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Thread: Dante Labs Long Read Test

  1. #1
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    Dante Labs Long Read Test

    https://www.dantelabs.com/collection...ome-sequencing
    WHOLE GENOMEL - LONG READS WHOLE GENOME SEQUENCING
    Whole GenomeL - based on Third-generation sequencing (also known as long-read sequencing). The first Long Reads Whole Genome Sequencing available commercially, worldwide. Leveraging Third-generation sequencing technology in the Dante Labs Oxford Nanopore-certified lab
    Out of curiosity I ordered the test. I don't really know that much about the Oxford Nanopore technology. If anyone is up on that I would like to learn more.
    YFull: YF14620 (Dante Labs 2018)

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  3. #2
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    Quote Originally Posted by pmokeefe View Post
    https://www.dantelabs.com/collection...ome-sequencing
    WHOLE GENOMEL - LONG READS WHOLE GENOME SEQUENCING
    Whole GenomeL - based on Third-generation sequencing (also known as long-read sequencing). The first Long Reads Whole Genome Sequencing available commercially, worldwide. Leveraging Third-generation sequencing technology in the Dante Labs Oxford Nanopore-certified lab
    Out of curiosity I ordered the test. I don't really know that much about the Oxford Nanopore technology. If anyone is up on that I would like to learn more.
    Wow. I've been trying to follow this technology, I think Thomas Krahn at YSEQ has been experimenting with a MinION himself and posted about it on fb but recently said it wasn't quite ready for market yet. He prefers this approach to the Chromium barcode stuff.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  5. #3
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    I'm very interested in that for research, like scaffolding Y-chromosome for structural variation, but that price is bit tough on many people's budgets! I'm not sure if one should expect significant discount on this. The costs of BGI-seq isn't clear, they might be getting very low price on it themselves, although the strategy seems to always have been to sell them at loss to establish themselves on the market. The Oxford Nanopore long read sequence may be pretty close to at-cost too, though I should check the latest estimates for flowcell yield & price.

    Note though:
    https://www.dantelabs.com/collections/our-tests

    Long-read sequencing doesn't include their standard variant interpretation, which might be as well, as the order page states: "Optimized for analysis of repeated sequences, copy number variations and structural variations". The best results have been achieved by using Oxford Nanopore long reads for chromosome structure and short reads for individual variants. Of course both technologies provide both types of information, so technologies for combining them are active research topic.

    Edit: Just checked, e-mail I received from Dante Labs announcing this says among other things:
    "Combined with your existing whole genome sequencing, long reads will give you the best genomic map of your DNA.

    A special offer for you

    As a valued Dante Labs customer, we are glad to share with you a 20% discount for this new test."

    They're sort-of hinting at combining the results themselves, but I see no mention or reference of them doing it yet. 20% for existing customers is interesting though. The problem with running large discounts like the Black Friday special is that you're always expecting better offer, though
    Last edited by Donwulff; 04-08-2019 at 07:05 AM.

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  7. #4
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    It would be great to see comparison between a PacBio test and a nanopore one if you are still doing the former. I agree the Dante price is too good to let it pass. The PacBio price at FGC is a bit painful though.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  9. #5
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    Quote Originally Posted by Donwulff View Post
    A special offer for you

    As a valued Dante Labs customer, we are glad to share with you a 20% discount for this new test."
    Oops, sounds like I should have rechecked my emails before ordering!
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content

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  11. #6
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    When I ordered my original Dante Labs test, they lowered the price by $50 right after. I immediately e-mailed them and they reimbursed me with $50 Amazon gift-card (Which I think I never got around to using, ouch). If you forgot to use the discount code, it's worth e-mailing their customer support, though I can't blame them if they've decided to offer no reimbursements since then.
    As an aside, I probably shouldn't mention this, but I originally created my Dante Labs account under different e-mail address from the one I ordered the test with, and I'm getting the discounts etc. on both e-mail accounts even though I didn't order anything on the second one. I don't think we're still supposed to share the discount code though, they might check if you've actually ordered before

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    Yeah I did fire off a contact message about it, fingers crossed :-)
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content

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  15. #8
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    I apologize if this is not state of the art, because I believe I've seen better results, but for a bit of what to expect:
    https://www.nature.com/articles/s41467-019-09025-z

    "The accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule sequencing, which has a per-nucleotide error rate of ~5–15%. Meeting this demand, we developed Clairvoyante, a multi-task five-layer convolutional neural network model for predicting variant type (SNP or indel), zygosity, alternative allele and indel length from aligned reads. For the well-characterized NA12878 human sample, Clairvoyante achieves 99.67, 95.78, 90.53% F1-score on 1KP common variants, and 98.65, 92.57, 87.26% F1-score for whole-genome analysis, using Illumina, PacBio, and Oxford Nanopore data, respectively. Training on a second human sample shows Clairvoyante is sample agnostic and finds variants in less than 2 h on a standard server. Furthermore, we present 3,135 variants that are missed using Illumina but supported independently by both PacBio and Oxford Nanopore reads. Clairvoyante is available open-source (https://github.com/aquaskyline/Clairvoyante), with modules to train, utilize and visualize the model."

    As said, long read sequencing's real strength is in structural variation, and genomic locations that are so repetitive/similar that it's impossible to place 160 (or 100) basepair reads into just one location. Y chromosome should have a lot of these, so as I suggested on the BigY-700 thread, I think this will eventually be a boon for Y chromosome phylogeny. Short reads aligned against the long sequencing read could provide evidence that the variant is a real one, and of course Sanger sequencing (up to 1000 basepairs for single read) could be used to validate any phylogenetically important variants. Or, just assume it's good enough for drawing phylogeny trees

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    Double post (Why does that always happen...)

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    There will be a second example of this test result under R1b-S1121 to compare with pmokeefe's. There's about 1600 years separating them with roughly accurate Eóganachta pedigrees going back that far, so it should be interesting from the Y DNA perspective.

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