National Geno 2.0 Next Gen Y SNPs

[TigerMW]

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]

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]

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]

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]

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]

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]

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]

" ...
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]

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]

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.