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  #11  
Old 21st July 2017, 09:56 AM
Martin Potter Martin Potter is offline
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STR vs SNP testing

For those who might be interested :

http://acreetree.net/ydnaadvanced.html

a transcript of an article ("Advanced Y-DNA Testing for the Acree One-Name Study") about a surname project which has replaced Y-STR testing with Y-SNP testing, thus "reducing cost" and "eliminating ambiguity", according to the author, Charles Acree.

The article has been or is being published in the "Journal of One-Name Studies" (Jul-Sep 2017), which I have not yet seen.

... Martin
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  #12  
Old 21st July 2017, 11:11 AM
TwiddlingThumbs TwiddlingThumbs is offline
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Originally Posted by Martin Potter View Post
An interesting article. However, the kit grouping in the Acree project is identical to what one would get based purely off of their current STR results (based on their public data, which I ran through my program), so while the SNP testing provided definitiveness for those who took the test and matched, I don't think it saved any money or made any difference for grouping the kits.

Big Y and similar tests are expensive. If you just take a terminal SNP test with someone who has done the testing, it's a bit of a shot in the dark. I tried that route and it was a miss. Then I took a SNP panel test and found my terminal SNP, but no one else with my surname who had done SNP testing had that SNP. Then I took a 67 STR test, which showed I was not related to the guy who had taken the Big Y test but was related to another guy who we established, through genealogical evidence, shared a common ancestor with me.

STR test results are still useful and currently still have a number of advantages over SNP tests. In order to determine if you match with someone, you need to take a test that provides results that you can compare with the other person's results. A lot of people have taken 12, 25, 37, 67 and 111 STR tests. A match on any of these tests gives some affirmative evidence of a possible relationship. While a match at 12 or 25 is weak evidence, it's still worth a look, and the results of 37, 67 and 111 tests are quite suggestive. With SNP testing, you can only base a match on a SNP that probably originated within the genealogical time frame, which means that both you and the other person need to have done Big Y or tested for the terminal SNP. There are a lot fewer people out there who have done that testing, so you are currently much less likely to match with other people. I guess the choice is between finding more people who you might be a match with or finding a lot fewer or no people who you are definitely a match with.

Last edited by TwiddlingThumbs; 21st July 2017 at 11:40 AM.
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  #13  
Old 21st July 2017, 08:52 PM
Martin Potter Martin Potter is offline
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Originally Posted by TwiddlingThumbs View Post
... the vast majority of the members of most surname projects have not done SNP testing ...
Are you sure of that? I don't have any figures to prove you wrong but you have to consider the large number of people who belong to the many haplogroup projects. They *all* came from surname projects. And all of them have done at least some SNP testing, while many have done extensive SNP testing, not to mention the ones who do Big-Y and other genomic type tests in order to provide the leading edge for haplogroup researchers to work on. I think the field is larger than you imagine.
... Martin
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  #14  
Old 21st July 2017, 09:33 PM
TwiddlingThumbs TwiddlingThumbs is offline
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Quote:
Originally Posted by Martin Potter View Post
Are you sure of that? I don't have any figures to prove you wrong but you have to consider the large number of people who belong to the many haplogroup projects. They *all* came from surname projects. And all of them have done at least some SNP testing, while many have done extensive SNP testing, not to mention the ones who do Big-Y and other genomic type tests in order to provide the leading edge for haplogroup researchers to work on. I think the field is larger than you imagine.
... Martin
I've looked at maybe about 100 of the larger surname groups and in all of them the number of people with green haplotypes (indicating that they have been confirmed by SNP testing) is a distinct minority. 'Vast majority" and 'distinct minority" are subjective, of course. Just to quantify, I took a look at a couple of project. For the Adams project about 135/550 had their haplotype confirmed by SNP testing. For the Adkins group the number was about 43/150. Pretty consistent that only about 1/4 to 1/3 of kits with STR results had done SNP testing. So, based on those numbers, I would estimate that there are 3-4 times as many people who have done STR testing as have done SNP testing. Moreover, the number of people who have done Big Y (or have otherwise done testing that establishes their terminal SNP) is a small subset of those who have done SNP testing and only Big Y (or have otherwise done testing that establishes their terminal SNP) is useful for affirmatively matching people within the genealogical time frame.

