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Problem with Chromosome Painting Being Random (Couples are randomized?)

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  • Problem with Chromosome Painting Being Random (Couples are randomized?)

    I saw my chromosome painting results, but unlike the examples FTDNA provided, my chromosome couples are all randomly mixed, there is no distinction between paternal and maternal chromosomes. It shows like my father and mother are from the same population, which is not the truth, I am mixed.


    As you can see in the image, blue, pink, dark green genes are all shown in both chromosomes. However, both my mother and father cannot have all of them because I know they are from different populations. Can you please help me with this? ftdnaaa.JPG

  • #2
    The "chromosome painting" algorithm, like almost every aspect of autosomal genetic genealogy, does not automatically know which SNP's come from which parent. SNP's are tested individually without regard to the DNA sequences on either side of them. This is very different from the ideal way of "sequencing" DNA, but it is right now the only feasible way to analyze autosomal DNA for the mass market. Eventually, I expect "long read sequencing" will become the standard, and with it, the possibility of establishing the actual sequences of long pieces of individual chromosomes (still without knowing which parent any segment came from).

    For now, almost all autosomal genetic genealogy attempts to guess what the actual sequences are, starting with individual SNP scores.

    This is not to say that the "chromosome painting" methodology is as good as it can be. There have already been some reports here for individual cases that suggest the need for a major improvement: Rather than letting some algorithm guess what the "ethnically informative" sequences are, it would make sense first to deduce actual sequences through an analysis of triangulating segment matches. The sequences deduced through the existence of robust triangulation groups can then be run through the "chromosome painting" methodology with a greatly reduced risk that the results are artifactual -- the result of randomly switching from one homologous sequence to the other. Likewise, when kits from both parents are available, it should be possible to produce almost perfect phasing results to reconstruct almost all of the child's paternal and maternal chromosomes, and those reconstructed sequences should produce more reliable results for "painting" the child's kit, and, as well, correctly identifying the homologous sequences in each parent (but without attributing these to a particular grandparent).

    For now, all you know is that the "chromosome painting" algorithm has deduced the probable existence of some ethnic markers and segments in your kit. It does not know where they came from, and there is not yet a guarantee that every one of them is even real.

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    • #3
      Originally posted by John McCoy View Post
      The "chromosome painting" algorithm, like almost every aspect of autosomal genetic genealogy, does not automatically know which SNP's come from which parent. SNP's are tested individually without regard to the DNA sequences on either side of them. This is very different from the ideal way of "sequencing" DNA, but it is right now the only feasible way to analyze autosomal DNA for the mass market. Eventually, I expect "long read sequencing" will become the standard, and with it, the possibility of establishing the actual sequences of long pieces of individual chromosomes (still without knowing which parent any segment came from).

      For now, almost all autosomal genetic genealogy attempts to guess what the actual sequences are, starting with individual SNP scores.

      This is not to say that the "chromosome painting" methodology is as good as it can be. There have already been some reports here for individual cases that suggest the need for a major improvement: Rather than letting some algorithm guess what the "ethnically informative" sequences are, it would make sense first to deduce actual sequences through an analysis of triangulating segment matches. The sequences deduced through the existence of robust triangulation groups can then be run through the "chromosome painting" methodology with a greatly reduced risk that the results are artifactual -- the result of randomly switching from one homologous sequence to the other. Likewise, when kits from both parents are available, it should be possible to produce almost perfect phasing results to reconstruct almost all of the child's paternal and maternal chromosomes, and those reconstructed sequences should produce more reliable results for "painting" the child's kit, and, as well, correctly identifying the homologous sequences in each parent (but without attributing these to a particular grandparent).

      For now, all you know is that the "chromosome painting" algorithm has deduced the probable existence of some ethnic markers and segments in your kit. It does not know where they came from, and there is not yet a guarantee that every one of them is even real.
      thank you so much for your detailed answer.

      I also thought they cannot know which one came from which parent. But in FTDNA MyOrigins 3.0 paper there are misleading images showing that father and mother chromosomes are not mixed but separated perfectly.
      ftdna 2.JPG


      Look at this image, shouldn't my chromosomes be like that, If not, why FTDNA shared this image? My father and mother are from different countries. So my chromosome painting should have been like this image, am I wrong?

      Comment


      • #4
        You are correct, the figure shows the "real" state of a hypothetical child of parents grandparents with ancestry from different "colors" of chromosomes. But, that's not what the Chromosome Painting feature does, because it only works with fragments of chromosomes! The discrepancy between how the chromosomes really are, and how the autosomal genetic genealogy process sees them, is huge!

        I had noticed that a lot of the "white paper" on Chromosome Painting fell into the category of "thought experiments" as opposed to real data. I missed the implications of this figure, which is "conceptually" informative but not at all similar to the results that the actual methodology can produce!

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        • #5
          John McCoy Thank you so much for your help, you've been really helpful.

          I am sorry in last post I tried to show my curiosity but I noticed it looked rather rude, the site doesn't let me to edit. Sorry for that, English is not my native language

          Originally posted by Revolver View Post


          Look at this image, shouldn't my chromosomes be like that, If not, why FTDNA shared this image? My father and mother are from different countries. So my chromosome painting should have been like this image, am I wrong?
          sorry for being unconsciously rude in this quoted sentences.
          Last edited by Revolver; 22 September 2021, 08:42 AM.

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          • #6
            No, you were perfectly clear and your observation was exactly right! The discrepancy you noticed is surprising and unexpected.

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