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Thread: Dante Labs Long Read Test

  1. #11
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    The order page says "LONG READ RAW DATA Download your FASTQ, BAM and VCF files, with no extra charge." I wonder if downloads will actually be available this time, or if it'll be separate order again?

    Also regarding raw data, "Meanwhile, it also has been found that electrical signals in Nanopore sequencing are sensitive to epigenetic changes in the nucleotides [12, 13, 14]. Several studies have demonstrated that Nanopore sequencing can be used to detect DNA methylation." DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

    I wonder if we have to ask Dante Labs whether they already do methylation calling, and if raw electrical signal data (Known as FAST5 files) is available. While likely not interesting from genealogical perspective, being able to extract methylation data from the results would make this extremely valuable for medical curiosity.
    Last edited by Donwulff; 04-08-2019 at 11:59 AM.

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  3. #12
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    Quote Originally Posted by Donwulff View Post
    The order page says "LONG READ RAW DATA Download your FASTQ, BAM and VCF files, with no extra charge." I wonder if downloads will actually be available this time, or if it'll be separate order again?

    Also regarding raw data, "Meanwhile, it also has been found that electrical signals in Nanopore sequencing are sensitive to epigenetic changes in the nucleotides [12, 13, 14]. Several studies have demonstrated that Nanopore sequencing can be used to detect DNA methylation." DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

    I wonder if we have to ask Dante Labs whether they already do methylation calling, and if raw electrical signal data (Known as FAST5 files) is available. While likely not interesting from genealogical perspective, being able to extract methylation data from the results would make this extremely valuable for medical curiosity.
    I've got an epigenome test pending elsewhere, I agree its all fascinating.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    GEDMatch: A828783 (autosomal DNA), 9427684 (GEDCOM) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT
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    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  4. #13
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    Quote Originally Posted by MacUalraig View Post
    I've got an epigenome test pending elsewhere, I agree its all fascinating.
    I asked Dante Labs about the raw data online download, FAST5 signal files, methylation calling (On second thought I'm not sure how this would be affected by using saliva sample, but it's worth a try), combining with the previously done WGS to "polish" the assembly and SNP's in the final result files. Lets see if I get any useful answers.

    Anyway even if we get raw data on disk, everything except methylation calling should be doable without FAST5 files.

    That's perhaps bit on the "research" side since previous hybrid assembly polishes have used Illumina short reads, but I don't see any reason BGIseq shouldn't work at least as well.

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  6. #14
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    My first sample to Full genomes took 9 weeks and by that time I'd sent another sample( I have no idea if the second sample has arrived as yet even though I sent it tracked about a month ago... I must check! which is supposed to be 5 to 10 days). That sample at Full genomes is still awaiting processing for a 20X ( sent back mid January). I think it would very diifficult, if not impossible, to send blood overseas from Australia. I can get blood collected easily though.

    i have posted a 30X to Dante..it's still in the mail to get there (been about 6 weeks so far).
    BUT it is going to the US, as I ordered from the US and they enclosed a fully paid return mail (from the US, so I could have returned for free postage if I had flown the US with it..which I have known people to do).

    Does it then get sent to Italy? I think the saliva sample may not be optimal by the time it gets there for nanopore IF I was allowed to upgrade? Also I've read on Full Genomes section that blood is better., and I can't see much point if one can't get an optimal sample to the lab.
    It's been what I've been waiting for though.

    My other concern is the size of the data. How much bigger than a standard 30X would it be? Any idea?

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  8. #15
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    If they're both 30X, then by definition the basecalls will be equivalent size. https://www.dantelabs.com/collections/our-tests supports this as both WGS and Long Read are "Average Data Size: +180 GB" (I have no idea what that means, though. The BAM's are like 100G, but that's uncompressed, real size much larger than 180GB. 3 billion bases genome times 30X is 90 GB "data" plus some metagenome).

    Side note, I just noticed that the table shows "Read Length PE150" for the second generation sequencing options, so it seems they have indeed upgraded to 150 basepair reads.

    Shipping blood internationally would, even in best circumstances, be quite a mess (no pun intended). Plus it would need to be shipped chilled, 6+ weeks shipping time? I think even on FGC thread the benefit of using blood was inconclusive. In terms of current price Oxford Nanopore is not "bleeding edge", FGC Long Read costs $2900 at which point indeed it's worth putting several hundred down for best sample possible.

    IMO main reason you would want to use blood though would be less contamination. I don't know how Dante Labs is running the Oxford Nanopore sequencing, those sequencers should be the capability of being selective about which molecules they sequence, if it's not human they could reject it. Then again, some people will be specifically interested in the metagenome in their saliva as well.

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  10. #16
    For nanopore sequencing, the basecalling accuracy seems to be about 2 orders of magnitude worse than NGS.
    According to this paper, quality scores for PromethION basecalls hover around 8-10 (80-90% confidence per basecall):
    https://www.biorxiv.org/content/bior...34118.full.pdf Raw Fastq data: https://www.ebi.ac.uk/ena/data/view/PRJEB26791

    Does anyone know what the aggregate confidence for the consensus basecall in the BAM is, after combining the ~30 reads?

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  12. #17
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    See https://anthrogenica.com/showthread....l=1#post559602

    Problem is nanopore sequence has high "systematic error" rate, that means all reads will have the error. Indeed, the Dante Labs product page doesn't even talk about returning SNP's/SNV's or variant interpretation reports, just CNV and SV. However, the way this is "normally" done is the assembly is polished using short read sequencing, with long reads used for structure. This could be potentially very bad PR for Dante Labs if people don't fully understand the product and think it's just "better sequence". But yeah, combining it with WGS would be best of both words, and honestly I'm not sure anybody knows the real accuracy of the latest flowcell chemistry + analysis software, they've been improving by leaps and bounds.

    Unfortunately I've not yet got any reply (or confirmation of receipt) to my questions about it to Dante Labs, although the questions were highly technical.

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  14. #18
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    Here's a quick update on the status of my order. I submitted the order on Monday morning April 8th (Rome time). Tuesday morning, the next day, Dante Labs emailed me the the tracking number for the shipment. This morning (Wednesday) the shipper's web site shows the package has been picked up and is in transit. So far so good, though obviously this is just the very beginning of a long process. Will update again when I actually receive the kit.
    YFull: YF14620 (Dante Labs 2018)

  15. #19
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    Quote Originally Posted by pmokeefe View Post
    Here's a quick update on the status of my order. I submitted the order on Monday morning April 8th (Rome time). Tuesday morning, the next day, Dante Labs emailed me the the tracking number for the shipment. This morning (Wednesday) the shipper's web site shows the package has been picked up and is in transit. So far so good, though obviously this is just the very beginning of a long process. Will update again when I actually receive the kit.
    Mine seems to be meandering around Germany at the moment, where was yours sent out from?
    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 ;-)
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  16. #20
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    Quote Originally Posted by MacUalraig View Post
    Mine seems to be meandering around Germany at the moment, where was yours sent out from?
    Likewise
    Date Time DPD parcel centre Parcel status
    10.04.2019 03:14 Aschaffenburg (D ... In transit. Preload.
    09.04.2019 17:02 DPD data centre Order information has been transmitted to DPD
    09.04.2019 15:40 Mittenwalde (DE) ... In transit.
    YFull: YF14620 (Dante Labs 2018)

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