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Thread: Full Y Chromosome Sequencing: Phase III Pilot

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    Quote Originally Posted by Rory Cain View Post
    I am hoping to see that demonstrated when two Y Elite 2.0 tests for O'Cathain (variants) arrive, compared with two O'Cathain (variants) Big Y results and my Y Elite 1.0. My Y Elite 1.0 found 18 more new SNPs in my sample than Big Y found in a close relation, even though we should have been either identical or perhaps one SNP apart. Not 18 SNPs. For our clan, Big Y is not reading some 18 of our derived state SNPs, but Y Elite 1.0 is, so bring on Y Elite 2.0!
    One reason for the extra delay was that we made the decision to have the team do a thorough review of procedures so we could continue to improve data quality from Batch 9004 to Batch 9005. Secondly, we do our own alignment of the raw data rather than use the alignments from the supplier and do additional quality control processing ourselves which takes additional time. The quality review did result in improvements in data quality in 9005 over 9004, so that approach was justified.

    Another factor was that we recruited a specialist in single-cell DNA sequencing who has worked as a research academic to do DNA extractions. In that way we would have two separate teams do the DNA extractions so we could compare the results.

    In this case, that works out to an additional amount of computational processing, approximately just under 300 hours of computational time for each of these batches. That time is used to doing our own alignments rather than using the alignments that our supplier gives us.

    Thus far, we believe that our alignments are better than those of the suppliers that we have used, so the extra computational time is justified.
    Last edited by FGC Corp; 11-12-2015 at 04:10 AM.
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    Quote Originally Posted by FGC Corp View Post
    One reason for the extra delay was that we made the decision to have the team do a thorough review of procedures so we could continue to improve data quality from Batch 9004 to Batch 9005. Secondly, we do our own alignment of the raw data rather than use the alignments from the supplier and do additional quality control processing ourselves which takes additional time. The quality review did result in improvements in data quality in 9005 over 9004, so that approach was justified.

    Another factor was that we recruited a specialist in single-cell DNA sequencing who has worked as a research academic to do DNA extractions. In that way we would have two separate teams do the DNA extractions so we could compare the results.

    In this case, that works out to an additional amount of computational processing, approximately just under 300 hours of computational time for each of these batches. That time is used to doing our own alignments rather than using the alignments that our supplier gives us.

    Thus far, we believe that our alignments are better than those of the suppliers that we have used, so the extra computational time is justified.
    Happy with that. Timeliness has been a problem for FGC from it's inception but when given good reasons for it, clients generally accept, I think. With O'Cathain clan members having tried both products, FGC or Big Y, and finding Big Y overlooks 18 potentially key SNPs and InDels that FGC delivers, we have decided to accept whatever timeframe FGC takes in order to get the better product. The long timeframe is a frustration but one we have decided to live with, to get a better genome coverage.

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    Quote Originally Posted by Rory Cain View Post
    The long timeframe is a frustration but one we have decided to live with, to get a better genome coverage.
    From what Justin just told me yesterday the usual Elite 1.0 yielded roughly 3 gigs of data whereas my Elite 2.0 is roughly 4.6 gigs. So absolutely there is a marked increase in coverage and we will have to wait and see, hopefully not more than a few days, what shows up especially in novel snps which may help our FGC17938 group show more branches.

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    Quote Originally Posted by dkm1987 View Post
    From what Justin just told me yesterday the usual Elite 1.0 yielded roughly 3 gigs of data whereas my Elite 2.0 is roughly 4.6 gigs. So absolutely there is a marked increase in coverage and we will have to wait and see, hopefully not more than a few days, what shows up especially in novel snps which may help our FGC17938 group show more branches.
    I think that means Elite 2.0 has 53% more coverage than Elite 1.0. That makes having an upgrade from Elite 1.0 to Elite 2.0 attractive if the cost is affordable.
    Last edited by Eldon; 11-14-2015 at 05:40 PM.
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    Quote Originally Posted by Eldon View Post
    With Elite 2.0 having 53% more coverage than Elite 1.0 it really makes having an upgrade from Elite 1.0 to Elite 2.0 attractive if the cost can be reasonable.
    To clarify, gigabases translates into the number of bases read. Overall, the greater the amount of data, the higher the data quaity and the greater the accuracy of the results. In terms of the coverage, the number of Callable Loci in the two tests in similar. The greater read length means that the quality of coverage of the same sections of the Y chromosome will be greater.

