489/ At the same time you'll never know until you get one of those tests unless you wait ten years or more for another test to come along that might find SNPs that puts your Y-DNA into a new downstream branch.

vettor
03-26-2016, 05:33 PM
Your only options for possibly finding downstream SNPs from CTS8862 are BigY and FGC but even then you might end up in that same group without a new branch. https://www.yfull.com/tree/T-CTS8489/ At the same time you'll never know until you get one of those tests unless you wait ten years or more for another test to come along that might find SNPs that puts your Y-DNA into a new downstream branch.

your opinion is exact in the sense that it will be a long time

I have better luck with my mtdna H95a or my sons with K1a4 ...............more correspondence with people with these markers

ChrisR
04-07-2016, 03:09 AM
Have mt- and autosomal/X SNPs on the NG chip the same error rates? This could limit if not falsify mt-Haplogroup as well as admixture and IBD-matching.

wombatofthenorth
04-09-2016, 09:04 PM
Wow, I'm pretty disappointed with this. For all their talk about how they radically improved mtDNA and Y-haplogroups, not only did my dad not get any new haplogroup info at all, he actually got less info that he did on the old test! And not a single bit more than he got on even 23!
They kept going on and on about how the upgrade was well worth it since it tested to deeper levels. Well it seems it is actually more shallow!

TigerMW
04-09-2016, 11:39 PM
Wow, I'm pretty disappointed with this. For all their talk about how they radically improved mtDNA and Y-haplogroups, not only did my dad not get any new haplogroup info at all, he actually got less info that he did on the old test! And not a single bit more than he got on even 23!
They kept going on and on about how the upgrade was well worth it since it tested to deeper levels. Well it seems it is actually more shallow!
I take it you are L20. Did people in L20 discover new branches with Big Y the first year Big Y testing? That's really key to what apparently National Geographic did as far as additional Y SNPs. As Armando pointed out we still need NGS testing to discover new branches.

wombatofthenorth
04-10-2016, 12:37 AM
I take it you are L20. Did people in L20 discover new branches with Big Y the first year Big Y testing? That's really key to what apparently National Geographic did as far as additional Y SNPs. As Armando pointed out we still need NGS testing to discover new branches.

I don't know what year they found them, but FTDNA offers a slew of downstream SNPs you can order. Also, I noted that the old test tested a couple of those downstream ones and the new test does not! How can they have gone backwards even?

(And his mtDNA results, now they just stop at V! Before they covered the entire next level plus a few little bits of next level beyond that! How can they have made it not even just the same but much worse. Even 23 tested one full level deeper! What happened to their talk about radically expanded haplogroups, by far the best you can get from any general do it all test? It covers even less than the old test!)

Amerijoe
04-10-2016, 03:53 AM
I concur that Geno 2+ has inconsistencies. FTDNA replied to my email, stating a fix should be initiated in the next few weeks. Results, Geno 2+ R-Z94, J1c4; FTDNA R-Y15121, J1c. Positive snps put me in every haplogroup. I provided my resulting snps to indicate the scope of the issue.

