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Nat Geo 2.0 Next Gen Y-DNA haplogroup prediction seems wrong

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  • #16
    Nevermind, I see that you are using the nomenclature of Ray Banks' tree and not the official ISOGG tree.

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    • #17
      You don't need to check every SNPs, some SNPs will not give a correct call in Chip test. And Geno 2+ not test F845's downstreams, so you end at a marker 6300 years ago, still very rough. subgroup include: SK1036, K511, etc.
      http://yfull.com/tree/C-F845/

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      • #18
        Originally posted by owen View Post
        You don't need to check every SNPs, some SNPs will not give a correct call in Chip test. And Geno 2+ not test F845's downstreams, so you end at a marker 6300 years ago, still very rough. subgroup include: SK1036, K511, etc.
        http://yfull.com/tree/C-F845/
        Yeah, the subgroup that has K511 is the C2e1b1 subclade that ddxue said isn't tested by Geno 2.0 NextGen. I've verified that that by cross-referencing all of the SNPs in the subclade that are listed at Ray Banks' site https://sites.google.com/site/compositeytree/c2 Not a single one is included in the NextGen results of other people.

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        • #19
          Originally posted by Armando View Post
          Are you sure that you don't have F1673 in your CSV file? It shows up in the CSV file of other people that had the Geno 2.0 NextGen test and it is one of the SNPs that define C2e1b1.

          Are there more than 13,000 SNPs in the file that you are looking at? If not, then you don't have the right file.
          You are right, I was using Ray Bank's google doc for C2 that has different subclade nomenclature. Under the 2016 ISOGG tree I would be C2e2 F845+.

          I contacted the Nat Geo project last week about my incorrect Y-DNA haplogroup and they have yet to respond. I really hope this isn't happening to a lot of other people.

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          • #20
            Originally posted by ddxue View Post
            I contacted the Nat Geo project last week about my incorrect Y-DNA haplogroup and they have yet to respond. I really hope this isn't happening to a lot of other people.
            They have been making a lot of mistakes. They have given a R1b-U106 person a terminal SNP that belongs to the R1b-M222 subclade, They have given three R1b-DF27 people a terminal SNP that is way downstream of R1b-U152, and another person that is probably positive for Z2103 was given a terminal SNP above that because Geno 2.0 NextGen doesn't test for it.

            Those are just the ones I know about which means there are probably hundreds of people out there that don't know any better that are being given bad information. It seems to be a very big problem.

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            • #21
              Originally posted by Armando View Post
              They have been making a lot of mistakes. They have given a R1b-U106 person a terminal SNP that belongs to the R1b-M222 subclade, They have given three R1b-DF27 people a terminal SNP that is way downstream of R1b-U152, and another person that is probably positive for Z2103 was given a terminal SNP above that because Geno 2.0 NextGen doesn't test for it.

              Those are just the ones I know about which means there are probably hundreds of people out there that don't know any better that are being given bad information. It seems to be a very big problem.
              I just don't understand how they even got my general haplogroup wrong. It should have been easy to run my SNP results through their automated program and determine I could not be haplogroup J since I tested negative for many of the SNP's that define the top level haplogroup J-M304. Their algorithm can't be that bad... I think.

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              • #22
                Originally posted by ddxue View Post
                I just don't understand how they even got my general haplogroup wrong. It should have been easy to run my SNP results through their automated program and determine I could not be haplogroup J since I tested negative for many of the SNP's that define the top level haplogroup J-M304. Their algorithm can't be that bad... I think.
                There are way too many false positives in the test. The algorithms can only do so much with that situation. The BigY test is much better. There aren't so many false positives but it still takes analysis by haplogroup admins and/or a professional analysis by a company such as YFull for the best placement.

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                • #23
                  FTDNA finally updated their prediction of my Y-DNA haplogroup from 'pending' to F-P135.

                  It took less than 5 minutes for me to Ctrl+F through my raw Y-DNA SNP results to conclude I cannot be F-P135. Using the Haplogroup F tree, I did test positive for ANY of the Haplogroup F SNP's that are highlighted green on my FTDNA page.

                  How can FTDNA/Nat Geo be this incompetent? I contacted FTDNA and Nat Geo customer support and they of course gave me no response.

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                  • #24
                    My FTDNA & NatGeno Experience

                    Also had some questionable results from NatGeno as well. First, I contacted my project administrators to review the results. I was assured that corrections will be made in the near future. With this information I contacted NatGeno stating the questionable results.

                    Request Received Yesterday@1:02PM

                    Hi: kit# XTJPA3P3XR. Your mt haplogroup J1c4 designation is wrong. I checked with FTDNA project manager who reviewed and stated it is in error and my mt is still J1c. Also, checked with R1a FTDNA manager on the Y Haplogroup and indicated it should have been closer to R-Y2123. I'm assigned to R-Y15121*. There were an additional 22 positive snps in file that I'm now told are false positions. Hope this helps your project. Here are the emails indicating a 2 hr. response time from Geno Project.a

                    Thanks, Joe


                    Request Update Yesterday@3:32PM

                    Hello,

                    Thank you for contacting The Genographic Project, I have requested that the Raw Data regarding the results of your kit:XTJPA3P3XR be reviewed. As soon as I hear anything back from this investigation, I will notify you immediately.

