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  • SNP testing and genealogy

    I know you can use SNP testing to prove that two men DO NOT have a genealogical relationship, but can even Big Y and deep SNP testing show that people DO have a common male ancestor within the past 500 years? According to YFull, my current terminal SNP originated 1450 years ago. And, based on haplotype group studies, it seems that several other surnames share the SNP (which is not surprising since it originated before the start of surnames). It is therefore useless for proving that I DO have a relationship within the genealogical time frame with another male with my surname.

  • #2
    Originally posted by TwiddlingThumbs View Post
    I know you can use SNP testing to prove that two men DO NOT have a genealogical relationship, but can even Big Y and deep SNP testing show that people DO have a common male ancestor within the past 500 years? According to YFull, my current terminal SNP originated 1450 years ago. And, based on haplotype group studies, it seems that several other surnames share the SNP (which is not surprising since it originated before the start of surnames). It is therefore useless for proving that I DO have a relationship within the genealogical time frame with another male with my surname.
    The Big Y test, which tests about 10 million locations on the y chromosome, will find previously unknown SNPs. That's what it make it different from and superior to the testing technology in SNP packs. SNP packs are limited to testing about 160 already known SNPs specific to a particular branch.

    The average mutation rate for new SNPs found in Big Y tests is estimated to be about 120 years. A similar test that covers more locations on the y, offered by Full Genomes Corp., has a mutation rate of about 90 years. So, Big Y can find new SNPs that occurred within the last 4 or so generations and the FGC test within the last 3 generations.

    That's obviously well within the range of time since surnames came into common use among Europeans. The fact that YFull gives you a terminal SNP that's 1,450 years old probably means that they don't have many men in their database that share more recent common ancestors with you than that period of time or your haplogroup/subclade is uncommon and no other men in your subclade have taken the Big Y test.

    Big Y, although expensive, can be used to break down a brick wall in the last few hundred years. The best strategy is to submit your unshared Big Y novel variants to YSEQ to have them made testable by development of primers for Sanger sequencing (another testing technology). Then if you have anyone with whom you think share a common paternal line ancestor around the time period of your brick wall, have him test your unshared novel variants at YSEQ at a very cheap price compared to a Big Y test.

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    • #3
      MMadi - Thanks for the explanation. Make sense. In comparing SNP testing and STR testing, would it be fair to say that, while both can be used to help establish a relationship within the genealogical time frame, the key differences are (i) SNP testing is much more definitive than STR testing, (ii) to get information relevant in the genealogical time frame, SNP testing is a lot more expensive than STR testing, and (iii) since there a lot fewer men who have taken the necessary level of SNP testing than have done STR testing, one is are currently less likely to find a match by SNP testing than by STR testing.

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      • #4
        Originally posted by TwiddlingThumbs View Post
        MMadi - Thanks for the explanation. Make sense. In comparing SNP testing and STR testing, would it be fair to say that, while both can be used to help establish a relationship within the genealogical time frame, the key differences are (i) SNP testing is much more definitive than STR testing, (ii) to get information relevant in the genealogical time frame, SNP testing is a lot more expensive than STR testing, and (iii) since there a lot fewer men who have taken the necessary level of SNP testing than have done STR testing, one is are currently less likely to find a match by SNP testing than by STR testing.
        The answer to all your points is yes, especially your first point. Given that STRs can easily back mutate, they aren't as reliable as SNPs.

        However, when you use the term SNP testing, the "yes" answer only applies to newly discovered SNPs found in Big Y tests. Results from SNP packs will not give you the resolution required to prove a common ancestor within the last few hundred years.

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        • #5
          Here's a link - http://acreetree.net/ydnaadvanced.html - to a summary of an actual case study of how one surname project has used SNP testing to conduct their research and track branches from a common ancestor. These quotes from the press release are relevant to the questions you're asking:

          "During the past two years, our project has been replacing conventional Short Tandem Repeat ('Y-STR') Y-DNA testing with Single Nucleotide Polymorphism ('Y-SNP') testing for most of our comparative efforts. This transition has greatly reduced the cost of testing after recovering an acceptable initial investment. Equally important, it has eliminated ambiguity in our comparisons....

