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  • Y-DNA Markers

    I have been informed by another DNA testing company that the markers used for Y-DNA testing are proprietary information and as such cannot be disclosed to the individual.

    Which markers are the most common in identifying Y-DNA haplogroups or is this a very silly question?


  • #2
    Are sure that they use markers? I believe you are actually talking about SNPs, since most companies (such as 23AndMe) use SNPs instead.

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    • #3
      23andMe and FTDNA use SNPs to determine Y Haplogroups. FTDNA uses STRs from the 1st panel of their Y-DNA tests to predict a Y Haplogroup. Both companies name the SNPs used and FTDNA names the STRs tested along with the number of repeats for each STR.

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      • #4
        KMC1, I don't know to which DNA testing company you refer, but it seems odd that they regard the SNPs as proprietary information.

        The last time I checked, a raw data file from 23andMe showed Y-DNA results between the X and mtDNA results. 23andMe gives RSID ("Reference SNP cluster ID") and position information for each SNP (including autosomal, X, Y, and mtDNA). I am not sure if there is a website or other source to use to match up RSID numbers, or their positions on the chromosome, with any Y-DNA SNPs. But if you view the Scientific Details tab for the paternal haplogroup report, 23andMe provides a tree showing the SNPs tested which leads to the haplogroup they predict.

        Other than 23andMe, I believe LivingDNA is the only other of the main "DNA for genealogy" type companies which actually gives a Y-DNA haplogroup prediction as part of autosomal results (as Jim Barrett pointed out, at FTDNA a separate Y-DNA test must be done, as no Y-DNA markers are included in the Family Finder autosomal test). Ancestry and MyHeritage files also may include some Y-DNA SNPs, but not as many as 23andMe (I'm not sure how many LivingDNA tests), and neither Ancestry nor MyHeritage gives a prediction in a customer's results. See Louis Kessler's blog post, "Comparing Raw Data from 5 DNA Testing Companies," for reference; scroll down to the heading "Number of SNPs by Chromosome."

        If someone who tested with LivingDNA downloaded their raw data file, it should show the actual Y-DNA SNPs used (according to the "How do I interpret my raw data?" page in the LivingDNA Support Center, under the heading "Your mtDNA and/or Y DNA file").

        Under that heading mentioned, part of it says:
        Your mitochondrial and (if you're genetically male) your Y DNA data file will contain a list of DNA markers that make up your mt or Y genetic signature.

        We will provide you with the most common name for a particular genetic marker and any alternative names that this marker may have - for example, if you have one row of your file like this "F83/M1185/PF5861" - this means that you have tested positive for marker "F83" which is also known as "M1185" and "PF5861".

        Please note that we do not include genetic markers you have not tested positive for in these files.

        We have used these positive markers to assign you your haplogroup and subclade (if applicable). Each haplogroup has a defining marker and, often, a set of supporting markers. We search for which defining and supporting markers you have in order to assign you your haplogroup - we always read as far down the mt and/or Y DNA phylogenetic tree as we can within scientific reason.

        You may find that you possess markers for haplogroups or subclades lower down the tree than the one we have assigned you.
        (there is a bit more)

        SNPedia has a page with links to pages for each of the main Y-DNA haplogroups, and on those pages they show the SNPs for derived subclades. Perhaps those would be of help in deciphering the Y-DNA SNPs included in either the 23andMe or LivingDNA raw data files. The FTDNA Y-DNA Haplotree should also allow one to follow Y-DNA SNPs to the predicted haplogroup or subclade given at LivingDNA.
        Last edited by KATM; 9 September 2021, 12:13 PM.

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        • #5
          I don't know if this adds anything to the discussion, but the left part of a new SNP shows which company isolated it.

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          • #6
            Thank you to all for your comments. I will follow up on each point.

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            • #7
              Originally posted by georgian1950 View Post
              I don't know if this adds anything to the discussion, but the left part of a new SNP shows which company isolated it.
              Yes, the prefixes are assigned by the research groups, and Haplogroup.org has a list of them, if anyone is interested.

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              • #8
                Originally posted by KATM View Post

                Yes, the prefixes are assigned by the research groups, and Haplogroup.org has a list of them, if anyone is interested.
                Thanks, that is a big list.

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                • #9
                  " Ancestry and MyHeritage files also may include some Y-DNA SNPs, but not as many as 23andMe (I'm not sure how many LivingDNA tests)"

                  LivingDNA has a whopping 34,216 Y SNPs. Compared to only 3733 at 23andMe (V5). Nine times as many. Although TBH, I dont know if LDNA gets any more bang out of all those SNPs.


                  MH has almost as many as 23andMe, with 3495 Y SNPs. Ancestry has 1691. Too bad they dont try to make a simple report.

                  source: ISOGG page

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                  • #10
                    Originally posted by mabrams View Post
                    " Ancestry and MyHeritage files also may include some Y-DNA SNPs, but not as many as 23andMe (I'm not sure how many LivingDNA tests)"

                    LivingDNA has a whopping 34,216 Y SNPs. Compared to only 3733 at 23andMe (V5). Nine times as many. Although TBH, I dont know if LDNA gets any more bang out of all those SNPs.


                    MH has almost as many as 23andMe, with 3495 Y SNPs. Ancestry has 1691. Too bad they dont try to make a simple report.

                    source: ISOGG page
                    Thanks for catching that. I should have checked the ISOGG Autosomal DNA testing comparison chart, as I usually do for these things, but I guess when I did a web search the Louis Kessler post came up, and seemed to have some information. Obviously not enough, and I should have looked further.

                    Not having Y-DNA results from LivingDNA for the managed kit I transferred there, I don't know if they report Y-DNA results in the form of a tree, such as what 23andMe provides. But, as I posted above, at least when a male downloads his raw data from LivingDNA he can check for the Y-DNA SNPs.

                    With all that being said, now is the time for me to take an overdue break from the forums. Stay safe, everyone!

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