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Thread: The Insoluble Dilemma of Commercial Haplogroup Predictors used by FTDNA/Genographic

  1. #51
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    Quote Originally Posted by ArmandoR1b View Post
    Wow, I just read your thread about your Geno 2.0 Haplogroup J prediction from Feb 2016 http://www.anthrogenica.com/showthre...6-Punjabi-Jatt

    Ali16 really had been giving you great advice and posts for the most part including that you are H-M69 and that Geno 2.0 NextGen has bad results and that you should test with Yseq.

    I really like the post by Ali16 with the link to the explanation by Charles Moore about how Chromo2 and the first version of Geno 2.0 had a lot of false positives that were taken out before even before they released the results but that for Geno 2.0 NextGen "Ray is seeing the same problems, not surprisingly, but he seems to be indicating that they haven't been doing as good a job of deleting the results from the false positives."

    Charles Moore also states:

    "Although the Geno Next Gen test covers more SNPs than the old Geno 2.0 test, it's not the best alternative for serious genetic genealogists in comparison to other tests that are available today. It's a test for newbies coming in from National Geographic.

    The better alternatives at the high end, are the NGS-type tests from FGC or FTDNA, or otherwise the SNP Pack/Panel tests from FTDNA or YSEQ. Although these alternatives yield more reliable results, their real benefit is that they take you further down your line of descent, matching you to fewer people more closely related to yourself.
    "

    https://groups.yahoo.com/neo/groups/...messages/42150

    I got more SNP both positive and negative from Geno 2 than any other company ...............I got more help from Geno 2 than anyone else............I got the first truly accurate ydna and mtdna than anyone else ...................and the worst is 23andme ......
    In 23andme v3 I had T marker ( which I am ) since november 2015 they are using v4 format and have placed me under F marker , because my v3 SNP's are no longer in their v4 system. Utterly useless company


    My Path = ( K-M9+, LT-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+, Y349970+ )


    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna

  2. #52
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    Quote Originally Posted by vettor View Post
    I got more SNP both positive and negative from Geno 2 than any other company ...............I got more help from Geno 2 than anyone else............I got the first truly accurate ydna and mtdna than anyone else
    That was the first version of Geno 2.0 and not Geno 2.0 NextGen. There is a higher percentage of people that get an incorrect haplogroup or subclade with Geno 2.0 NextGen than did with the first version of Geno 2.0 or with 23andme. I haven't seen you post that you have had a BigY test so you could see that with a YFull or FGC analysis it would give you more positive and negatives than any other company. The FTDNA FMS tests more of the mtDNA than any other company except a much more expensive FGC test. With a BigY test you would probably create a new subclade at https://www.yfull.com/tree/T-CTS8489/

    Quote Originally Posted by vettor View Post
    ...................and the worst is 23andme ......
    In 23andme v3 I had T marker ( which I am ) since november 2015 they are using v4 format and have placed me under F marker , because my v3 SNP's are no longer in their v4 system. Utterly useless company
    23andme tests a far too low of a number of Y-DNA SNPs. There are less than 1,000 Y-DNA SNPs without no-calls. 884 in one of the files that I looked at. The first version of Geno 2.0 had about 12,000. Geno 2.0 NextGen probably has the same number or even less if all of the extra false positives and false negatives are removed. BigY has almost 36,000 SNPs in the VCF file the actual number of usable SNPs will be far less but a lot more than Geno 2.0.

  3. #53
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    Quote Originally Posted by ArmandoR1b View Post
    Jatt, thank you for posting what happened. I wish I had known.

    I haven't had any bad experiences in any of the FTDNA groups that I have joined. Some of the group admins are people that post at Anthrogenica and used to post at other DNA forums, or still do, and are extremely knowledgeable and helpful people even if I disagree with a statement or two. If the FTDNA groups and Anthrogenica didn't exist we would only have a little more knowledge than we had in 2009 for Y-DNA and mtDNA. You really have no idea how much they have helped. These past seven years have sped along a lot thanks to increased testing by FTDNA, the first version of Geno 2.0, Yseq, FGC, and YFull. The first version of Geno 2.0 was also done in the lab of FTDNA but it was a good test for the most part. YSEQ was started by Dr. Thomas Krahn former scientist at FTDNA that developed the chip for the first version of Geno 2.0. YFull analyzes FTDNA BigY testing and is a very good service. If you had lived through all of the advances you would understand.
    I really appreciate all the support that I have got from you and all the forum members. I do understand that this is an evolving science and that discrepancies, honest mistakes etc. would always be there and that is patience is required to have things sorted out. I am sure that most of the administrator are friendly and with a professional attitude but I just happened to get connected to a bad one. This forum has been very helpful in broadening my understanding about haplogroups and once again , I thank you all for your time and assistance.