          "A persistent disadvantage of Y-STR testing has been that it requires laborious comparisons of lengthy strings of differing marker totals (called 'haplotypes') that can be indeterminate, even when a maximum number of markers are compared at substantial cost. Y-SNP testing, in dramatic contrast, permits unambiguous comparison of sequential, cumulative mutations. It is definitive, overruling any apparent Y-STR-based contradictions that may arise."

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          • #6
            Originally posted by MMaddi View Post
            Here's a link - http://acreetree.net/ydnaadvanced.html - to a summary of an actual case study of how one surname project has used SNP testing to conduct their research and track branches from a common ancestor. These quotes from the press release are relevant to the questions you're asking:

            "During the past two years, our project has been replacing conventional Short Tandem Repeat ('Y-STR') Y-DNA testing with Single Nucleotide Polymorphism ('Y-SNP') testing for most of our comparative efforts. This transition has greatly reduced the cost of testing after recovering an acceptable initial investment. Equally important, it has eliminated ambiguity in our comparisons....

            "A persistent disadvantage of Y-STR testing has been that it requires laborious comparisons of lengthy strings of differing marker totals (called 'haplotypes') that can be indeterminate, even when a maximum number of markers are compared at substantial cost. Y-SNP testing, in dramatic contrast, permits unambiguous comparison of sequential, cumulative mutations. It is definitive, overruling any apparent Y-STR-based contradictions that may arise."
            That is brilliant! But I would think Y-STRs would allow some clearer pictures after in-depth SNP testing to really determine the relationship between individuals.

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            • #7
              Originally posted by MMaddi View Post
              It is definitive, overruling any apparent Y-STR-based contradictions that may arise."
              Definitive, yes. But in this case, and in the case of most males with the same surname, there were no contradictions. The Acree STR results result in the same family groupings as are currently shown on their surname project web page.

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              • #8
                Terminal SNP

                A quick question, and I apologise if this has been dealt with earlier, I have done SNP testing down through R-Z8 pack and ended up with an SNP below R-Z323 to R-CTS1747, from my understanding only one or two tested individuals have returned this SNP. Is this the end of the line? (I didn't have the funds to complete Big Y) Looking at the data, this mutation occurred several hundred years B.C. with no real geographical estimate as to location. Would Big Y have given me much more information?

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                • #9
                  Originally posted by Mustik View Post
                  Looking at the data, this mutation occurred several hundred years B.C. with no real geographical estimate as to location. Would Big Y have given me much more information?
                  A SNP pack is limited to testing for about 160 already known SNPs on a specific branch. In most cases, the most downstream SNP pack will get you down to a SNP that's about 2,000 years old, in some cases somewhat younger than that.

                  Big Y tests the y chromosome for about 10 million locations and is able to find previously unknown SNPs. Some of these SNPs will eventually match other men who take the Big Y test later or men who've taken a later version of a SNP pack to which previously unknown Big Y SNPs are added. That will get you down to SNPs that are 1,000 years old or sometimes less.

                  Also, Big Y will find SNPs that are unique to the last several generations of your paternal line, the last few or several hundred years. Those private SNPs may be useful in breaking down a genealogical brick wall. This is why haplogroup project administrators overwhelmingly recommend Big Y over SNP packs.

                  Big Y is on sale until Aug. 31 for $395. That's the lowest price it's ever had. Now's a good time to get the youngest SNPs possible through Big Y.

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                  • #10
                    Originally posted by MMaddi View Post
                    A SNP pack is limited to testing for about 160 already known SNPs on a specific branch. In most cases, the most downstream SNP pack will get you down to a SNP that's about 2,000 years old, in some cases somewhat younger than that.