    As I mentioned earlier, there will also be SNP discoveries that could not be made with lower read lengths, such as the 100bp of Y Elite 1.0.

    Say region A is covered in Y Elite 1.0 and 2.0. Some SNPs in region A cannot be discovered by 1.0 even though it falls under the coverage of 1.0. The read length improvement accounts for the difference.
    Last edited by FGC Corp; 11-14-2015 at 05:42 PM.
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    Quote Originally Posted by FGC Corp View Post
    ... In terms of the coverage, the number of Callable Loci in the two tests in similar. The greater read length means that the quality of coverage of the same sections of the Y chromosome will be greater.

    As I mentioned earlier, there will also be SNP discoveries that could not be made with lower read lengths, such as the 100bp of Y Elite 1.0.

    Say region A is covered in Y Elite 1.0 and 2.0. Some SNPs in region A cannot be discovered by 1.0 even though it falls under the coverage of 1.0. The read length improvement accounts for the difference.
    Ok, same callable loci but greater clarity. My genetic group's tests now include my Y Elite 1.0, two
    Big Ys, and shortly two Y Elite 2.0. The two versions of Y Elite cover the same callable loci so I assume that my old Y Elite 1.0 could be found to have SNPs not previously found until compared with the new Y Elite 2.0

    If I am right so far, then my question is, would this also apply to the Cain and Kain who ordered Big Y. Are the same callable loci covered in Big Y, just with lesser clarity, or are less loci covered in Big Y? After all, the ultimate value of DNA results is all in the comparison.

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    Quote Originally Posted by Rory Cain View Post
    Ok, same callable loci but greater clarity. My genetic group's tests now include my Y Elite 1.0, two
    Big Ys, and shortly two Y Elite 2.0. The two versions of Y Elite cover the same callable loci so I assume that my old Y Elite 1.0 could be found to have SNPs not previously found until compared with the new Y Elite 2.0

    If I am right so far, then my question is, would this also apply to the Cain and Kain who ordered Big Y. Are the same callable loci covered in Big Y, just with lesser clarity, or are less loci covered in Big Y? After all, the ultimate value of DNA results is all in the comparison.
    The Y Elite 1.0 and 2.0 captures are comparable to the coverage that one gets via whole genome sequencing. The alternatives target a smaller set of the Y, and thus achieve lower costs, as the cost is proportional to the number of probes and the amount of the Y covered, so Elite has more CallableLoci and more coverage for those reasons.

    If a SNP isn't in Big Y, then it could be Sanger sequenced or checked in 2.0.

    Certain aspects of the other company's product were discussed in the I4GG talk, which you can see here:
    http://i4gg.org/product/thomas-krahn/

    See there for details.
    Last edited by FGC Corp; 11-14-2015 at 08:36 PM.
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    Quote Originally Posted by Rory Cain View Post
    Are the same callable loci covered in Big Y, just with lesser clarity, or are less loci covered in Big Y? After all, the ultimate value of DNA results is all in the comparison.
    This community member commented on this in this blog post:
    http://www.it2kane.org/2015/11/which-ngs-test-to-take/

    Y Elite covers more of the Y, in short.
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    Something I didn't mention in that post is Y Elite is consistently close to the theoretical limit for what has been included in the hg37 reference. I believe Alex calculated that to be 22984529 bases which are not 'N'. The Y Elite BAMs were averaging 22772412. The single WGS that was shared hit 22824490 on the Y.

    I'm looking forward to comparing the 2.0's that are in the next few batches.

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    Quote Originally Posted by JamesKane View Post
    Something I didn't mention in that post is Y Elite is consistently close to the theoretical limit for what has been included in the hg37 reference. I believe Alex calculated that to be 22984529 bases which are not 'N'. The Y Elite BAMs were averaging 22772412. The single WGS that was shared hit 22824490 on the Y.

    I'm looking forward to comparing the 2.0's that are in the next few batches.
    We're upgrading to the hg38 reference, with batches 8001 onward.
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