                    I deeply apologize for any inconvenience this has caused you, your patience and understanding throughout this entire process has been greatly appreciated.

                    Best Regards,


                    Alyssa G
                    Information Specialist
                    The Genographic Project

                    I understand the frustration involved when things are off-track, but the companies involved do not want an inferior product. I for one, know that errors will be less frequent as time proceeds, it's how science works. This is is a new and developing science and some erroneous results will arise during the on-going process. Remember a positive approach leads to positive results.

                    Comment


                    • #25
                      Originally posted by Amerijoe View Post
                      Also had some questionable results from NatGeno as well. First, I contacted my project administrators to review the results. I was assured that corrections will be made in the near future. With this information I contacted NatGeno stating the questionable results.

                      Request Received Yesterday@1:02PM

                      Hi: kit# XTJPA3P3XR. Your mt haplogroup J1c4 designation is wrong. I checked with FTDNA project manager who reviewed and stated it is in error and my mt is still J1c. Also, checked with R1a FTDNA manager on the Y Haplogroup and indicated it should have been closer to R-Y2123. I'm assigned to R-Y15121*. There were an additional 22 positive snps in file that I'm now told are false positions. Hope this helps your project. Here are the emails indicating a 2 hr. response time from Geno Project.a

                      Thanks, Joe


                      Request Update Yesterday@3:32PM

                      Hello,

                      Thank you for contacting The Genographic Project, I have requested that the Raw Data regarding the results of your kit:XTJPA3P3XR be reviewed. As soon as I hear anything back from this investigation, I will notify you immediately.

                      I deeply apologize for any inconvenience this has caused you, your patience and understanding throughout this entire process has been greatly appreciated.

                      Best Regards,


                      Alyssa G
                      Information Specialist
                      The Genographic Project

                      I understand the frustration involved when things are off-track, but the companies involved do not want an inferior product. I for one, know that errors will be less frequent as time proceeds, it's how science works. This is is a new and developing science and some erroneous results will arise during the on-going process. Remember a positive approach leads to positive results.
                      Additional info:

                      RE: Update on Your Request {385959}
                      Today@1:03PM

                      ## Open Requests only: Reply ABOVE THIS LINE to add a note ##
                      Request Update Request ID: 385959

                      Hello Joe,

                      For Kit B82688, I see the problem you are addressing. We are working on a resolution. FTDNA is not exactly the same as the Genographic project and we are working on getting the SNPs to resolve. The solution is not implemented but we expect it to be soon.



                      Thank you


                      Best Regards,

                      Tom
                      Family Tree DNA

                      I'm usually impatient, I want the answer yesterday, but when people are honestly trying to resolve the issue, I graciously extend my patience. I hope my correspondence will show fellow members that solutions soon will be implemented.

                      Comment


                      • #26
                        Originally posted by Amerijoe View Post
                        There were an additional 22 positive snps in file that I'm now told are false positions. Hope this helps your project.
                        Too many false positives like I had said - http://forums.familytreedna.com/show...2&postcount=22

                        Comment


                        • #27
                          Also, as far as I've seen, they actually use LESS SNPs than they did on the old test! I see they tested less SNPs on R-L20 branch than on the old test and less on the V branch for mtDNA (in fact all they give is a basic V! the old test and even 23 which hasn't bothered to update in years gives more!). I thought at the least they'd ADD a few, hopefully all the basic ones, but at least a few extra R-L20 branch SNPs for all their talk about a radical improvement in Y-testing, almost as good as the full test! And that they could at least say turn V3 into V3c (and hopefully even another level). Instead it is just plain V!

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                          • #28
                            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.

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                            • #29
                              Nat Geo S7123 Mess

                              I have a project member that Nat Geo reported to be S7123+ so FTDNA assigned him to Haplogroup R-S7123. The problem is that he is reported as negative for every SNP in SNP Pack L513, many of which are upstream of S7123.

                              Comment


                              • #30
                                Originally posted by Jim Barrett View Post
                                I have a project member that Nat Geo reported to be S7123+ so FTDNA assigned him to Haplogroup R-S7123. The problem is that he is reported as negative for every SNP in SNP Pack L513, many of which are upstream of S7123.
                                Nat Geo Geno 2.0 or Nat Geo Geno 2.0 NextGen? What does he get at Nat Geo for the terminal SNP? What is the allele he gets in the raw data for S7123? In at least one NextGen file that I have an allele that is not compatible with ISOGG or Ybrowse is reported. In the FTDNA tree S7123 has
                                L193, Z16332, S5982, S5990, A5, A6, A4, S5992, BY208 as phylogenetic equivalents and YFull is in agreement and so is ISOGG. Out of those only S5982, S5990, and S5992 are included in the L153 SNP Pack.

                                It is technically possible to be positive for only one phylogenetic equivalent and for a person to create a new branch but since S7123 looks to be falsely called a positive by FTDNA it is doubtful.

                                Luckily not a lot of people will be getting false positives anymore since the Nat Geno NextGen test will now be done by Helix. http://cruwys.blogspot.co.uk/2016/11...-app-with.html But there will only be about 10,000 Y-DNA SNPs tested. The SNP Packs at FTDNA are still better.

                                Both the Geno 2.0 test and the SNP Pack show that a BigY test is still more valuable because it has the ability to find new subclades when a person is negative for all known subclades.

                                Comment

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