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

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

    Hi Folks,

    I am writing this article/post in wake on my experience dealing with different genetic testing companies namely FTDNA and Geongraphic regarding ancestry testing in particular Y Haplogroup assignments.These companies use a DNA Microarray (also commonly known as DNA chip or Biochip) for SNP detection, some capable of testing as many as around 700,000 SNPs. for autosomal and 13,600 for Y-DNA. Based on the tested positive and negative SNP’s, a data set is generated which is most commonly called as “ RAW DATA” is available to download for the clients. Once the Raw data is generated, it has to go through a “Computation stage “ where an algorithm is used to predict your possible haplogroup. This stage is the most important one and this computation/algorithm would decide your predicted haplogroup. Please note that I am using the term “predicted” haplogroup because these algorithms are prone to make errors and get confused easily. I will give you an example at the later stage of this discussion.


    How this algorithms works : These are basically computer programs that filter your positive/negative SNPS and assign you a haplogroup based on programming logic . It could be as simple as an excel spread sheet with functional programming ( If and then Loops/vlookups or index match). For instance if Cell value = P62 then assign Haplogroup H , if Cell value = M98 then assign Haplogroup T. The real programming can be complex but I am giving this example just to make people understand how these algorithms works.

    What is wrong with these programs/algorithms?

    These algorithms are prone to make incorrect predictions, the higher the number of SNPs the more unreliable the prediction becomes. To support my argument, I am pasting a screen shot of one such prediction tool. Please note that the predictor assigned me Haplogroup J based on the following tested positive SNPs by FTDNA (provided at the end of this post). When I investigated the issue, it came out that I did not have the basal SNPs – the top most SNP that are a pre-requisite for a person to be placed under the J Haplo. Genographic/FTDNA Haplogroup predictor and also Morley Predictor got confused and incorrectly assigned me J, F and R so on. The tools do not have the intelligence and lack the programing logic to read a pattern and instead incorrectly assign haplogroups based on the very last positive tested SNP. To clarify the point further, please look at the screen shot 1 pasted below



    As you can see that the Predictor calculated me as J but I was negative for M410 and M174 (basal SNPS for J) and if you are negative for that you cannot be a J, but the predictor was not smart enough to see that. The quality control at Genographic/FTDNA were not smart either to pick this error until I brought this to their attention. They acknowledged the problem but were unable to resolve it and kept on assigning me different haplogroups from J to R to H to F and so on to the point that I no longer trust their prediction. Not that it’s their fault but this is a system limitation and more to do with weaknesses in the overall testing platform . The Chip based technology at this point in time is not so mature and many of the clients are assigned a wrong haplogroup by FTDNA/NATGEO without even knowing it.

    The margin of error is more if you are non- European because most Y-DNA datasets/samples lack adequate information about people of non -European decent. Many of the non european haplogroups lack the SNP density required to correctly assign a correct subclaude. Some of the weaknesss, I have noticed are :


    • False positives, False Negatives and No Calls
    • Reverse Mutations - how would these be addressed?
    • Poorly programmed Haplogroup predictors.
    • Poor or Lack of indequate Quality control




    Would love to hear from other forum members of what they think of this issue.

    Thanks and regards,
    Jatt2016

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    Last edited by jatt2016; 08-07-2016 at 12:37 PM.

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    There has been more than one forensic DNA crime lab scandal where
    errors were made and then hidden with the knowledge that lives could
    possibly be ruined or even extinguished. I assume these were held to
    a much higher legal and quality control standard then a genealogy
    oriented DNA testing lab with no outside oversight and which targets
    people looking to see if they are related to Jessie James.

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    Quote Originally Posted by rock hunter View Post
    There has been more than one forensic DNA crime lab scandal where
    errors were made and then hidden with the knowledge that lives could
    possibly be ruined or even extinguished. I assume these were held to
    a much higher legal and quality control standard then a genealogy
    oriented DNA testing lab with no outside oversight and which targets
    people looking to see if they are related to Jessie James.
    The irony is that many laymans like me think that the science of assigning a haplogroups is as concrete as testing your blood group and this is how these vendors also portray and say that " YOUR ASSIGNED HAPLOGROUP is this n that " and brag about: " that we test around 700,000 SNPS across your entire genome", whereas the fact of the matter is that there is a huge amount of uncertainty involved which these vendors do not communicate to their clients because they will lose business. Testing 700,000 SNPS with a genochip is no big deal but do you have the tool and the quality control to interpret the results for the 700,000 SNPS correctly? I will share more on my experience and hoping that it would serve as an eye opener for us all. You would be surprised to hear some of the very unprofessional responses and rather bizarre experiences that I had with them.

    More to come as this thread proceeds !
    Last edited by jatt2016; 08-07-2016 at 04:26 AM.

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    Jatt,

    There are several very important things that need to be clarified in this thread.

    1. Your thread should have been in the Geno 2.0 sub-forum because the chip was designed and paid for by Genographic. The DNA testing is done in the FTDNA lab but it is not a chip owned by FTDNA, nor did they specify which autosomal, Y-DNA, or mtDNA SNPs should be tested, nor is there an equivalent test by FTDNA.

