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  • Well, so much for that...

    I'm a member of the McDonald project, in their R1a group. The key SNP to dig under is L176.1.

    I got my Big Y results back aaaaand.....

    There's a test available for L176.1. Big Y didn't pick it up. After all the hype and dramaz, all it tells me is that I'm R-M417. Which I already knew. And all negative down to M458, which I didn't know, but stops short of where I needed to go.

    This thing was supposed to blow the Y-tree wide open, and it didn't even take me to the end of the current tree.

    What a load of.....
    Last edited by Varego; 2 April 2014, 11:55 PM.

  • #2
    After reading the explanatory page at FTDNA, I have to conclude that I haven't learned anything useful from my Big Y results.

    From reading the forums, it seems the next step is to download something called a BAM file, send that to YFull, and do some more waiting for YFull to see if results expand the tree. Or wait for FTDNA to produce a new tree.

    Is there nothing the individual can do with these results? I just want to know how close I am (in generations) to other cases on the ISOGG and FTDNA trees. Is there any way to do that?

    Comment


    • #3
      This test is the best thing to ever hit FTDNA, for the price it's amazing what it provides. I am still waiting on my results but have seen others.

      It was very clear the test was targeted at advanced users who wanted to advance science.

      I am not an advanced user and I did try and post here and elsewhere a few times over the last few months to try and ask everyone else how they planned to analyse and use their results with little response.

      This test provides gigabytes upon gigabytes of data about our DNA. I have tried to spend the last few months while the tests were being run reading as much as I can to prepare to be able to understand what I might get and how I might use it. This included understanding sequencing, coverage, reads, BAM files, idels, the human reference genome, free analysis tools, relevant discussion forums I could join so I was signed up and ready to participate when my results hit. Others have spent the time creating and sharing spreadsheets to help understanding the results. I have looking at my Y STR matches and trying to establish who has tested for BigY and what projects they are in as these are the people I might most usefully compare BigY with.

      Some people will be lucky and have an active project administrator who has prepared well in terms of deciding how they would analyse and compare results and will be able to help them, even then many project admins have more than 100 results to go through so we need to be patient.

      In the past we have relied to admins to guide us through all these SNP's and that was possible for the SNP's that were a few thousand years old shared by large numbers of people. In many cases BIGY may have provided an SNP that is unique to you or your father and perhaps another that is unique to your great, great grandfather and so on. On average there should be an SNP in your direct linage that has developed every 100 years or so. Working on some of these details will require a knowledge of actual family trees and cousins within the last 1,000 and 500 years to test. In this period from the last 1,000 it will be down to each individual rather than Haplogroup admins to work out the recent phylogenetic tree hopefully with help from the useful surname administrators who will have work very closely in collaboration with each other to work out exactly at what point in the last 1,000 years specific surnames diverged from each other.

      It's going to take some time to work all this out that's why I have been so eager for these results, there is so much data to go through it's going to be amazing for the next few years as knowledge floods out.

      Comment


      • #4
        Originally posted by Earl Davis View Post
        This test is the best thing to ever hit FTDNA, for the price it's amazing what it provides. I am still waiting on my results but have seen others.
        For my purposes, the $40 L176.1 test would have been far more informative. And, most likely, faster.

        Hopefully your results are more informative and pertinent.

        Comment


        • #5
          Earl,

          What about non-relatives? If you had two cases on the same branch but with different terminal SNPs, could you compare their Big Y results and tell how many generations have passed since the common branching point?

          Comment


          • #6
            That is the the theory yes. Of course it's not going to be quite that easy. As I understand the current thinking a new SNP occurs every 1.5 generations, however because of the issues for working with DNA and current technology limitations only enough of your DNA can be read to pick up an SNP every 3 generations.

            At a simple level, if you and your father had tested and you shared 80 novels variants and one that you were positive and he was negative for the same one then you have identified the SNP that is unique to you (in theory) that will be passed on then to all your descendants. It's not simple as there are some things to be careful about like coverage and no calls and so on.

            Apply the same logic to the next level out. If you and your 3rd cousin share 80 novels and two where you don't then between your results, your fathers and your cousins you can start to say in which individual ancestor those very recent SNP's originated.

            Comment


            • #7
              Once you move further out than known cousins you are comparing novel variants which should give you an indication within a few generations exactly when your common ancestor lived. I am sure the estimates on these times will change as understanding grows from the analysis of the results but we should soon be able to see family trees being drawn from DNA without the ancestors names been known. Cont...
              Last edited by Earl Davis; 3 April 2014, 04:01 AM.

