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

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  • wombat
    replied
    Well I finally got an answer on the BY2171. And it turns out that is one of the ones they read strand reversed. So Geno 2.0 NG and FTDNA putting as down as negative for that is correct. The RAW data download from FTDNA is confusing though since the ones that are strand reversed are not labelled so off-hand there would be no way to know.

    I guess that is sort of interesting. Between the old Geno 2.0 (which did actually test more R-L20 sub-branches than the new one!) and the new Geno 2.0 NG which did test a new and major BY2171 sub-branch that the old test did not it seems that we are negative all of the known R-L20 sub-branches then.

    The question is, is that just nothing much and just an artifact that not enough R-L20 have tested anywhere yet or it is some clue that there is something unusual about our R-L20. We do know that R-L20 is found only very rarely in our main country of ancestry (I see only one other person on all of FTDNA reporting the same country.) so might this hint that R-L20 maybe could go way back in the Baltics and that there could be some unique, old, very rare branch there from way back when and it's not something that snuck in from some other region more recently? Hard to say yet. But interesting.

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  • Armando
    replied
    Originally posted by KATM View Post
    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.
    I don't know of any website and I don't know why they don't publicize the SNPs that are tested. I do think that you will be able to determine if he is I1a, I2b, etc because there are 179 I1 and I2 SNPs tested. Just be sure to have a haplogroup admin check the results for you once you get them transferred to FTDNA. You'll also be able to download the CSV file yourself and compare the results with what is found at http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html and if you know how to use Vlookup or Index Match functions then you can automate the process.

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  • wombat
    replied
    Originally posted by Armando View Post
    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.
    Actually the thing where I said he had a - and + for something downstream of mixed negative results I don't think points to Geno 2.0 NG error at all. Looking over a bunch of BigY and such results it seems like many others have similar stuff going on so I think the problem is actually with the "needs more research tentative" item ISOGG has directly under their L20 branch, it seems that many get some of those negative and yet get L20 line and the line two below with some positive.

    It could also be that I misinterpreted what they meant by the first line below L20. They might mean those were just a bunch of various potential branch points and that not all of them should be positive before being able to get to the next line below that one. So there may not even be any conflict at all possibly.

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  • wombat
    replied
    Hmm this is becoming confusing. For L20 using old or new I have what the ISOGG lookup calls derived which makes sense since am L20+. For Z291 and YSC0000193 branches on the old test (not tested on the new) have what it calls the ancestral values which makes sense since Z291- and YSC0000193-.

    But for this new BY2171 that the new test has according to the ISOGG SNP lookup it would seem the derived value (AA) is showing up and yet FTDNA appears to be showing me on the chart as untested (which it might mean to be negative).

    So does this mean FTDNA is messing up handling this SNP transfer, that a problem has been found with that probe so they are ignoring it on purpose or that this is one of the SNPs that they measured on the - strand instead of the + strand and you need to interpret ancestor and derived in opposite fashion?

    If BY2171 actually is derived then maybe the new test has found a new sub-L20 branch that we are actually on. Perhaps in time they will update the terminal SNP on their site to show this when and if it appears as an official ISOGG in a year or two or when they get around to deciding how to handle it?

    I'll have to contact them.

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  • wombat
    replied
    Originally posted by wombat View Post
    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. (confusingly the old test did test for a CTS2171 on the Y, not sure if that is the same thing, maybe it already had it?) Actually I found the ancestral/derived for it on ISOGG YBrowse. But that would suggest he has positive for some of these. FTDNA transfer appears to suggest either not tested or negative. It could be a positive/negative strand issue. Or FTDNA transfer not working properly.

    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.

    It seems I found another branch of L20 sub the old test tested for that the new one doesn't. So now it seems that is two subs for the old test and one for the new.

    But it's complex since SNP names change.

    I wish I knew what Geno/FTDNA considered to be the ancestral for each of the SNPs. I read that the chip sometimes uses different strand +/- for different SNPs in a few cases so how do you know when trying to parse it yourself?

    Maybe L20 is not studied enough. Until I hear from them it's hard to know what is going on. Maybe the L20 handling is reasonable and maybe not. The V mtDNA is bad though for sure and that is what really got me going.

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  • KATM
    replied
    Originally posted by wombat View Post
    If you ask me the SNPs you are looking for I can check.
    Thanks for the offer, but right now the person in question has done no testing whatsoever, so we have no idea of his Y haplogroup, or any SNPs. I only speculate that he might be in one of the "I" groups, since they are prevalent in Scandinavia. It could be otherwise, of course.

    I was just wondering if the "I" haplogroup SNPs were limited in the Geno 2.0 NextGen test.

    Leave a comment:


  • wombat
    replied
    Originally posted by wombat View Post
    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.

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  • wombat
    replied
    Originally posted by KATM View Post
    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.

    Leave a comment:


  • KATM
    replied
    Originally posted by Armando View Post
    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.

    Leave a comment:


  • wombat
    replied
    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.

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  • wombat
    replied
    Originally posted by Armando View Post
    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?

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  • Armando
    replied
    Originally posted by wombat View Post
    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/

    Originally posted by wombat View Post
    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.

    Originally posted by wombat View Post
    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?

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  • Armando
    replied
    Originally posted by wombat View Post
    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?




    Originally posted by wombat View Post
    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.

    Originally posted by wombat View Post
    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.

    Originally posted by wombat View Post
    (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.

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  • Armando
    replied
    [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

    Originally posted by wombat View Post
    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.

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  • wombat
    replied
    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+

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