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Thread: 23andme v5 GEDMATCH & MyHeritage completely different MyHeritage matches!

  1. #1
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    23andme v5 GEDMATCH & MyHeritage completely different MyHeritage matches!

    So, I uploaded a relative's recent 23andme test to GEDMATCH a couple of months ago, then took advantage of the free tools upload for MyHeritage a few weeks ago, and was somewhat shocked, that basically all of the matches marked MyHeritage on GEDMATCH from 45cM downwards, simply do not appear as matches on the same data uploaded to MyHeritage. The matches on GEDMATCH had some surprising matches (as someone of mostly British Isles ancestry) of Russians, Germans, Czechs, Brazilians, Argentines who seemed to have Volga German ancestry, but none of these matches appear on MyHeritage. Can anyone explain what is going on here? Is it possible the GEDMATCH matches are IBD or IBS matches, and MyHeritage is filtering these out? Are Volga German populations particularly endogamous and perhaps show closer matches to Anglo-Saxon descended populations than is actually reflective of their most recent common ancestor?

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    Speaking only in terms of matches in general, IMO MyHeritage matches should be checked thoroughly and questioned always. I have my paid swab kit, my Ancestry and my 23andMe V5 kits on there. What I've noticed over the years, is that the matches vary between kits and some known matches on Ancestry for example, do not match my Ancestry kit on MyHeritage. I have many 3rd-5th cousins (~0.5% DNA matches) with trees at MyHeritage that I simply cannot determine a MRCA, when theoretically I should be able to (mostly French, Scandinavian and German lines that I have already been able to genetically confirm and have well documented branches for). To be fair, I have seen an influx of French matches recently (this is my only source of French matches), but anything less than a 1% match without another known relative to triangulate (my maternal grandparents for example), I would question.

    I have also noticed my paternal chromosomes 1, 15 and 18 (maybe 21 and 22, but I cannot confirm yet) appear to have more NW German/Dutch matches and also have mysterious British matches that I have suspected to be IBS, pile up regions.

    I cannot speak much on Gedmatch, but I have noticed the same as my previous statement from the projects I am a member of (Lower Saxony, Danish, Prussian) - paternal chromosomes 1, 15 and 18 appear to be heavily from this area with several close British matches that I cannot explain other than IBS. I have not been able to confirm any matches here (outside of the known ones), they are simply too small.

    Sorry this is not more helpful, but I started questioning MyHeritage matches about 2 years ago. Good luck with your searches!




    edit - I should've mentioned another example of the inconsistency with MyHeritage matches and glitches in general. One of my more recent confirmations only matched me on my swab kit. They and they're siblings are confirmed 4C matches to me (I think that's right) - we match a set of French 3x great grandparents and we are all around 0.5%, 35 cMs.

    My grandma is a much closer match to them ~1.2%, 156 cMs (2Cs I think to my grandma). She matches them on her 23andMe V5 kit.

    My point is, without the swab kit I would've missed this excellent genetic verification to myself and without my grandma's kit, I may have missed them altogether. When I click on their profiles, they do not list my grandma as a common match - even though I am ~22% match to my grandma (makes sense for a grandparent). Frustrating to say the least. That begs the question - what relatives am I missing? What relatives are my grandparents' kits missing?

    I also had a recent phenomenon with my Danish line. I have a known paternal cousin that I also match on 23andMe, who matches me on MyHeritage. We match two Danes (makes sense) and all overlap on Chromosome 9. The issue? When I click on the overlapping DNA triangulation function, the two additional matches are not common matches to each other...even though we all triangulate and overlap with my known paternal cousin!!!
    Last edited by boilermeschew827; 03-22-2021 at 05:24 PM.
    AncestryDNA (2020 update): Eastern European and Russia 33%, Germanic Europe 32%, Sweden 10%, Norway 7%, Baltics 7%, France 5%, Scotland 4%, Finland 1%, Malta 1%

    23andMe (v5.9): French and German 41.1%, Eastern European 38%, Scandinavian 8%, Finnish 1.6%, British and Irish 0.8%, BNWE 10.2%, North African 0.2%, Broadly European 0.1%

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    Quote Originally Posted by boilermeschew827 View Post
    Speaking only in terms of matches in general, IMO MyHeritage matches should be checked thoroughly and questioned always. I have my paid swab kit, my Ancestry and my 23andMe V5 kits on there. What I've noticed over the years, is that the matches vary between kits and some known matches on Ancestry for example, do not match my Ancestry kit on MyHeritage. I have many 3rd-5th cousins (~0.5% DNA matches) with trees at MyHeritage that I simply cannot determine a MRCA, when theoretically I should be able to (mostly French, Scandinavian and German lines that I have already been able to genetically confirm and have well documented branches for). To be fair, I have seen an influx of French matches recently (this is my only source of French matches), but anything less than a 1% match without another known relative to triangulate (my maternal grandparents for example), I would question.

    I have also noticed my paternal chromosomes 1, 15 and 18 (maybe 21 and 22, but I cannot confirm yet) appear to have more NW German/Dutch matches and also have mysterious British matches that I have suspected to be IBS, pile up regions.