Tests Taken

A531+, A91+, BY1142+, BY1237+, BY1357+, BY136_FGC19909_Z18229+, BY1551+, BY1734+, BY20+, BY2211+, BY2402+, BY2463+, BY2510+, BY65_Z18181+, BY763+, BY876+, CTS10031+, CTS10147+, CTS10188+, CTS10229+, CTS103+, CTS10300+, CTS10428+, CTS10433+, CTS10448+, CTS10552+, CTS10572+, CTS10615+, CTS10648+, CTS1066+, CTS10723+, CTS10745+, CTS10761+, CTS10821+, CTS10847+, CTS10993+, CTS11012+, CTS11041+, CTS11071+, CTS11088+, CTS11126+, CTS11184+, CTS11190+, CTS11261+, CTS11354+, CTS114+, CTS1141+, CTS11436+, CTS11441+, CTS1148+, CTS11503+, CTS11530+, CTS1164+, CTS11651+, CTS1171+, CTS11710+, CTS11731+, CTS11759+, CTS11816+, CTS11907+, CTS11913+, CTS11949+, CTS11962-, CTS11970+, CTS12023+, CTS12058+, CTS1211-, CTS1216+, CTS12449+, CTS12450+, CTS12578+, CTS1276+, CTS12856+, CTS12933+, CTS12934+, CTS12948+, CTS12950+, CTS12976+, CTS1340+, CTS1353+, CTS1413+, CTS1436+, CTS1633+, CTS1710+, CTS1733-, CTS1758+, CTS1806+, CTS191+, CTS202+, CTS2067+, CTS210+, CTS2105+, CTS2134+, CTS2230+, CTS2275+, CTS2284+, CTS2289+, CTS2413+, CTS2488+, CTS2515+, CTS262+, CTS2670+, CTS278+, CTS2800+, CTS2848+, CTS2906+, CTS2947+, CTS305+, CTS316+, CTS3202+, CTS3268+, CTS3366+, CTS3402-, CTS3403+, CTS3466+, CTS347+, CTS3519+, CTS352+, CTS3534+, CTS3543+, CTS3551+, CTS3654+, CTS3663+, CTS3700+, CTS3802+, CTS3837+, CTS3868+, CTS3902+, CTS3943+, CTS3984+, CTS4053+, CTS4086+, CTS4089+, CTS4094+, CTS4178+, CTS4179-, CTS4209+, CTS4235+, CTS4259+, CTS4326+, CTS4385-, CTS4406+, CTS4463+, CTS4608+, CTS4643+, CTS4715+, CTS4781+, CTS4784+, CTS4793+, CTS4853+, CTS4984+, CTS501+, CTS5052+, CTS5152+, CTS5156+, CTS5254+, CTS5304+, CTS5334+, CTS5359+, CTS5370+, CTS5649+, CTS5690+, CTS58+, CTS5828+, CTS585+, CTS5860+, CTS5933+, CTS5936+, CTS5939+, CTS597+, CTS5979+, CTS5998+, CTS6062+, CTS6063+, CTS6090+, CTS6117+, CTS6265+, CTS6285+, CTS6352+, CTS636+, CTS6365+, CTS6394+, CTS6403+, CTS6438+, CTS6447+, CTS6449+, CTS6468+, CTS6481+, CTS6506+, CTS656+, CTS6613+, CTS6631+, CTS6677+, CTS6704+, CTS6848+, CTS687+, CTS6918+, CTS6967+, CTS7022+, CTS7101+, CTS7147+, CTS7186+, CTS7193+, CTS7227+, CTS7266+, CTS7275+, CTS7285+, CTS7299+, CTS730+, CTS7317+, CTS736+, CTS7451+, CTS7598+, CTS7601+, CTS7611+, CTS7626+, CTS7642+, CTS7803+, CTS7810+, CTS7925+, CTS7929+, CTS7942+, CTS8027+, CTS8126+, CTS8203+, CTS8216+, CTS8277-, CTS8300+, CTS8440+, CTS8492+, CTS8506+, CTS8521+, CTS860+, CTS8645+, CTS8723+, CTS8746-, CTS8815+, CTS8816-, CTS903+, CTS9056+, CTS9154+, CTS9240+, CTS9322+, CTS9325+, CTS9335+, CTS9387+, CTS9471+, CTS9518+, CTS9525+, CTS9539+, CTS9558+, CTS97+, CTS9716+, CTS9739+, CTS9894+, CTS9900+, CTS9925+, CTS9975+, CTS9976+, DF109_FGC4101_S660_Y2845+, F1007+, F1013+, F1024+, F1055+, F1088_PF6160+, F1096+, F1108+, F1127+, F115+, F1159+, F1207+, F1221+, F1291+, F1302+, F1345-, F1367+, F1405+, F1412+, F142+, F1442+, F1474+, F1476+, F1539+, F1540+, F1567+, F1594+, F1703+, F1712+, F1796+, F1813+, F1848+, F1874+, F188+, F1924+, F1946+, F1956+, F2018+, F202+, F2028+, F2132+, F2149+, F2165+, F2208+, F2224+, F2236+, F2304+, F2332+, F2343+, F2370+, F2371+, F240+, F2480+, F2516+, F2546+, F2558+, F2600+, F2654+, F2684_PF6201+, F2724+, F2742+, F2753+, F2761+, F2767+, F2850+, F287+, F2873+, F2924+, F2947+, F2960+, F2961+, F2990+, F3032+, F3048+, F3056+, F3057+, F3108+, F313+, F3143+, F3166+, F3185+, F3195_PF1806+, F3337+, F3368_PF3566+, F3402_PF3567+, F3422+, F3444+, F3451+, F3491+, F3518+, F3551_PF6231+, F3582+, F3595+, F3692+, F3697+, F371+, F3735+, F3739+, F3806+, F386+, F3869+, F3892+, F3907+, F3949+, F3956+, F3994+, F4003+, F4099+, F4111+, F4176+, F4188_PF3539+, F4244+, F4251+, F4257+, F4282+, F47+, F492+, F526+, F557+, F565+, F61+, F646+, F716+, F719+, F736+, F741+, F743+, F819+, F836+, F837+, F862+, F886_PF6153+, F896+, F910+, F937+, F995+, FGC11678+, FGC11897_YP327+, FGC16362_Z18162+, FGC16683_Y5619+, FGC1721_Y5322+, FGC20866_ZS2566+, FGC20874_ZS2572+, FGC24646+, FGC28639_YP556+, FGC29572+, FGC3718_Y6369+, FGC6948_Y2703+, FGC7948+, FGC9988-, K257+, K386+, L1029-, L104+, L1093+, L1186+, L1247+, L132+, L1324+, L15+, L16+, L167+, L183+, L187+, L213+, L245+, L253+, L254+, L260-, L294+, L325+, L387+, L440+, L442+, L448-, L449+, L453+, L459+, L464_1+, L484+, L492+, L496+, L498+, L503+, L533+, L542+, L551+, L552+, L556+, L557+, L625+, L636+, L657-, L664-, L665+, L692+, L72+, L747+, L782+, L784+, L817+, L840+, L99+, M102+, M116+, M129+, M139+, M171+, M198+, M198+, M207+, M251+, M262+, M275+, M288+, M367+, M39+, M417+, M420+, M420+, M448+, M45+, M458-, M459+, M513+, M514+, M515+, M526+, M630+, M644+, M647+, M746_S4582_Z2479+, M784_Y216+, M89+, M94+, M9574+, M9588+, MC14+, N4+, P102+, P108+, P117+, P118+, P128+, P129+, P131+, P132+, P135+, P136+, P141+, P145+, P148+, P151+, P159+, P160+, P166+, P181+, P194+, P202+, P225+, P230+, P233+, P237+, P238+, P268+, P269+, P289+, P295+, P305+, P40+, P52+, P59+, P77+, P80+, P84+, P91+, PAGES00010+, PAGES00048+, PAGES00081+, PAGES00101+, PAGES00105+, PF1015+, PF1026+, PF1031+, PF1085+, PF1097+, PF1141+, PF1147+, PF1152+, PF1164+, 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PF7328+, PF7341+, PF7374+, PF7434+, PF747+, PF7514+, PF7521-, PF7522+, PF7527+, PF7531+, PF7534+, PF7552+, PF7557+, PF791+, PF794+, PF806+, PF829+, PF888+, PF907+, PF926+, PF93+, PF946+, PF95+, PF966+, PF968+, PF971+, PF997+, PK1+, PR805+, rs12116413+, rs16980396+, rs16980499+, rs17222573+, rs17250121+, rs17250535+, rs17307070+, rs17842387+, rs2032652+, rs2033003+, rs2075640+, rs28609124+, rs35249440+, rs3853054+, rs7067237+, rs7067486+, rs7892924+, rs7893044+, rs895530+, rs9306845+, rs9306848+, rs9785670+, rs9785717+, rs9785740+, rs9785846+, rs9785853+, rs9785905+, rs9785994+, rs9786043+, rs9786082+, rs9786139+, rs9786181+, rs9786247+, rs9786290+, rs9786325+, rs9786714+, rs9786770+, rs9786774+, S23201-, S23592-, S24902-, S2857-, S2858-, S2859-, S2880-, S2894-, S3207+, S3473-, S3477-, S4458-, S5153-, s5153+, S6842-, S7123+, SK1247_Y4915+, SK1410_Y5528_Z20169+, V174+, V187+, V21+, V216+, V221+, V227+, V250+, V29+, V32+, V59+, V78+, V79+, V8+, V90+, V94+, Y1038+, Y1049+, Y1083+, Y1113+, Y1122+, Y14244-, Y15121+, Y17491-, Y196+, Y209+, Y210+, Y2395-, Y2604-, Y2613-, Y2905-, Y2914-, Y2921-, Y32+, Y33-, Y35-, Y40-, Y4135-, Y4459-, Y47-, Y4864_Z16422+, Y4899+, Y5272+, Y5305_Z16500+, Y57-, Y5759_Z16420+, Y5992-, Y6181+, Y763+, Y874-, Y934+, YP1013-, YP1014-, YP1015-, YP1034-, YP1051-, YP1129-, YP1136-, YP1137-, YP1168 *, YP1178-, YP1182-, YP1211-, YP1214-, YP1272-, YP1337-, YP1341-, YP1364-, YP1368-, YP1567-, YP1570-, YP1703-, YP234-, YP237-, YP254-, YP256-, YP263-, YP276-, YP282-, YP285-, YP321+, YP340-, YP343-, YP355-, YP358-, YP360-, YP386-, YP3896-, YP3927-, YP398-, YP4101-, YP4102-, YP4123-, YP413-, YP4131-, YP4132-, YP414-, YP4141-, YP415-, YP416-, YP417-, YP418-, YP4243-, YP4289 *, YP430-, YP431-, YP432-, YP441-, YP442-, YP443-, YP444-, YP4444-, YP445-, YP4467-, YP451-, YP4514-, YP4515-, YP4517-, YP4519-, YP4535-, YP4557-, YP515-, YP517-, YP520-, YP541-, YP543-, YP544-, YP547-, YP556 *, YP582-, YP589-, YP593-, YP610-, YP621-, YP654-, YP694-, YP704-, YP728-, YP729-, YP870-, YP942 *, YP943-, YP951-, YSC0000081+, YSC0000150+, YSC0000186+, YSC0000216+, YSC0000288+, YSC0000292+, YSC0001071+, Z10274+, Z11180+, Z1149+, Z130+, Z133+, Z138+, Z1456+, Z1476+, Z148+, Z1483+, Z1504+, Z1518+, Z1589+, Z1593+, Z1616+, Z16267+, Z18133+, Z18140+, Z1817+, Z18186+, Z1835+, Z187+, Z189+, Z1975+, Z2035-, Z2069+, Z2082+, Z2094+, Z2121+, Z2122-, Z2123+, Z213+, Z2396+, Z269+, Z270+, Z274+, Z280-, Z281-, Z282-, Z283-, Z284-, Z284+, Z287-, Z2970+, Z2976+, Z2983+, Z30+, Z306+, Z315+, Z319+, Z347+, Z350+, Z3723+, Z39+, Z477+, Z515+, Z531+, Z544+, Z60+, Z625+, Z638+, Z685-, Z72+, Z75+, Z767+, Z92-, Z93+, Z93_F992+, Z94+, Z94+, Z966+, ZS1727+, ZS251+
Download SNPs as CSV