              Comment


              • #8
                So say you are in a surname project and match 6 other people fairly closely on STR markers who have ordered BigY but none of you can link your paper research. You don't currently know how closely you are related to these people. Then you compare novel SNP's. You find you differ on 3 SNP's from Bill and Simon, 5 SNP's from Ian, and 7 SNP's from Charles, John and Mike. You then compare them with each other. Suddenly you can start to draw a tree perhaps accurate to within 100 years of where each of your groups branches out.

                Now although you have 7 SNP's not in common with Charles and 7 not in common with John when they compare they have 3 not in common with each other so they can start to predict at which generation they split. This prediction will get better and better as more people test. And IF FTDNA include all the SNP's discovered through bigY on their next mass market Geno chip then we will start to be able to compare our recent BigY results with the masses.

                Cont...

                Comment


                • #9
                  Some of the current issues and challenges.

                  People have mentioned the FTDNA Y Tree. It's true that it is very outdated. A new one will be nice but I don't think it will help that much. They have no way of knowing of a novel SNP originated in you, your father or your x8 great grandfather. That's the genealogical work we need to do with our results.

                  A bigger issue is the FTDNA database. There are many thousand of SNP's being reported as novel that already well know in other databases such as at ISOGG. This will muddy the waters when we try and unravel our novel SNP's as it will make it more difficult to work on the true recent SNP's and ancient SNP's that are only being shown as novel because they are not in the FTDNA database. To me getting the database updated with all known SNP's is more important than the tree at least at this stage. Both would be nice.

                  The next bit is a challenge many of the project admins are working through now. BigY has discovered many new SNP's that are older than many peoples old terminal SNP prior to taking the BigY. It's important we all try and keep on top of this research If we want to understand which of our novels are recent and which are very old new discoveries. I would be interested in how FTDNA plans to handle this research. There seems to be some difference of opinion in the admin community on this.

                  Earl.

                  Comment


                  • #10
                    So can your analysis be reduced to a formula for estimating the TMRCA of two cases on a branch ---

                    1. Count the number of novel SNPs not shared.
                    2. Multiply that number by 1.5 or 3 to estimate the number of generations to the TMRCA.

                    Comment


                    • #11
                      At a basic level that is my understanding.

                      However more detailed analysis will be required in each comparison. For example two people may share an SNP genetically but BigY might not show that for various reasons, an obvious reason being that that pat of the DNA was covered for person A but not person B or there was a mis call.

                      But yes having done that analysis your formula is a fair starting point.

                      Of course the rate at which new SNP's occur will come under heavy debate as BIgY results continue to be analysed and new people test so I am in no way saying that 3 will ultimately be correct figure but it seems to be what several people are currently thinking.

                      Comment


                      • #12
                        Originally posted by Varego View Post
                        I'm a member of the McDonald project, in their R1a group. The key SNP to dig under is L176.1.

                        I got my Big Y results back aaaaand.....

                        There's a test available for L176.1. Big Y didn't pick it up. After all the hype and dramaz, all it tells me is that I'm R-M417. Which I already knew. And all negative down to M458, which I didn't know, but stops short of where I needed to go.

                        This thing was supposed to blow the Y-tree, wide open, and it didn't even take me to the end of the current tree.

                        What a load of.....

                        L176.1 is an 'indel' and therefore not reported in the result list. However, in your VCF file you can check at the
                        position 21,779,256 if you find a del to AAAAC variant.

                        A SNP slightly upstream of L176.1 is CTS4179

                        Comment


                        • #13
                          Yes, I'm CTS4179+, but there are at least three SNPs downstream including L176.1, none of which are in my Big Y results.

                          Comment


                          • #14
                            Originally posted by Varego View Post
                            I'm a member of the McDonald project, in their R1a group. The key SNP to dig under is L176.1.

                            I got my Big Y results back aaaaand.....

                            There's a test available for L176.1. Big Y didn't pick it up.
                            This thing was supposed to blow the Y-tree wide open, and it didn't even take me to the end of the current tree.

                            What a load of.....
                            Oh my!!!! I'm the Clan Donald data massager. Unfortunately
                            from your name I don't know who you are. But
                            I've got all the results up to yesterday fully
                            assigned. L176.1 CAN be determined, usually, from
                            the BED and VCF files, not always. One of the
                            people I analyzed, probably you, comes out ambiguous, so we'll need to get your bam file.

                            BUT ... its immaterial. The Big Y has already
                            provided several candidates for more reliable L176.1
                            substitute SNPs. We do need a few more results to be sure.

                            Don't be unhappy ... you've hit the jackpot. And if you
                            are who I think you are, you are an important person.

                            Send me a private email at [email protected]
                            with your kit number. I'll explain.

                            Oh yes ... the Big Y also includes L175. Being an
                            indel, they don't call it either. But I can.

                            Doug McDonald.

                            Comment


                            • #15
                              Work with Doug, Vareg there is so much to be learned from the results you have.

                              Earl.

                              Comment

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