Not all members of haplotype groups have done SNP testing. Most FTDNA haplotype groups accept members based on "predicted haplotype" which is based purely on their STR results.
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  #15  
Old 22nd July 2017, 06:55 AM
Jim Barrett Jim Barrett is offline
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Originally Posted by TwiddlingThumbs View Post
Big Y and similar tests are expensive. If you just take a terminal SNP test with someone who has done the testing, it's a bit of a shot in the dark. I tried that route and it was a miss. Then I took a SNP panel test and found my terminal SNP, but no one else with my surname who had done SNP testing had that SNP. Then I took a 67 STR test, which showed I was not related to the guy who had taken the Big Y test but was related to another guy who we established, through genealogical evidence, shared a common ancestor with me.
The SNP Pack you ordered probable did not find your terminal SNP. It only found the most down stream SNP included in that SNP Pack.
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  #16  
Old 22nd July 2017, 07:48 AM
TwiddlingThumbs TwiddlingThumbs is offline
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Originally Posted by Jim Barrett View Post
The SNP Pack you ordered probable did not find your terminal SNP. It only found the most down stream SNP included in that SNP Pack.
Maybe a definitional issue with "terminal SNP"? I ordered the YSEQ Northwest Irish Panel about 18 months ago based on my STRs indicating that I was probably R-M222. The SNP farthest down the tree for which I tested positive was S588. All the results included in the panel for SNPs below S588 were negative. According to ISOGG, "terminal SNP" is the defining SNP of the latest subclade known by current research. I think that means that, at the time I took my test, S588 was my terminal SNP because there were no SNP tests for subclades I might fit in below that. YSEQ has since add a few more SNP tests for subbranches below S588, so in theory I could fit in one of those and find I had a new terminal SNP. However, tracking the discussion in the M-222 project, there seem to be a fair number of men with different surnames who are "stuck" on S588 despite Big Y testing. So, for some on the S588 branch of the tree, it seems like SNPs have not yet been identified which would allow them to identify relatives within the genealogical time period even if their relatives have taken Big Y. I guess that is a bit of a chicken and the egg situation, however, because if they and some relatives took Big Y, the results could be used to identify a defining SNP downstream of S588, identify a new subclade, and establish a new terminal SNP.

Last edited by TwiddlingThumbs; 22nd July 2017 at 07:59 AM.
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  #17  
Old 23rd July 2017, 06:12 AM
Jim Barrett Jim Barrett is offline
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Originally Posted by TwiddlingThumbs View Post
According to ISOGG, "terminal SNP" is the defining SNP of the latest subclade known by current research.
How many new SNPs have been found when Big-Y was used?

If you subscribe to the ISOGG list you know there are many members who don't like the term "Terminal SNP" and prefer something like "Most Down Stream Tested SNP". If you have been a member of ISOGG since its inception you also know they are continually updating their definitions.
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  #18  
Old 23rd July 2017, 08:53 AM
TwiddlingThumbs TwiddlingThumbs is offline
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Originally Posted by Jim Barrett View Post
How many new SNPs have been found when Big-Y was used?
Do you mean how many new SNPs have been identified by comparing Big Y results of men who are S588+ but for which YSEQ is not yet offering a SNP test?

Quote:
Originally Posted by Jim Barrett View Post
If you subscribe to the ISOGG list you know there are many members who don't like the term "Terminal SNP" and prefer something like "Most Down Stream Tested SNP". If you have been a member of ISOGG since its inception you also know they are continually updating their definitions.
Not a subscriber, but I am not surprised.
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  #19  
Old 24th July 2017, 06:13 AM
Jim Barrett Jim Barrett is offline
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Originally Posted by TwiddlingThumbs View Post
Do you mean how many new SNPs have been identified by comparing Big Y results of men who are S588+ but for which YSEQ is not yet offering a SNP test?
Since FTDNA started offering Big Y - How many SNPs have been discovered that were not on anyone's tree at the time of the discovery.
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