Here are the my mt results.


Chromosome Position Result
mt 12705 C
mt 13973 T
mt 13276 A
mt 11914 G
mt 16069 T
mt 16230 A
mt 11204 C
mt 228 A
mt 8468 C
mt 15452 A
mt 2885 T
mt 8655 C
mt 10873 T
mt 4312 C
mt 769 G
mt 14798 C
mt 16519 T
mt 2758 G
mt 8701 A
mt 150 T
mt 13830 C
mt 13708 A
mt 794 A
mt 10688 G
mt 9540 T
mt 12083 T
mt 11251 G
mt 4216 C
mt 3399 A
mt 489 C
mt 16126 C
mt 295 A
mt 247 G
mt 4104 A
mt 825 T
mt 16278 C
mt 7256 C
mt 3594 C
mt 7521 G
mt 7772 G
mt 16129 G
mt 195 T
mt 10810 T
mt 13506 C
mt 3010 A
mt 13650 C
mt 185 A
mt 12612 G
mt 13105 A
mt 1018 G

wombatofthenorth
04-12-2016, 12:01 AM
I've noticed some weird things. After transferring Geno results old and new tests, FTDNA's Y haplogroup tree offers various SNPs under L20 for purchase. But the thing is that for the old test while it marks off some that were taken as being negative it fails to mark off all as negative so it tries to offer some SNPs that you've already taken. For the new transfer it seems offer for a sale the new L20 sub-SNP the new test has even though it was already taken. So you really can't seem to trust what they show as potential SNPs to buy. Make sure to look at the download file since there may be ones you actually already have data for.

Another weird thing is that BY2171 is on the new test (says AA) and looking at ISOGG SNP Lookup it says A is the derived value but FTDNA shows the SNP as either untested or negative (who knows what they mean when they show untested, in some cases they mean negative in some cases they mean untested) instead of positive. So is FTDNA messing up and failing to mark a positive result as positive, has it been determined that BY2171 is unreliable so they are ignoring it or is it one of the few SNPs where you need to read the transfer as a - strand so that A is actually ancestral?

ArmandoR1b
04-12-2016, 02:17 AM
I've noticed some weird things. After transferring Geno results old and new tests, FTDNA's Y haplogroup tree offers various SNPs under L20 for purchase. But the thing is that for the old test while it marks off some that were taken as being negative it fails to mark off all as negative so it tries to offer some SNPs that you've already taken. For the new transfer it seems offer for a sale the new L20 sub-SNP the new test has even though it was already taken. So you really can't seem to trust what they show as potential SNPs to buy. Make sure to look at the download file since there may be ones you actually already have data for.

Another weird thing is that BY2171 is on the new test (says AA) and looking at ISOGG SNP Lookup it says A is the derived value but FTDNA shows the SNP as either untested or negative (who knows what they mean when they show untested, in some cases they mean negative in some cases they mean untested) instead of positive. So is FTDNA messing up and failing to mark a positive result as positive, has it been determined that BY2171 is unreliable so they are ignoring it or is it one of the few SNPs where you need to read the transfer as a - strand so that A is actually ancestral?

