Wow, Geno 2.0 NG gave LESS haplogroup info for my dad than the old test!

[wombat]

Wow, I'm very upset.
They went on about how they had radically expanded the haplogroup testing and how it's well worth the upgrade but not only did they not test more than on the old test, they actually tested less!
I see on the free FTDNA transfer that they tested LESS SNPs for my dad's Y-haplogroup. LESS! And they did the same for his mtDNA haplgroup too!

They don't even give V1,V2,V3,etc. much less say break V3 down into V3c or more. All they give now is a V!

The old test and even 23 which hasn't bothered to update their haplogroups in years gave my dad more info!

[Armando]

From your other posts I see that L20 is the Y-DNA haplogroup that you are concerned about.

The original Geno 2.0 tested these SNP downstream from L20 which are all in the 3 April 2016 ISOGG tree as R1b1a1a2a1a2b1a1~ - L737, L739, Z291, Z383 and for R1b1a1a2a1a2b1a1a which are CTS11795 and PF121 in the same ISOGG tree. The only SNPs missing from the Geno 2.0 NextGen are L737, Z291, and Z383 which are phylogenetically equivalent to L739 anyway.

There are 12,051 SNPs in the original Geno 2.0 test and there are 13,630 SNPs in the Geno 2.0 NextGen test. The BigY tests more than 36,400 Y-DNA positions. With a sale and a coupon the BigY is a better deal because only one other company tests more Y-DNA positions but for a higher price.

The mtDNA test from Geno 2.0 NextGen is already known not to test the whole mitochondrion and not to provide matching.

[Armando]

Have you downloaded your father's Y-DNA CSV file after doing a transfer to FTDNA? You can see where to download it from at http://i.imgur.com/gcRTGZr.jpg

[wombat]

From your other posts I see that L20 is the Y-DNA haplogroup that you are concerned about.

The original Geno 2.0 tested these SNP downstream from L20 which are all in the 3 April 2016 ISOGG tree as R1b1a1a2a1a2b1a1~ - L737, L739, Z291, Z383 and for R1b1a1a2a1a2b1a1a which are CTS11795 and PF121 in the same ISOGG tree. The only SNPs missing from the Geno 2.0 NextGen are L737, Z291, and Z383 which are phylogenetically equivalent to L739 anyway.

There are 12,051 SNPs in the original Geno 2.0 test and there are 13,630 SNPs in the Geno 2.0 NextGen test. The BigY tests more than 36,400 Y-DNA positions. With a sale and a coupon the BigY is a better deal because only one other company tests more Y-DNA positions but for a higher price.

The mtDNA test from Geno 2.0 NextGen is already known not to test the whole mitochondrion and not to provide matching.

All I can say is testing LESS L20 SNPs than the old test and LESS for mtDNA V3 is pretty poor for all their bragging about how the Y testing would be as good as BigY SNPs for most people and that the mtDNA was noticeably expanded as well.

Not only did they not add for everyone they actually took away many SNPs! They barely added anything new for anyone.

[wombat]

From your other posts I see that L20 is the Y-DNA haplogroup that you are concerned about.

The original Geno 2.0 tested these SNP downstream from L20 which are all in the 3 April 2016 ISOGG tree as R1b1a1a2a1a2b1a1~ - L737, L739, Z291, Z383 and for R1b1a1a2a1a2b1a1a which are CTS11795 and PF121 in the same ISOGG tree. The only SNPs missing from the Geno 2.0 NextGen are L737, Z291, and Z383 which are phylogenetically equivalent to L739 anyway.

There are 12,051 SNPs in the original Geno 2.0 test and there are 13,630 SNPs in the Geno 2.0 NextGen test. The BigY tests more than 36,400 Y-DNA positions. With a sale and a coupon the BigY is a better deal because only one other company tests more Y-DNA positions but for a higher price.

The mtDNA test from Geno 2.0 NextGen is already known not to test the whole mitochondrion and not to provide matching.

According to the old test he was negative for CTS4069 (which is two branches down from Z291). But they didn't even test that SNP this time. The old test also had him negative for L144 (two branches down from CTS9733) (edit: from what I read L144 was broken on the old test and always registered negative). The new one didn't test that either. It had him positive for Z383. And the new one didn't test that either. (maybe they found everyone downstream has it????)

For the already did before he test T for PF121.2 which appears to be the positive value.

The only SNPs missing from the Geno 2.0 NextGen are L737, Z291, and Z383 which are phylogenetically equivalent to L739 anyway.

Hmm well a problem I see (although maybe I just don't know how this is supposed to work) is that he seems to be L739- and yet Z383+ and yet he is also PF121.2+ which was listed on the ISOGG as being downstream if you have all those but he is only positive for some of the upstream values. So something doesn't seem to add up. He is also CTS11795.2-. But now Geno doesn't even test for Z383 and some others in that tentative branch they have one spot down from L20 on ISOGG. What if they figure out a split and now Geno won't be able to handle it properly? And if a place that tests tons of people like Geno has removed some of the various bits won't it make it less likely they figure out how to get it worked out?

