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Thread: Full Y Chromosome Sequencing: Phase III Pilot

  1. #1321
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    Quote Originally Posted by FGC Corp View Post
    "Once I mailed it off I noticed the 2 kit bags had something hand written on them which is probably the kit#. Is this going to cause a problem?"

    Those are the kit codes. No problem.
    Good to know. Thanks
    Last edited by MitchellSince1893; 12-09-2015 at 01:14 AM.
    37% English, 26% Scot/Ulster Scot, 14% Welsh, 14% German, 3% Ireland, 3% Nordic, 2% French/Dutch, 1% India
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  3. #1322
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    Quote Originally Posted by FGC Corp View Post
    Probably 65% plus as an estimate.
    Agreed, with the 111 panel and Big Y it comes out to about a 50% per father-son transmission so it should be higher with more coverage.

    It's still a bit frustrating that "averages" aren't smooth so it all depends on the fits and starts of these mutations. However, I think the good point is that the opportunity or mutation is improved with both SNPs, STRs and other types of variants. These things are additive in improving opportunities.
    Last edited by Mikewww; 12-09-2015 at 02:31 PM.

  4. #1323
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    Quote Originally Posted by Mikewww View Post
    Agreed, with the 111 panel and Big Y it comes out to about a 50% per father-son transmission so it should be higher with more coverage.

    It's still a bit frustrating that "averages" aren't smooth so it all depends on the fits and starts of these mutations. However, I think the good point is that the opportunity or mutation is improved with both SNPs, STRs and other types of variants. These things are additive in improving opportunities.
    If one combines improved capture technology, the new reference sequence, and refinements to the software, it may be possible to get 1 marker at least 65% of the time, and tighten the confidence intervals.
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  6. #1324
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    Quote Originally Posted by FGC Corp View Post
    We can do better as I mentioned in an email, beyond 30x, the sample can be upgraded for $45/1x, up to 100x coverage.

    Overall, a 100x test would be $4750 in total. The same option exists for incremental upgrades; ie 40x would be 30x ($1600) + 10*$45 or $2050.

    Essentially, the primary reason to do 100x is if you want very high certainty and you are going to take this to genetics specialists to analyze your results (Note: we do not do medical analysis).
    Just of curiosity: can a similar upgrade also be offered for Y-Elite 2.0 for example to 50x?
    Particularly interested in: DNA/Admixture from Central Europe (Alps, Tyrol, Dolomites); Y-DNA J2a-PF5169, J2a-L210, R1a-M17, R1b-U106; mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects in which I work:Hidden Content , Hidden Content , J2a-PF5197, ISOGG Wiki, GenWiki (german)

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  8. #1325
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    Quote Originally Posted by ChrisR View Post
    Just of curiosity: can a similar upgrade also be offered for Y-Elite 2.0 for example to 50x?
    Essentially, the only path here would be to re-run the sample and add both data sets which would probably yield about 60x mean coverage.
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  10. #1326
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    Quote Originally Posted by FGC Corp View Post
    To an extent, we're already doing this because we use our own customer database as well as the public datasets to identify the unique variants for each sample within each haplogroup. The private SNP section of haplogroup compare report identifies the newly identified high-quality private SNPs and also shows which of these may be shared by other customers' kits.

    That also means that as the database grows larger, SNPs in older customer samples may be re-evaluated to be higher quality, precisely because the database has improved.

    Also, we add newly available public samples from research papers as they become available, so our database is continually expanding via both new public samples and new customer samples.
    Ah, that's good. It answers concerns arising from FGC's original statement when starting out in 2013 that FGC results would be compared with an already ageing and racially selective (it excluded Ireland and Wales from it's "British Isles" sample) 1K Genomes database.

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  12. #1327
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    Just ordered Y-Elite 2.0, I was informed that I will get mtDNA too and in addition the interpretation that's included in the price, can someone confirm this?

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  14. #1328
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    Quote Originally Posted by wmehar View Post
    Just ordered Y-Elite 2.0, I was informed that I will get mtDNA too and in addition the interpretation that's included in the price, can someone confirm this?
    Yes, interpretation is included ($50 value) as well as mtDNA results.
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  16. #1329
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    My experience with Y Elite 1.0 shows that mtDNA coverage and accuracy is not 100 %. I don't know if 2.0 is better or not.
    Regarding interpretation I think Yfull is much better.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
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  17. #1330
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    Quote Originally Posted by Petr View Post
    My experience with Y Elite 1.0 shows that mtDNA coverage and accuracy is not 100 %. I don't know if 2.0 is better or not.
    Regarding interpretation I think Yfull is much better.
    Thus far, the mtDNA coverage appears to be consistently better in 2.0 than 1.0.
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