There is obviously a glitch with Geno 2.0+. BY2171 (http://ybrowse.org/gb2/gbrowse_details/chrY?ref=ChrY;start=23615856;end=23615856;name=BY2 171;class=Sequence;feature_id=97733;db_id=chrY%3Ad atabase) is T>A at position 23615856. So T is ancestral and A is derived. There are no other SNPs in that position either.

wombatofthenorth
04-12-2016, 02:55 AM
There is obviously a glitch with Geno 2.0+. BY2171 (http://ybrowse.org/gb2/gbrowse_details/chrY?ref=ChrY;start=23615856;end=23615856;name=BY2 171;class=Sequence;feature_id=97733;db_id=chrY%3Ad atabase) is T>A at position 23615856. So T is ancestral and A is derived. There are no other SNPs in that position either.

Well it would be a glitch with FTDNA. Since it's on the FTDNA site where they fail to list it as positive. On the Geno site they don't seem to be ready to use anything downstream of L20 as the terminal SNP just yet so they don't say anything about it at all. But it could also be one of the ones where the Geno chips tests reverse strand and so T swaps with A and G swaps with C so A would become ancestral and T derived. In which case it would be negative and FTDNA would be correct (although I still say they are very misleading it marking both not tested and negative results as not tested).

ArmandoR1b
04-12-2016, 12:11 PM
Well it would be a glitch with FTDNA. Since it's on the FTDNA site where they fail to list it as positive. On the Geno site they don't seem to be ready to use anything downstream of L20 as the terminal SNP just yet so they don't say anything about it at all. Correct. I did mean to write it's a glitch with FTDNA.


But it could also be one of the ones where the Geno chips tests reverse strand and so T swaps with A and G swaps with C so A would become ancestral and T derived. In which case it would be negative and FTDNA would be correct (although I still say they are very misleading it marking both not tested and negative results as not tested).I truly doubt that it has anything to do with testing the reverse strand. Of course, both FTDNA and Geno should be reporting negative results and FTDNA should be reporting untested SNPs. They are reasons that people should not get a Geno 2.0 test.

wombatofthenorth
04-13-2016, 04:37 AM
I truly doubt that it has anything to do with testing the reverse strand. Of course, both FTDNA and Geno should be reporting negative results and FTDNA should be reporting untested SNPs. They are reasons that people should not get a Geno 2.0 test.

The raw Y data from Geno shows both positive and negative. Something about when you use FTDNA to view the tree seems to be muddled though as FTDNA seems to randomly decide to show some negative SNPs as negative and some as untested (two rather different things, assuming it's not just because they have legit decided some SNP is not reliable).

To be fair, Ancestry and basic FTDNA don't even give you any haplogroups at all. And 23 presents them in very outdated form and present much less info about haplogroup results than the very nice presentation Geno gives people.

As for reverse strand, I've heard that people found the prior test did report certain Y SNPs on the reverse strand, mostly not, but a small few. I'll have to contact them and try to get the real story on BY2171.

ArmandoR1b
04-13-2016, 01:11 PM
The raw Y data from Geno shows both positive and negative.Right. That is why I tell people to download the CSV file.


Something about when you use FTDNA to view the tree seems to be muddled though as FTDNA seems to randomly decide to show some negative SNPs as negative and some as untested (two rather different things, assuming it's not just because they have legit decided some SNP is not reliable).Partly right. SNPS that are black are Presumed Negative and SNPs that are red are Tested Negative. FTDNA does not show Tested Negative SNPs in red from the Geno 2.0+ test. They only show Presumed Negative SNPs in black even though the CSV file will have the ancestral values of the SNPs which means they are Tested Negative. The ones that show untested can't be presumed to be negative because there aren't positive SNPs from other branches and because FTDNA does not use the negative SNPs from Geno 2.0+. If the kit has Tested Negative SNPs they are from testing other than Geno 2.0+. It's too much of a mess for the money.


To be fair, Ancestry and basic FTDNA don't even give you any haplogroups at all. And 23 presents them in very outdated form and present much less info about haplogroup results than the very nice presentation Geno gives people.No, but FTDNA have developed SNP packs and they have the BigY which is way better than Geno 2.0+ and it doesn't have as many false positives.


As for reverse strand, I've heard that people found the prior test did report certain Y SNPs on the reverse strand, mostly not, but a small few. I'll have to contact them and try to get the real story on BY2171.A file of a person that it not U152 also has A for BY2171 so I think it is a false positive like many other false positives in the test. You could always get that tested at Yseq for $17.50 + $5.00 shipping after choosing Wish an SNP (http://www.yseq.net/product_info.php?products_id=108) and paying $1 for the test to be made available.

GoldenHind
04-15-2016, 09:48 PM
Can anyone tell me if the Geno 2 next gen test actually gives a result for R-P312? I know for a fact that P312 was NOT included in the earlier version. I have been looking at the results of someone who got only a "presumed" positive for P312, though he got an actual positive for P310 (the next step above P312).