    Regards,
    Jatt2016
    Last edited by jatt2016; 08-12-2016 at 10:06 PM.

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  5. #54
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    Quote Originally Posted by ArmandoR1b View Post
    That was the first version of Geno 2.0 and not Geno 2.0 NextGen. There is a higher percentage of people that get an incorrect haplogroup or subclade with Geno 2.0 NextGen than did with the first version of Geno 2.0 or with 23andme. I haven't seen you post that you have had a BigY test so you could see that with a YFull or FGC analysis it would give you more positive and negatives than any other company. The FTDNA FMS tests more of the mtDNA than any other company except a much more expensive FGC test. With a BigY test you would probably create a new subclade at https://www.yfull.com/tree/T-CTS8489/


    23andme tests a far too low of a number of Y-DNA SNPs. There are less than 1,000 Y-DNA SNPs without no-calls. 884 in one of the files that I looked at. The first version of Geno 2.0 had about 12,000. Geno 2.0 NextGen probably has the same number or even less if all of the extra false positives and false negatives are removed. BigY has almost 36,000 SNPs in the VCF file the actual number of usable SNPs will be far less but a lot more than Geno 2.0.
    Thanks

    I will not get better than Samargyl reading for me even if I do a bigY
    from semargyl below

    T1a2 L131>Y6033/L446>CTS933>CTS11984>CTS8862+ Europe

    The only benefit is IF i branch out from brand new branch and that cannot happen with CTS8862


    My Path = ( K-M9+, LT-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+, Y349970+ )


    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna

  6. #55
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    Quote Originally Posted by vettor View Post
    Thanks

    I will not get better than Samargyl reading for me even if I do a bigY
    from semargyl below

    T1a2 L131>Y6033/L446>CTS933>CTS11984>CTS8862+ Europe

    The only benefit is IF i branch out from brand new branch and that cannot happen with CTS8862
    That's not true. You have more SNPs that are yet to be named or to be tested by any other test besides BigY or FGC.

    At least one of the people that created Semargl is also part of YFull which does the analysis of BigY tests and they created YFull for a reason - because BigY is important for learning more about the phylogeny of the Y-DNA tree. http://isogg.org/wiki/YFull

    Go to https://www.yfull.com/tree/T-CTS8489/ the click on info next to where it says formed 2800 ybp, TMRCA 2200 ybp. You'll see that they have 13 more SNPs. Those SNPs are unnamed but they have been tested for them by 1000 Genomes another test. You will also see that there are 3 people in that group. One of them is even brand new and is from Cagliari. So between you, the person from Cagliari, the Puerto Rican, and the Iberian you will create a new subclade out of those 13 SNPs that might or might not include one or two of them. Downstream from them are two more that have been tested by BigY. They have a common ancestor in about the last 375 years. You are very unlikely to match them.

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  8. #56
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    I'll say this for Nat Geno's 2.0 next gen: It seems to do a pretty good job for some haplotypes (like R1b?). In my case, it went far past R1b>P312>DF19>DF88 to R-S4281, which is pretty darn specific for a first test.
    FTDNA's custom bundled SNP pack only moved me along two more steps. It's gonna take a BigY to find out any more.
    Last edited by Dewsloth; 08-16-2016 at 04:52 PM.

  9. #57
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    Quote Originally Posted by Dewsloth View Post
    I'll say this for Nat Geno's 2.0 next gen: It seems to do a pretty good job for some haplotypes (like R1b?). In my case, it went far past R1b>P312>DF19>DF88 to R-S4281, which is pretty darn specific for a first test.
    FTDNA's custom bundled SNP pack only moved me along two more steps. It's gonna take a BigY to find out any more.
    There are people that are R1b>P312>DF27>etc, etc based on other testing but Geno 2.0 NextGen put them into U152 even though they were negative for U152.

