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Retesting Novel Variants

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  • Retesting Novel Variants

    I wanted to retest some novel variant results to check FTDNA ‘s accuracy.
    Because of the expense of testing , 50 of my 90 variants were initially considered by someone more knowledgeable than I . Of these 50 , 22 were selected to be retested. The results showed

    1 location showed to be an Indel rather than the reported value
    1 location , were instead of the derived value reported by FTNA , it was the ancestral value on the retest.
    1 location that could not be reported after multiple attempts at retesting

    19 values were identical. So in my case it was 86 % accurate as far as independent retest

    I thought this result may be helpful to know if two people were comparing results of novel variants.

  • #2
    Originally posted by Brunetmj View Post
    I wanted to retest some novel variant results to check FTDNA ‘s accuracy.
    Because of the expense of testing , 50 of my 90 variants were initially considered by someone more knowledgeable than I . Of these 50 , 22 were selected to be retested. The results showed

    1 location showed to be an Indel rather than the reported value
    1 location , were instead of the derived value reported by FTNA , it was the ancestral value on the retest.
    1 location that could not be reported after multiple attempts at retesting

    19 values were identical. So in my case it was 86 % accurate as far as independent retest

    I thought this result may be helpful to know if two people were comparing results of novel variants.
    There seems to be a lot of problems with the Big-Y tests and I will wait until they get it right before I think about testing.

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    • #3
      [QUOTE]There seems to be a lot of problems with the Big-Y tests and I will wait until they get it right before I think about testing. [QUOTE]

      I certainly can understand that. I personally am trying to avoid all testing here. Extraordinary long waiting times, a breakdown in company communication and an increase in alternatives have led to my decision. Since I have previously taken every major test offered here , this is not any big deal. However it becomes increasing more difficult for me to recommend testing here to others.

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      • #4
        Originally posted by Brunetmj View Post
        1 location showed to be an Indel rather than the reported value
        1 location , were instead of the derived value reported by FTNA , it was the ancestral value on the retest.
        1 location that could not be reported after multiple attempts at retesting
        #1 is a known and previously disclosed difficulty with FTDNA's interpretation method. From the BAM file, YFull is able to distinguish between a transition/transversion and an indel.

        #3 is a limitation of ordinary sequencing ("retesting"), not necessarily of FTDNA's results.

        I would be suspicious of #2 as well. It may also be a limitation of conventional sequencing (which may confuse a Y chromosome sequence with a very similar sequence elsewhere on the Y or on another chromosome).
        Last edited by lgmayka; 21 August 2014, 01:23 AM.

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        • #5
          So what would be the conclusions of all this?
          Big y results cannot be replicated elsewhere?


          Originally posted by lgmayka View Post
          #1 is a known and previously disclosed difficulty with FTDNA's interpretation method. From the BAM file, YFull is able to distinguish between a transition/transversion and an indel.

          #3 is a limitation of ordinary sequencing ("retesting"), not necessarily of FTDNA's results.

          I would be suspicious of #2 as well. It may also be a limitation of conventional sequencing (which may confuse a Y chromosome sequence with a very similar sequence elsewhere on the Y or on another chromosome).

          Comment


          • #6
            Originally posted by Brunetmj View Post
            Big y results cannot be replicated elsewhere?
            DNA testing results from one technology cannot always be replicated in another technology. Each technology has its advantages and limitations. Your own experience shows that most, but not all, SNPs found by next-generation sequencing can be reproduced in conventional (Sanger) sequencing.

            Perhaps because the primary use of a Y-DNA haplotree is (arguably) to guide test customers in choosing the next individual SNP to test (by conventional sequencing), ISOGG's listing criteria say that:
            - A SNP found by next-generation sequencing (e.g., Big Y or FullGenomes) but not yet confirmed with conventional sequencing must appear in italics.
            - A SNP found by a microarray (e.g., Geno 2.0 or Chromo2) but not yet confirmed by other means cannot appear at all.
            Last edited by lgmayka; 21 August 2014, 06:55 PM.

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