TigerMW
04-15-2016, 09:55 PM
Can anyone tell me if the Geno 2 next gen test actually gives a result for R-P312? I know for a fact that P312 was NOT included in the earlier version. I have been looking at the results of someone who got only a "presumed" positive for P312, though he got an actual positive for P310 (the next step above P312).
I haven't seen a P312 result yet so my guess is no. I'm sure there is no DF27, which is of greater concern to me. How about DF99, DF19 and L238?

GoldenHind
04-16-2016, 01:55 AM
I haven't seen a P312 result yet so my guess is no. I'm sure there is no DF27, which is of greater concern to me. How about DF99, DF19 and L238?

I have it on very good authority that DF99 is not included. DF19 was included in the initial version of the test (which has helped a great deal to identify them), so is probably in the new version as well. I don't believe L238 was tested in the original version, but I don't know about the new one.

I hardly need to point out that R1b-P312 probably constitutes the most numerous haplogroup subclade in western Europe. There really is no excuse for not including it in their new test.

ArmandoR1b
04-16-2016, 02:23 AM
I haven't seen a P312 result yet so my guess is no. I'm sure there is no DF27, which is of greater concern to me. How about DF99, DF19 and L238?


I have it on very good authority that DF99 is not included. DF19 was included in the initial version of the test (which has helped a great deal to identify them), so is probably in the new version as well. I don't believe L238 was tested in the original version, but I don't know about the new one.DF19 and L238 are definitely tested in Geno 2.0 NextGen. DF99 and P312 definitely are not.

I hardly need to point out that R1b-P312 probably constitutes the most numerous haplogroup subclade in western Europe. There really is no excuse for not including it in their new test.[/QUOTE]
100% agree.

Huntergatherer1066
04-16-2016, 03:15 AM
P312 was on the original Geno 2.0 chip it just did not work. That may be the case again for Geno 2.0+

leo76
04-16-2016, 03:42 AM
I hardly need to point out that R1b-P312 probably constitutes the most numerous haplogroup subclade in western Europe. There really is no excuse for not including it in their new test.

Sincere question: Why is it a big a deal to not include P312 as a specific tested SNP? There are so many hundreds of SNPs downstream of P312 that it does test for, that if you're say, positive for Z195 and Z220 and M153, then obviously you're P312. It might be unhelpful for any P312* men, but are there really many of those?

ArmandoR1b
04-16-2016, 03:32 PM
Sincere question: Why is it a big a deal to not include P312 as a specific tested SNP? There are so many hundreds of SNPs downstream of P312 that it does test for, that if you're say, positive for Z195 and Z220 and M153, then obviously you're P312. It might be unhelpful for any P312* men, but are there really many of those?
It's also unhelpful for DF99, L238, and DF27 men that are negative for SNPs downstream from those SNPs that are tested by Geno 2.0, (not all downstream SNPs are tested or are reliable) since DF99, L238, and DF27 aren't included either. So they still have to get a M343 test at FTDNA or individually test SNPs until they find their subclade if they even know the tests are available. It pretty much sums up to a waste of money for those people and it creates more work for people trying to find others with the same subclade or for admins trying to help the FTDNA customers.

GoldenHind
04-16-2016, 05:28 PM
Sincere question: Why is it a big a deal to not include P312 as a specific tested SNP? There are so many hundreds of SNPs downstream of P312 that it does test for, that if you're say, positive for Z195 and Z220 and M153, then obviously you're P312. It might be unhelpful for any P312* men, but are there really many of those?

There are reasons to believe that the P312* group is much larger than currently thought. If they had been identified in the nearly 750,000 people who have ordered a Genographic DNA test, we would have a far better idea of their number. I also suspect that one reason that DF19 currently appears to be so much larger than DF99 is that the former has been included in the Geno test from the beginning, while the latter is still not. I don't know how many SNPs below DF27 are included in the new test, but my guess is that a significant percentage of DF27 is not covered, perhaps close to half.

Can you, or anyone else, tell me now many of the nearly 750,000 tested P310*, as I did? Of course one would have to add to that number those who got false positive results for SNPs such as Z2970 etc. in the Next Gen test.

wombatofthenorth
04-19-2016, 01:08 AM
I have it on very good authority that DF99 is not included. DF19 was included in the initial version of the test (which has helped a great deal to identify them), so is probably in the new version as well. I don't believe L238 was tested in the original version, but I don't know about the new one.

I hardly need to point out that R1b-P312 probably constitutes the most numerous haplogroup subclade in western Europe. There really is no excuse for not including it in their new test.

