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No calls with MtDNA FGS

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  • No calls with MtDNA FGS

    I'm waiting for my mtDNA FGS which is supposed to be a full mtdna results and the final test for mtDNA. Now with that said what does FTDNA do about nocalls. Do they incorrectly label them as deletions with the minus sign or do they a fixed number retries to verify a true deletion? Just curious what the procedure is since the machines reading the DNA can't be 100% perfect .. nothing in science ever seems to be.

  • #2
    There's a FAQ for that!

    http://www.familytreedna.com/faq/answers.aspx?id=10#338

    Elise

    PS. And to specifically address the no-call concern... you'll never get an FGS result with no-calls.
    Last edited by efgen; 8 August 2011, 05:26 PM.

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    • #3
      Thanks for the quick response. Yes I read the FAQ. There is no mention of nocalls but deletions are explained. So back to my original question I would like to understand the procedure FTDNA uses to evaluate nocalls and deletions. I could be wrong , but don't expect the machine to be 100% accurate. If it is why not use the same technology for autosomal test? Is it just too costly?

      Part of this just understanding why it takes 8 weeks for mtDNA FGS when Y-DNA markers or snps seem to take a few weeks.
      Last edited by thetick; 8 August 2011, 06:14 PM.

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      • #4
        Originally posted by thetick View Post
        I'm waiting for my mtDNA FGS which is supposed to be a full mtdna results and the final test for mtDNA. Now with that said what does FTDNA do about nocalls. Do they incorrectly label them as deletions with the minus sign or do they a fixed number retries to verify a true deletion? Just curious what the procedure is since the machines reading the DNA can't be 100% perfect .. nothing in science ever seems to be.
        No-calls are not an issue with direct sequencing, which doesn't care which bases are there.

        Microarrays (chips) are different -- they use probes designed to latch on to a specific short sequence of SNPs. For instance, I have an unusual mutation 236C. That confuses the probe designed to look for a mutation at 235, so I (and my mtDNA kin) get a no-call there. Poly-C regions are tricky, and there are other miscellaneous random causes for no-calls. Interestingly, someone with a known heteroplasmy at FTDNA got a no-call for that position, as did her mother. But that's an exceptional case.

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        • #5
          It's definitely way too costly to do the autosomal SNP tests with the sequencing method that is used for the FGS.

          As shown in the FAQ that I posted, it takes 96 test panels to complete a full FGS test. The FGS has 16,569 bases.

          Family Finder has over 710,000 *pairs* of bases being tested -- that's 85 times more bases than the FGS.

          Would you be willing to pay $299*85 (over $25,000) for the autosomal SNP test for 100% accuracy?

          (I don't know that it would necessary cost that, but the point is, there's an astronomical difference in how much testing would need to be done.)

          Elise
          Last edited by efgen; 8 August 2011, 06:27 PM.

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          • #6
            Originally posted by thetick View Post
            Part of this just understanding why it takes 8 weeks for mtDNA FGS when Y-DNA markers or snps seem to take a few weeks.
            Partly because they need to ensure accuracy for the 96 panels of tests for one FGS. Unlike Y-DNA, partial FGS results will not be posted -- all 96 panels need to be complete (with the exception of HVR1 & HVR2 -- those can be posted separately).

            Elise
            Last edited by efgen; 8 August 2011, 06:22 PM.

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