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Thread: Why don't companies compare phased kits for DNA matches?

  1. #1
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    France France Bretagne

    Why don't companies compare phased kits for DNA matches?

    DNA testing alone don't separate DNA from the father and from the mother.
    This gives false positives in matches with other members.

    A technique makes it possible to differentiate the two DNAs: phasing.
    For this, it's of course necessary to test at least one of the parents.

    To my knowledge, no company practices phasing for matches!
    Even 23andme, who practices phasing for ethnicity, does not do for DNA matches.

    However, it is essential!
    If they did, they could lower the detection thresholds, while maintaining a certain reliability.
    Because many real segments are not detected because of the too high thresholds.


    Since Geneanet easily accepts files, I was able to send phased and non-phased kits, and see the difference.
    I was able to phase my kit with my father's kit: which gave me a kit with DNA that I received exclusively from my father and another that I received exclusively from my mother
    Then, I was able to extract from my father's kit, the DNA that I did not receive from him. For this kit, there will be genetic cousins ​​that he has, but not me.

    Before phasing:
    My kit: 17 matches
    My father's kit: 43 matches

    After phasing:
    My kits: (paternal and maternal): 3 matches
    My father's kits: (what he gave me and what he did not gave me): 5 matches

    Difference:
    I lost 82% of my matches
    My father lost 88% of his matches


    Here is the graph of the segments that remained (green - True) and the segments that disappeared after phasing (Red - False)
    We see that it is not the total of centimorgan which is important, but the length of the longest segment.
    segments-phased.png


    Another thing: the length of the real segments varies according to the method.
    This means that segments that have disappeared after phasing can be real segments, but the phasing
    gave them their true size and become below the threshold defined by the company.

    Example of my father's 5 segments:

    With phasing (my father) - Without phasing (my father) - segment transmitted to me (without phasing)
    14.5 cM - 19.85 cM - 14.5 cM
    13.7 cM - 13.7 cM - 14.3 cM
    13.2 cM - 13.2 cM - 13.2 cM
    16.8 cM - 20.3 cM - X
    16.3 cM - 16.9 cM - X


    Thus 4 out of 8 segments increased their length when the kit was not phased.
    The average, when the segment increases in size is 2.5 centimorgan

    These statistics are probably too few to make any definitive conclusions.
    I would love to send phased kits on myheritage, because I have a lot more connections than on geneanet, but they don't accept phased kits.
    That said, we can do it by hacking the kits. I managed to do it for my phased kit on the maternal side. But I had a lot of trouble getting there!

    What seems obvious to me is the immense interest in phasing our kit with at least one of his parents, or one of his children.
    This would avoid wasting time with fake cousins ​​and having a more limited number of matches to be able to study all of them!
    Y haplogroup: R1b: L21 --> DF13 --> BY145002
    The oldest L21 known are I2457 et I2565 from Stonehenge (Beaker Culture, 2400-1900 BC)

    MTDNA: U4c1
    The oldest U4c1 known are "poz224", Yamnaya culture (2882-2698 BC), and 2 Bell-Beaker in Germany (Karsdorf, 2314-2042 BC)

    Paternal MTDNA: K1b2b
    The oldest K1b2 are Eastern European Mesolithic: Kunda Donkalnis5 (Lithuania), 6000 BC and Meso-Ene Lepenski Vir Lepe28 in Serbia, 5900 BC.
    The oldest K1b2b is Alt-3, Corded-Ware Germany (2500 BC)

  2. The Following 3 Users Say Thank You to Tolan For This Useful Post:

     Calamus (06-30-2020),  dosas (06-30-2020),  jstephan (06-30-2020)

  3. #2
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    Yes, of course.
    But what do they get out of it?
    In order to push this, you need to persuade companies that, in some way, their revenue would increase.*
    I'm sure it is possible to make a case for that: if possible with a real example of how they made more money from a phased kit being uploaded.
    I am used to developing a new product and then having to present a marketing department with a ready-made case for it they can take to management. You basically have to show how ignoring your proposal will lose potential earnings.

    The best most of us can do is to phase our kit at GEDmatch.
    Or to do it off-line and upload to a site that will accept phased kits.

    *without too many "this is not working" type enquiries generated from it.
    Last edited by Saetro; 06-30-2020 at 09:14 PM.

  4. The Following User Says Thank You to Saetro For This Useful Post:

     Tolan (07-01-2020)

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