Yeah there is no D99 or P312, but there is D19.

wombatofthenorth
04-19-2016, 01:10 AM
It's also unhelpful for DF99, L238, and DF27 men that are negative for SNPs downstream from those SNPs that are tested by Geno 2.0, (not all downstream SNPs are tested or are reliable) since DF99, L238, and DF27 aren't included either. So they still have to get a M343 test at FTDNA or individually test SNPs until they find their subclade if they even know the tests are available. It pretty much sums up to a waste of money for those people and it creates more work for people trying to find others with the same subclade or for admins trying to help the FTDNA customers.

L238 is included

ArmandoR1b
04-19-2016, 02:03 AM
Indeed it is and I had found it when I looked for it in post #71. I included L238 in post #74 in error.

wombatofthenorth
04-20-2016, 05:08 AM
Just a quick word of note. The new FTDNA R-L2 SNP pack is NOT a universal L2 pack good for everyone. It's totally useless if you are DF49+ or L20+. It has less SNPs for those types of L2 branches than Geno 2.0, Geno 2.0 NG or even 23. They are going to come out with special DF49 and Z367 packs. Of course whether even those will be worthwhile for anyone who took a comprehensive general (mtDNA, y-haplo, autosomal ancestry) test or not I don't know. L20 seems kind of understudied. And if you've had both Geno 2.0 and Geno 2.0 NG you already have the bulk of the main sub-branch tests for L20 that FTDNA seems to cover. if you notice you are negative for all of those then even the Z367 pack might not be worth anything (perhaps it would test Z1910 branch and the one other, although this one other appears to have like only two people ever so far positive for it) and it might be either go BiY or something even more for general future research purposes or don't bother at all.

I should say this does show the value of the general tests as opposed to the FTDNA and Ancestry methods where they have no general test. By the time you do some basic y-haplo test and a few exploratory SNP packs you could've had even more for less money with a general test to start out. It seems like people should start either with a full general test or, if they know they will go all-out BigY or better and full mtDNA right away then get the basic test and add the giant extra tests. The whole get the basic test and then try various small scale and SNP add-ons seems like you'd pay a lot to get less and only seems to make sense if you plan to do nothing at all for haplogroups or go all-in 100% in with them right away.

wombatofthenorth
04-20-2016, 05:15 AM
And actually another plus for some to start with a full general test, especially the Genos since 23 really doesn't tell you a whole ton about the haplogroups these days in terms of detailed mapping and background info is that Geno gives the best general presentation of haplogroup tracking and background info out of Africa out there. If you will eventually go all out it does make it a bit more expensive than the FTDNA or Ancestry route (although same as the 23 route) but you do get that nice presentation and you get an extra look at autosomal ancestry (well with Ancestry you do too, although some say the Ancestry autosomal is so-so, although, especially for people with long Colonial roots that does get you into their database too, of course all the money goes to a profit and none to research as with Geno).

TigerMW
04-20-2016, 01:01 PM
Just a quick word of note. The new FTDNA R-L2 SNP pack is NOT a universal L2 pack good for everyone. It's totally useless if you are DF49+ or L20+. It has less SNPs for those types of L2 branches than Geno 2.0, Geno 2.0 NG or even 23. They are going to come out with special DF49 and Z367 packs.

There over 120 downstream SNPs in the new R1b-L2 SNP Pack, and may be closer to 140 with the late adds that have been requested. Details are available on this thread in the U152 category.
http://www.anthrogenica.com/showthread.php?6928-U152-SNP-Packs-from-FTDNA

The L2 pack should be thought of as the R1b-L2 top-layer and misc. subclades SNP Pack with the "misc." being all of the subclades except the large Z49 (not DF49) and large Z367 subclades. Both of those two will get their own SNP Packs that are yet available. L20 fits under Z367. Another way to think of the L2 pack is as the R1b-L2 (xZ367 xZ49) pack. Please note that L2, Z367 and Z49 are each in the R1b-M343 Backbone SNP Pack. This means for the newbie R-M269 who take the Backbone test and are L2+ of some type, they will be able to jump straight to the right specialized pack, be it L2 top-layer and misc, Z49 or Z367.


Of course whether even those will be worthwhile for anyone who took a comprehensive general (mtDNA, y-haplo, autosomal ancestry) test or not I don't know. L20 seems kind of understudied. And if you've had both Geno 2.0 and Geno 2.0 NG you already have the bulk of the main sub-branch tests for L20 that FTDNA seems to cover. if you notice you are negative for all of those then even the Z367 pack might not be worth anything (perhaps it would test Z1910 branch and the one other, although this one other appears to have like only two people ever so far positive for it) and it might be either go BiY or something even more for general future research purposes or don't bother at all.