    2. You should specify that it is the Geno 2.0 Next Generation test. The first Geno 2.0 was with a different chip.

    3. The 700,000 SNPs are for the autosomal portion of the test but your post is mostly about the Y-DNA portion of the test. There are only about 13,600 Y-DNA SNPs tested by Genographic.

    4. You can't use IF THEN loops with Excel for naming a haplogroup with Geno 2.0 results just because of the huge number of SNPs. You have to use INDEX MATCH or VLOOKUP.

    5. The Morley SNP predictor was made for the first version of the Genographic test and not for Genographic 2.0 NextGen.

    6. FTDNA is not at fault that Genographic has a chip that provides false positives, false negatives, or a read on a reverse strand. They use what is sent to them by the Genographic team.

    7. Even though you never mentioned this, though it could have been inferred by readers, but FTDNA BigY doesn't have the problem that you experienced with Genographic NextGen especially when a haplogroup admin or a professional company analyzes the results for about $49.

    8. BigY results are being used to create SNP packs at FTDNA which are very useful, relatively inexpensive, and don't have false negatives or false positives and don't put people into an incorrect haplogroup.
    Last edited by ArmandoR1b; 08-07-2016 at 11:49 AM.

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    Quote Originally Posted by ArmandoR1b View Post
    Jatt,

    There are several very important things that need to be clarified in this thread.

    1. Your thread should have been in the Geno 2.0 sub-forum because the chip was designed and paid for by Genographic. The DNA testing is done in the FTDNA lab but it is not a chip owned by FTDNA, nor did they specify which autosomal, Y-DNA, or mtDNA SNPs should be tested, nor is there an equivalent test by FTDNA.

    Please note that National Geographic is not a DNA testing company but a global nonprofit organization committed to scientific exploration and educational projects. They started the Genographic project as a joint collaboration with FTDNA. FTDNA owns the Labs and their staff does all the work from DNA analysis to compilation of raw data and so on. Genographic probably just uploads the results/raw data they get from the FTDNA Lab. It is like you arrange/book a hall for a party but the food is provided by catering service ( FTDNA). If there is something wrong with the food , the catering service is likely to get more blame from a legal perspective. The onus is on both of them to sort out that who is responsible for the discrepancies in results caused by lab error or wrong haplogroups calling. I could have put the thread under Genographic too, I am really not so sure about who is more to be accountable here as I do not know their business model or joint venture agreement.
    Readers are free to have their opinions and share.


    2. You should specify that it is the Geno 2.0 Next Generation test. The first Geno 2.0 was with a different chip.

    The purpose of the thread is to highlight the short comings and limitations of chip based technology and the chip versions does not matter.

    3. The 700,000 SNPs are for the autosomal portion of the test but your post is mostly about the Y-DNA portion of the test. There are only about 13,600 Y-DNA SNPs tested by Genographic.

    Corrected to 13,600 SNPS for YDNA.

    4. You can't use IF THEN loops with Excel for naming a haplogroup with Geno 2.0 results just because of the huge number of SNPs. You have to use INDEX MATCH or VLOOKUP.

    I did mention that the actual logic could be more complex than a simple if and then command, vLOOKUP and index matches are more probable but the purpose of my referring to ifs and thens was just to give readers an example of how the logic works in the simplest context.

    5. The Morley SNP predictor was made for the first version of the Genographic test and not for Genographic 2.0 NextGen.

    Irrespective of that, the FTDNA/Genograpgic Predictors both made the same mistake as the Morley Predictor. Had I have access to the commercial predictors they use , I would have pasted their screen shots as example but I guess they are not open to the public. But please note that FTDNA/Geongraphic Joint ventured gave me the same results J and then R based on their alogrithyms. My finding was supplemented by the Y -Haplogroup result tree FTDNA maintains on their website in collaboration with Genographic and it showed that I was positive for some isolated R Haplo SNPs and J Haplo SNP. Their Haplogroup predictors got confused and made the same errors as the Morley Predictor. I brought this to the attention of both the vendors and they acknowledged the problem.

    6. FTDNA is not at fault that Genographic has a chip that provides false positives, false negatives, or a read on a reverse strand. They use what is sent to them by the Genographic team.

    Do you have the complete process of how it works between the two organizations? Chip is owned by Genographic but who does the lab test? and raw data compilation and how would a client know that what has gone wrong at what stage and the accountability ?

    Chip error = Geongrapic responsible
    Lab error = FTDNA responsible
    Incorrect Raw Data = who would be responsible?
    Incorrect Haplogroup assignment = is this a shared responsibility or just one party responsible?

    This needs to be clearly formulated by both parties in their own as well as client's interest.


    7. Even though you never mentioned this, though it could have been inferred by readers, but FTDNA BigY doesn't have the problem that you experienced with Genographic NextGen especially when a haplogroup admin or a professional company analyzes the results for about $49.