    I cannot speak much on Gedmatch, but I have noticed the same as my previous statement from the projects I am a member of (Lower Saxony, Danish, Prussian) - paternal chromosomes 1, 15 and 18 appear to be heavily from this area with several close British matches that I cannot explain other than IBS. I have not been able to confirm any matches here (outside of the known ones), they are simply too small.

    Sorry this is not more helpful, but I started questioning MyHeritage matches about 2 years ago. Good luck with your searches!




    edit - I should've mentioned another example of the inconsistency with MyHeritage matches and glitches in general. One of my more recent confirmations only matched me on my swab kit. They and they're siblings are confirmed 4C matches to me (I think that's right) - we match a set of French 3x great grandparents and we are all around 0.5%, 35 cMs.

    My grandma is a much closer match to them ~1.2%, 156 cMs (2Cs I think to my grandma). She matches them on her 23andMe V5 kit.

    My point is, without the swab kit I would've missed this excellent genetic verification to myself and without my grandma's kit, I may have missed them altogether. When I click on their profiles, they do not list my grandma as a common match - even though I am ~22% match to my grandma (makes sense for a grandparent). Frustrating to say the least. That begs the question - what relatives am I missing? What relatives are my grandparents' kits missing?

    I also had a recent phenomenon with my Danish line. I have a known paternal cousin that I also match on 23andMe, who matches me on MyHeritage. We match two Danes (makes sense) and all overlap on Chromosome 9. The issue? When I click on the overlapping DNA triangulation function, the two additional matches are not common matches to each other...even though we all triangulate and overlap with my known paternal cousin!!!
    Thanks for this really detailed reply boiler. Could some of these issues be to do with overlap? It seems some of the chips are much more similar in the SNPs that they test than others, 23andme v5 an LivingDNA seems to be the least like, say a MyHeritage OR FTDNA kit, than 23andme v3

    https://www.youtube.com/watch?v=wPtsX_IMF5k Family History Fanatics video on GEDMATCH overlap
    https://youtu.be/wPtsX_IMF5k?t=561 table that shows the % in relation to the SNPs that GEDMATCH looks at

    Obviously we don't know exactly how MyHeritage handles uploads, whether it differs to the way GEDMATCH does or is similar. We also don't know if somehow MyHeritage is filtering out or deleting stuff with uploads that GEDMATCH does not. Ordering my GEDMATCH matches by largest segment size, I now have managed to find a few matches marked as MyHeritage on GEDMATCH that do also appear on my MyHeritage 23andmev5 upload. However, nearly all of the matches that were a surprise to me on GEDMATCH, the French, Polish, Czech, Russian, Brazilian/Argentinian matches do not appear at all. But these matches also appear from FTDNA, which I believe uses the same chip. So it seems like these may be pile up regions of ancient common (Germanic?) ancestry that MyHeritage are filtering out, but GEDMATCH does not do this? But I would also be interested to know how they determine what is a pile up region, and if sometimes they can be wrong, and the connection can be closer?

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    There are some issues for sure, some of them probably have to do with imputation when transferring the kit. See my post here for a similar issue - FWIW the guy did appear as a relative when I transferred my 23andMe to MyHeritage. It's very frustrating that they miss legitimate matches but show a bunch of people from distant countries with whom you share 6cM-10cM in pileup regions.

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  8. #5
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    Quote Originally Posted by peloponnesian View Post
    There are some issues for sure, some of them probably have to do with imputation when transferring the kit. See my post here for a similar issue - FWIW the guy did appear as a relative when I transferred my 23andMe to MyHeritage. It's very frustrating that they miss legitimate matches but show a bunch of people from distant countries with whom you share 6cM-10cM in pileup regions.
    Thanks. I think maybe we can rule out imputation, to MyHeritage at least, as I get the same phenomena i.e. the same unexpected matches from FTDNA kits, which use the same chip as MyHeritage on GEDMATCH. But I guess it could be a problem with the way the new GEDMATCH matching system deals with matching 23andme v5 kits and MyHeritage/FTDNA kits. It would be interesting to know if a similar problem occurs with Ancestry uploads - in fact, I have several and I can't say there anywhere near as obviously unexpected matches than with the 23andme. Did you get the results of the 23andme upload to MyHeritage i.e. have you been able to compare with your MyHeritage tested kit?

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    Quote Originally Posted by Rufus191 View Post
    Thanks. I think maybe we can rule out imputation, to MyHeritage at least, as I get the same phenomena i.e. the same unexpected matches from FTDNA kits, which use the same chip as MyHeritage on GEDMATCH. But I guess it could be a problem with the way the new GEDMATCH matching system deals with matching 23andme v5 kits and MyHeritage/FTDNA kits. It would be interesting to know if a similar problem occurs with Ancestry uploads - in fact, I have several and I can't say there anywhere near as obviously unexpected matches than with the 23andme. Did you get the results of the 23andme upload to MyHeritage i.e. have you been able to compare with your MyHeritage tested kit?
    Yeah I got the results for my 23andMe upload to MyHeritage, haven't done a serious effort to compare them but many matches overlap, which is good. I should probably export them to Excel and run comparisons.

    Do you know if MyHeritage phases your matches after you've tested both parents?

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