It seems like they have given up, pretty much, on L20 branch since they didn't add any of the branch SNP that FTDNA has downstream. FTDNA shows a lot of BY findings and some regular ones downstream. For all their talk, you'd think they'd have tossed a few in to expand research on this line and help build up a much larger database of research.

(and there is still his V mtDNA which is tested levels less deep than known and less deep than the last test! in this case it is 100% known that there are bunch of downstream variants and they are all established and many even used to be tested for, but not only did they not add they few they were missing, they now removed a bunch!)

[wombat]

I see some people are Z291- and Z383+ plus.

One confusing thing is I'm not seeing PF121 or CTS11795 under the L20 section of FTDNA's Y-haplotree. Do you know if they have called those SNPs something else?

It seems like they call L739 as CTS4069 (at least according to one website)? Odd that both versions of the test tested my dad for it but they only list it as negative when using his old kit and as untested when using his new kit???

[wombat]

According to the ISOGG and using the old test my dad got:
R1b1a1a2a1a2b1a1 L20/S144+
• R1b1a1a2a1a2b1a1~ L737-, L738 (not tested?), L739-, S256/Z291-, Z383+
• • R1b1a1a2a1a2b1a1a~ CTS11795.2-, PF121.2+

[Armando]

[QUOTE=wombat;424545]All I can say is testing LESS L20 SNPs than the old test and LESS for mtDNA V3 is pretty poor for all their bragging about how the Y testing would be as good as BigY SNPs for most people and that the mtDNA was noticeably expanded as well.[QUOTE=wombat;424545] I can't find anywhere that they claimed the Y testing would be as good as BigY SNPs. The only claim that turned out incorrect about Y-DNA SNPs is that was a news story at Genomeweb that there were going to be close to 20,000 of them but the FAQ pages states more than 15,000 which is accurate if the redundant names are counted. https://genographic.nationalgeograph...etween-1-geno2

Not only did they not add for everyone they actually took away many SNPs! They barely added anything new for anyone.

They definitely added SNPs for some people. Otherwise there wouldn't be more Y-DNA SNPs tested. Who they added SNPs for and who they didn't would take too much work.

Regardless, your bad experience, that of others, should be a warning to people to get tested at FTDNA and not with Geno.

[Armando]

According to the old test he was negative for CTS4069 (which is two branches down from Z291). But they didn't even test that SNP this time. The old test also had him negative for L144 (two branches down from CTS9733) (edit: from what I read L144 was broken on the old test and always registered negative). The new one didn't test that either. It had him positive for Z383. And the new one didn't test that either. (maybe they found everyone downstream has it????)

For the already did before he test T for PF121.2 which appears to be the positive value.

CTS4069 in the Geno 2.0+ CSV files of two different people. Did you do the transfer and download the CSV file that has about 12,630 SNPs?

Hmm well a problem I see (although maybe I just don't know how this is supposed to work) is that he seems to be L739- and yet Z383+ and yet he is also PF121.2+ which was listed on the ISOGG as being downstream if you have all those but he is only positive for some of the upstream values. So something doesn't seem to add up. He is also CTS11795.2-. But now Geno doesn't even test for Z383 and some others in that tentative branch they have one spot down from L20 on ISOGG. What if they figure out a split and now Geno won't be able to handle it properly? And if a place that tests tons of people like Geno has removed some of the various bits won't it make it less likely they figure out how to get it worked out?

The Geno 2.0+ also has a problem with false positives and possibly false negatives. This is another reason why Geno 2.0+ is not a very good test.

It seems like they have given up, pretty much, on L20 branch since they didn't add any of the branch SNP that FTDNA has downstream. FTDNA shows a lot of BY findings and some regular ones downstream. For all their talk, you'd think they'd have tossed a few in to expand research on this line and help build up a much larger database of research.

They have only claimed to have tested more SNPs and never claimed to be better for everyone. They don't do in-depth analysis of all lineages. They have their own Y-DNA tree and they have to operate on a limited budget. A lot of the gains with the ISOGG tree and FTDNA tree is from citizen scientists who are mainly concerned about western European lineages. The scientists at Geno are concerned about all Y-DNA lines so they have less time to concentrate on specific lineages.

(and there is still his V mtDNA which is tested levels less deep than known and less deep than the last test! in this case it is 100% known that there are bunch of downstream variants and they are all established and many even used to be tested for, but not only did they not add they few they were missing, they now removed a bunch!)

So I repeat, this should be lesson to people to not get the Geno 2.0 NextGen test.

[Armando]

I see some people are Z291- and Z383+ plus.

One confusing thing is I'm not seeing PF121 or CTS11795 under the L20 section of FTDNA's Y-haplotree. Do you know if they have called those SNPs something else?