I should say this does show the value of the general tests as opposed to the FTDNA and Ancestry methods where they have no general test. By the time you do some basic y-haplo test and a few exploratory SNP packs you could've had even more for less money with a general test to start out. It seems like people should start either with a full general test or, if they know they will go all-out BigY or better and full mtDNA right away then get the basic test and add the giant extra tests. The whole get the basic test and then try various small scale and SNP add-ons seems like you'd pay a lot to get less and only seems to make sense if you plan to do nothing at all for haplogroups or go all-in 100% in with them right away.

I think that Geno 2 Next Gen could be a greater starter test for those first time DNA testers as they will get a mix of different types of DNA and then they can get more deeply engaged and learn more and join us, the crazies. :) However, there are some false positives in Geno 2 Next Gen today screwing up haplogroup labeling and confusing things. Geno 2 needs to strip out the failing SNPs from their test, and/or FTDNA needs to filter out the failing SNPs when they transfer Geno 2 results into the FTDNA system.

In some sense, though, my (and our) feelings about Geno 2 Next Gen area moot point. The main audience for this is the vast unawashed masses. They don't know who we are or what we think. When and if they do find out, they will have already received their results for Geno 2 Next Gen and wondering what the transfer to FTDNA thing is about.

ArmandoR1b
04-20-2016, 02:32 PM
Please note that L2, Z367 and Z49 are each in the R1b-M343 Backbone SNP Pack. This means for the newbie R-M269 who take the Backbone test and are L2+ of some type, they will be able to jump straight to the right specialized pack, be it L2 top-layer and misc, Z49 or Z367.
That is a perfect example of how the SNP packs can be of more value than Geno 2.0+ and without so many invalid test results and having both positive and negative results reported.


In some sense, though, my (and our) feelings about Geno 2 Next Gen area moot point. The main audience for this is the vast unawashed masses. They don't know who we are or what we think. When and if they do find out, they will have already received their results for Geno 2 Next Gen and wondering what the transfer to FTDNA thing is about.
That's not a reason to not point out that Geno 2.0+ has a lot of problems and that there are better alternatives that might cost more but are of a lot more value. Informing the people that are willing to investigate before purchasing the test is something that should be done by people with the knowledge.

ph.
11-22-2016, 04:09 PM
Further to my comments way back in this thread.

I supported the original Genographic as well as the Geno2 due to their alleged purpose of using surplus funds for mapping global genetics.

It is disappointing if they are only subjected to the sampled corrections here rather than to open access and full peer review. On looking at the organisation in general, it would appear that they mainly are in the entertainment business rather than in research.

Any signs that they will at least be opening suitably anonymised databases ?

p.

Amerijoe
11-22-2016, 06:21 PM
I think that Geno 2 Next Gen could be a greater starter test for those first time DNA testers as they will get a mix of different types of DNA and then they can get more deeply engaged and learn more and join us, the crazies. :) However, there are some false positives in Geno 2 Next Gen today screwing up haplogroup labeling and confusing things. Geno 2 needs to strip out the failing SNPs from their test, and/or FTDNA needs to filter out the failing SNPs when they transfer Geno 2 results into the FTDNA system.

In some sense, though, my (and our) feelings about Geno 2 Next Gen area moot point. The main audience for this is the vast unawashed masses. They don't know who we are or what we think. When and if they do find out, they will have already received their results for Geno 2 Next Gen and wondering what the transfer to FTDNA thing is about.

Pardon me, I bathe every Saturday night, whether I need it or not. Growing up, this was the norm. Slums back then didn't have showers or bathtubs; so, you had to improvise. I remember being bathe in a washing machine. No, it wasn't going, then again, might have been fun! Where was I? O.K., I'm back to the present.

The mention of NG raises my 'Hackles' so to speak. I'm presently in hiatus, waiting for their support dept. to quit or be let go, either will do. My mtdna designation by them is J1c4. The other majors have me at mtdna J1c. Besides the numerous false positives, out of the two defining snps for J1c4, I have one with letters reversed and the other is not present. Even with this information in hand, she refused to admit any erroneous results and stuck to her guns that they were right. I've had my results looked at by two FTDNA group admins. and both concur the J1c designation is correct. Remember this is now part of the Murdoch 21st Century Fox Empire and what is their main product? Maybe pH is right as quoted from his post#83. ("On looking at the organisation in general, it would appear that they mainly are in the entertainment business rather than in research.")

They are taking orders as of today (US only). Results will be posting before you know it!B)

Ann Turner
11-23-2016, 11:44 AM
I started a new thread about Helix and the Genographic Project:

http://www.anthrogenica.com/showthread.php?9137-Helix-now-doing-the-testing-for-the-Genographic-Project

ArmandoR1b
11-23-2016, 01:11 PM
edit: Please delete. I posted in the wrong thread.