    I had a shocker experience of dealing with one of the FTDNA group administrator. You would be stunned if I share my experience of dealing with a religiously motivated fanatic who happened to be a volunteer working with FTDNA. He got very upset that I am wrongfully placed in J haplogroup. Trolled me for sometime and got my real name and address because I clicked on a link he provided me as administrator. Accused me of religious blasphemy and being falsely related to the Muslim Prophet. As per him only the lineage of the Prophet can claim that subclaude that I was placed in and that I being an ethnic Punjabi cannot have that group. He made some historical contexts to a bloody war that happened somewhere in Iraq back in 600 AD which neither myself or my ancestors had any part in. I reported him to FTDNA and the local police. I am luckly that I live in Canada and not in Iran, Pakistan or Afghanistan , this guy sent me harassing emails and had I been in the countries mentioned above , I would have been in real trouble. Religious blasphemy accusation is a death sentence there !

    FTDNA should do some reference checks/screening before they allow general public to become volunteer administrators for groups.


    8. BigY results are being used to create SNP packs at FTDNA which are very useful, relatively inexpensive, and don't have false negatives or false positives and don't put people into an incorrect haplogroup.
    Good suggestion but due to my bad experience, I am a little reluctant to choose them anytime in the near future. I went with 23andme and they placed me in Haplgroup F. At least their raw data is consistent with the haplogroup they have assigned me. I am in process of examining the raw data. The excel converter spreadsheet you provided is very useful. thanks for that !
    Last edited by jatt2016; 08-07-2016 at 01:32 PM.

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    Quote Originally Posted by ArmandoR1b View Post
    Jatt,

    There are several very important things that need to be clarified in this thread.

    1. Your thread should have been in the Geno 2.0 sub-forum because the chip was designed and paid for by Genographic. The DNA testing is done in the FTDNA lab but it is not a chip owned by FTDNA, nor did they specify which autosomal, Y-DNA, or mtDNA SNPs should be tested, nor is there an equivalent test by FTDNA.

    2. You should specify that it is the Geno 2.0 Next Generation test. The first Geno 2.0 was with a different chip.

    3. The 700,000 SNPs are for the autosomal portion of the test but your post is mostly about the Y-DNA portion of the test. There are only about 13,600 Y-DNA SNPs tested by Genographic.

    4. You can't use IF THEN loops with Excel for naming a haplogroup with Geno 2.0 results just because of the huge number of SNPs. You have to use INDEX MATCH or VLOOKUP.

    5. The Morley SNP predictor was made for the first version of the Genographic test and not for Genographic 2.0 NextGen.

    6. FTDNA is not at fault that Genographic has a chip that provides false positives, false negatives, or a read on a reverse strand. They use what is sent to them by the Genographic team.

    7. Even though you never mentioned this, though it could have been inferred by readers, but FTDNA BigY doesn't have the problem that you experienced with Genographic NextGen especially when a haplogroup admin or a professional company analyzes the results for about $49.

    8. BigY results are being used to create SNP packs at FTDNA which are very useful, relatively inexpensive, and don't have false negatives or false positives and don't put people into an incorrect haplogroup.
    Good point! When you are a novice rely on what more experienced members can convey. These companies use an algorithm because they test large numbers of samples. A human can take one look and give a better terminal SNP assignment. In this case, H-M69.

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    Quote Originally Posted by jatt2016 View Post
    Good suggestion but due to my bad experience, I am a little reluctant to choose them anytime in the near future. I went with 23andme and they placed me in Haplgroup F. At least their raw data is consistent with the haplogroup they have assigned me. I am in process of examining the raw data. The excel converter spreadsheet you provided is very useful. thanks for that !
    Your reluctance is unfounded which was the point of my post. Even 23andme put you in the wrong haplogroup.

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    Quote Originally Posted by jatt2016 View Post
    Please note that National Geographic is not a DNA testing company but a global nonprofit organization committed to scientific exploration and educational projects. They started the Genographic project as a joint collaboration with FTDNA. FTDNA owns the Labs and their staff does all the work from DNA analysis to compilation of raw data and so on. Genographic probably just uploads the results/raw data they get from the FTDNA Lab. It is like you arrange/book a hall for a party but the food is provided by catering service ( FTDNA). If there is something wrong with the food , the catering service is likely to get more blame from a legal perspective. The onus is on both of them to sort out that who is responsible for the discrepancies in results caused by lab error or wrong haplogroups calling. I could have put the thread under Genographic too, I am really not so sure about who is more to be accountable here as I do not know their business model or joint venture agreement.
    Readers are free to have their opinions and share.
    No need to cross-post. I have properly pointed out who owns the chip that is causing the erroneous results. FTDNA does not own any chips that causes that.

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    Quote Originally Posted by jatt2016 View Post
    The purpose of the thread is to highlight the short comings and limitations of chip based technology and the chip versions does not matter.
    It matters a lot. None of the other chip based technology has as many errors as the Geno 2.0 NextGen.

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    Quote Originally Posted by jatt2016 View Post
    I did mention that the actual logic could be more complex than a simple if and then command, vLOOKUP and index matches are more probable but the purpose of my referring to ifs and thens was just to give readers an example of how the logic works in the simplest context.
    The IF function exists in Excel but can't be used for Geno 2.0 NextGen.

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