                    Big Y tests the y chromosome for about 10 million locations and is able to find previously unknown SNPs. Some of these SNPs will eventually match other men who take the Big Y test later or men who've taken a later version of a SNP pack to which previously unknown Big Y SNPs are added. That will get you down to SNPs that are 1,000 years old or sometimes less.

                    Also, Big Y will find SNPs that are unique to the last several generations of your paternal line, the last few or several hundred years. Those private SNPs may be useful in breaking down a genealogical brick wall. This is why haplogroup project administrators overwhelmingly recommend Big Y over SNP packs.
                    Right, but if only 2 other people have tested at his current terminal SNP, chances are he will not match up with anyone at the lower SNPs. So, maybe useful in the future if and when a bunch of other people test, but until then?

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                    • #11
                      Originally posted by TwiddlingThumbs View Post
                      Right, but if only 2 other people have tested at his current terminal SNP, chances are he will not match up with anyone at the lower SNPs. So, maybe useful in the future if and when a bunch of other people test, but until then?
                      No one is guaranteed that they will find a match in the database. Finding a match is related to how common the haplogroup is, how many descendants are living today and, most importantly, how many descendants have tested and are in the database.

                      If you're looking for a quick answer, then genetic genealogy will many times disappoint you. But it does have the potential to be useful in the future. Of course, if you reject the idea of waiting for a future match and don't order the test, then there's 100% certainty that you won't find a match!

                      I was responding to someone who was disappointed that the SNP pack only got him down to a SNP that's over 2,000 years old. As long as he understands that Big Y will give him much younger SNPs, but that it may take a few years before someone comes along to match his private SNPs, then Big Y is probably a viable option for what he's trying to find out. There's not much doubt that, with the increasing number of men taking the Big Y test, he'll probably find matches with some of his Big Y SNPs that are around 1,000 years old.

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                      • #12
                        SNP test vs Big Y

                        So if I am understanding right...the Big Y test covers whatever is done in your recommended SNP test packet for my haplogroup but can dig down deeper?

                        So If I want to know more about my ancestry and get the most specific haplogroup possible, I should go with the Big Y over the SNP packet, right?

                        Lastly, If I just ordered my SNP pack and it is still processing, could I cancel that test and upgrade to the Big Y instead and apply the $119 I paid for the SNP pack to the Big Y price?

                        Thanks!

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                        • #13
                          Originally posted by Ayran View Post
                          So if I am understanding right...the Big Y test covers whatever is done in your recommended SNP test packet for my haplogroup but can dig down deeper?
                          To summarize what I posted in my previous post, each SNP pack is limited to about 160 known SNPs on a specific branch of the yDNA tree. The Big Y test covers about 10 million locations on the y chromosome and can find previously unknown SNPs which will be younger than the SNPs in a SNP pack, along with testing for all known SNPs. I think that answers your question.

                          Originally posted by Ayran View Post
                          So If I want to know more about my ancestry and get the most specific haplogroup possible, I should go with the Big Y over the SNP packet, right?
                          Yes.

                          Originally posted by Ayran View Post
                          Lastly, If I just ordered my SNP pack and it is still processing, could I cancel that test and upgrade to the Big Y instead and apply the $119 I paid for the SNP pack to the Big Y price?

                          Thanks!
                          If your order for the SNP pack has already been batched for testing, you're out of luck. FTDNA only allows changes in test orders before a test has been batched for the lab. Batching occurs every Monday afternoon and Wednesday afternoon.

                          This is why it's highly recommended that anyone interested in SNP testing join the appropriate haplogroup project and consult with a project administrator about what test will help him in whatever research he's doing on his paternal line. I've seen too often where members of the haplogroup project of which I'm a co-administrator have just wasted money by ordering a SNP pack that isn't even appropriate to his haplogroup/subclade or orders several single SNPs at $39 each when he could be testing for 160 SNPs on a branch for $99 or $119. He would have done better to just contribute to the project group fund and let us do the ordering for him.

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