ISOGG is the only tree that has PF121 and CTS11795 and they are in grey which means they are Investigational items. Z383 is not in the BigTree at http://www.ytree.net/DisplayTree.php...440&star=false or at YFull either https://www.yfull.com/search-snp-in-tree/

It seems like they call L739 as CTS4069 (at least according to one website)?

L739 is 16428800 G->A and CTS4069 is 15375055 C>G but CTS4069 so they are definitely different SNPs although they could be phylogenetically equivalent. CTS4069 is not in ISOGG, YFull, or the BigTree. I had to go to Ybrowse http://ybrowse.org/gb2/gbrowse/chrY/? in order to find it.

Odd that both versions of the test tested my dad for it but they only list it as negative when using his old kit and as untested when using his new kit???

Where do you see your dad shows untested for CTS4069? Is it in the CSV file from the default FTDNA page that has about 13,630 SNPs tested? Or are you just looking at the list of SNPs at the bottom of the FTDNA haplotree page?

[wombat]

The Geno 2.0+ also has a problem with false positives and possibly false negatives. This is another reason why Geno 2.0+ is not a very good test.

Although regarding CTS11759.2- and PF121.2+ he got the same on both the old and new so maybe those results are correct. And he got so many of the others all negative on the tentative branch just above on the old test you'd think there might be some truth to that, so perhaps the way ISOGG was guessing the extensions might work is wrong?

[wombat]

Well it's a bit confusing since FTDNA with the old test reports some of the negative results on the tree and won't let you order those SNPs (since they were already tested), but it doesn't do that for all of them (since it does let you order a few that I see were tested), it doesn't really make sense. With the new data it's claiming you might want to order everything under L20 even though I see in the full download that a few actually were tested.

They actually are still testing L144 (apparently it's very rare, ultra rare, so it's weird they are testing a SNP that seems to be a few stages past L20 and not an earlier one).

They no longer test for the Z291, L737, L739, Z383 as you said though. FTDNA has Z383 possibly the same as L20 so maybe that one doesn't matter. They have Z291 forming a new branch, so it's odd they got rid of it on the new test. My dad was negative for it anyway at least. They don't test a few other next branch points FTDNA has. I do see that they did add in one next test for L20 I think it was Z2191, I forget. I have to check to see if I can dig up any more. So it seems like they might have taken away one and added one new one. Not sure what ancestral and derived is for that, since FTDNA didn't bother to list it as tested (even though it was) I assume maybe that means he is negative for it?
And I guess they don't yet know where to place the PF121.2 yet so they don't bother listing it as a terminal SNP with info yet. So it seems like overall it's a wash. They could've added just a few more to cover the entire FTDNA base for the next level, but instead removed one, added one new one and didn't add the others.

[KATM]

CTS4069 in the Geno 2.0+ CSV files of two different people. Did you do the transfer and download the CSV file that has about 12,630 SNPs?

The Geno 2.0+ also has a problem with false positives and possibly false negatives. This is another reason why Geno 2.0+ is not a very good test.

They have only claimed to have tested more SNPs and never claimed to be better for everyone. They don't do in-depth analysis of all lineages. They have their own Y-DNA tree and they have to operate on a limited budget. A lot of the gains with the ISOGG tree and FTDNA tree is from citizen scientists who are mainly concerned about western European lineages. The scientists at Geno are concerned about all Y-DNA lines so they have less time to concentrate on specific lineages.

So I repeat, this should be lesson to people to not get the Geno 2.0 NextGen test.

Armando, can you refer me to a website where I can see which Y haplogroup SNPs that Geno 2.0 NextGen does test? I gave a NextGen kit to a male who is likely to have an "I" haplogroup, if he ever uses the kit. He is of direct line male Scandinavian descent, back to about the mid-1700s. I was hoping to get at least a general idea (I1a, I2b, etc.), but now not sure if that will show, from what you are saying.

[wombat]

Armando, can you refer me to a website where I can see which Y haplogroup SNPs that Geno 2.0 NextGen does test? I gave a NextGen kit to a male who is likely to have an "I" haplogroup, if he ever uses the kit. He is of direct line male Scandinavian descent, back to about the mid-1700s. I was hoping to get at least a general idea (I1a, I2b, etc.), but now not sure if that will show, from what you are saying.

If you ask me the SNPs you are looking for I can check.

[wombat]

I do see that they did add in one next test for L20 I think it was Z2191, I forget.

To correct my statement above the new sub-L20 test they added is for BY2171. I can't see to find what the ancestral value is. I assume my dad must have tested negative for this SNP change but since FTDNA seems a touch hit and miss in how they are tracking transferred SNPs I'm not 100% sure. They made it seem like he wasn't tested for it, but now going through the raw data I see that he was.

FTDNA is somewhat random in whether they say you should or shouldn't order a SNP because you have or haven't already been tested for it. They note some that were tested but fail to note others so that led to some confusion.