    There are people that are positive for the phylogenetic equivalents of R1b>M269>L23>Z2103>and another SNP I forget but the Geno 2.0 NextGen site told them they are just R1b>M269>L23.

    GoldenHind has other examples at http://www.anthrogenica.com/showthre...ss-and-Mystery

    lgmayka has an example also at http://www.anthrogenica.com/showthre...l=1#post133204

    The rate of incorrect placement of Geno 2.0 NextGen is too high even for R1b.

  10. #58
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    Quote Originally Posted by ArmandoR1b View Post
    That's not true. You have more SNPs that are yet to be named or to be tested by any other test besides BigY or FGC.

    At least one of the people that created Semargl is also part of YFull which does the analysis of BigY tests and they created YFull for a reason - because BigY is important for learning more about the phylogeny of the Y-DNA tree. http://isogg.org/wiki/YFull

    Go to https://www.yfull.com/tree/T-CTS8489/ the click on info next to where it says formed 2800 ybp, TMRCA 2200 ybp. You'll see that they have 13 more SNPs. Those SNPs are unnamed but they have been tested for them by 1000 Genomes another test. You will also see that there are 3 people in that group. One of them is even brand new and is from Cagliari. So between you, the person from Cagliari, the Puerto Rican, and the Iberian you will create a new subclade out of those 13 SNPs that might or might not include one or two of them. Downstream from them are two more that have been tested by BigY. They have a common ancestor in about the last 375 years. You are very unlikely to match them.
    Thanks

    food for thought

    Maybe it is worthwhile for me to test as I only have common ancestors with
    1 x catalan
    1 x East-central Italian
    3 x north Italians
    2 x tyrolese
    1 x baden-baden germany
    1 x hessian germany

    and some britsh isles ( usually welsh and irish only )

    The 2 from north and south carolina USA which are common ~375 years ago are linked with me via ftdna .............I already spoke to these members who both state they are of scottish origins.


    My Path = ( K-M9+, LT-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+, Y349970+ )


    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna

  11. #59
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    Quote Originally Posted by ArmandoR1b View Post
    There are people that are R1b>P312>DF27>etc, etc based on other testing but Geno 2.0 NextGen put them into U152 even though they were negative for U152.
    Are the Z195- (ZZ12+) 'half' of DF27 getting any indication they are DF27+ from Geno 2.0 NextGen?

  12. #60
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    Quote Originally Posted by corner View Post
    Are the Z195- (ZZ12+) 'half' of DF27 getting any indication they are DF27+ from Geno 2.0 NextGen?
    I don't know. What I can say, after cross-referencing http://www.ytree.net/SNPIndex.php, is that there are about 120 subclades of ZZ12, including ZZ12_1, that are tested by Geno 2.0 NextGen but only about 81 aren't false positives or another type of problem. For instance ZZ12_1 shows as A for a U106 person but the ancestral is T and the derived is C. P312 and DF27 are not tested by Geno 2.0 NextGen.

    These are the ZZ12 subclades that are possibly tested correctly -
    Code:
    FGC20761, CTS7204, CTS9952, BY837, BY1364, BY1717, PF6555, Z1513, FGC11413, FGC20750, FGC20756, FGC20748, FGC20769, CTS11087, CTS11565, BY1293, BY1356, BY1477, L617, DF81, PR4859, BY1380, BY2114, BY2533, PF6566, FGC22193, FGC20752, Z227, CTS7759, Z240, Z234, Z2567, BY834, FGC14936, BY1211, FGC20767, F1343, CTS1155, BY1485, BY1711, CTS7356, F1928, CTS9545, CTS6519, FGC14937, BY734, Y7352, FGC21119, Y7356, FGC21120, Y7354, FGC21122, Y7357, FGC21124, Y6954, FGC20554, BY1058, BY2285, Y5075, FGC22213, Y5076, FGC22190, A641, FGC19598, Y5058, FGC22195, Y5069, FGC22206, Y5077, FGC22203, FGC22225, Y5065, FGC22191, A431, Y3267, BY1246, FGC11394, FGC11398, FGC11378, FGC11379, CTS8308

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