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Thread: Dante Labs (WGS)

  1. #1201
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    U5a1b1g*

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    Quote Originally Posted by E_M81_I3A View Post
    Thanks, I have now received my results today, finally, after 11 months…. Do you know how I can now check the quality of the data ?
    Fastp: https://github.com/OpenGene/fastp - Tool to sample the read length, insert size, total bases, and quality of the reads in your FASTQ files.

    GATK: https://github.com/broadinstitute/gatk/releases - CollectWgsMetrics will yield the Mean and Median Coverage from the BAM as well as the depth percentages in buckets from 1x to 90x. The package includes a ton of other tools for assessing qualities and variant discovery.

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  3. #1202
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    Quote Originally Posted by E_M81_I3A View Post
    Thanks, I have now received my results today, finally, after 11 months…. Do you know how I can now check the quality of the data ?
    There are simpler tools
    1. WGSExtract (Software) http://37.187.22.93/wgsextract/WGSExtractBeta.zip
    2. https://bam.iobio.io/
    3. https://qual.iobio.io/

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     darethehair (03-30-2020),  E_M81_I3A (03-18-2020),  Jatt1 (03-19-2020)

  5. #1203
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    I3a1 (Steppe)

    France-Ile-de-France France Bouches-du-Rhône France Lyon France Dauphiné
    Quote Originally Posted by FreeAmin View Post
    Yes thanks, I have used qual.iobio.io already.
    Last edited by E_M81_I3A; 03-18-2020 at 02:09 PM.
    G25 scaled:Hidden Content Hidden Content Hidden Content
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    Y Dna: E-M81-->CTS12227-->BY8900 : The oldest M81 known are Guanches 2000 BP
    MtDna: I3a1 : The oldest I3a1 known is VK164, Viking from Oxford, UK, 880-1000 CE.


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  6. #1204
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    Y-DNA (P)
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    U7a3a5a
    Y-DNA (M)
    R1b-Z2109 > Y84821
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    M5a1a (185G)

    England United Kingdom India Punjab India
    Quote Originally Posted by E_M81_I3A View Post
    Thanks, I have now received my results today, finally, after 11 months…. Do you know how I can now check the quality of the data ?
    I would start with FQsum (https://workupload.com/file/Ctkj6RAw), as this determines whether or not you would be able to get a resequence from Dante Labs. They'll only resequence your sample if it's less than 90 GBases (all FASTQ files combined).
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-SK2142 > Y1383* - M5a1a (185G)
    * Maternal Uncle: R1b-Z2109 > Y84821 - U7a3a5a
    * MGMs MGF: R1a-Z93 > Y7 - ?

    Friends Haplos:
    * North Moroccan Berber: E-M35 > M81 - R0
    * Han Chinese: O-M117 > F1531 - M7e
    * Gujarati Lohana: T-M70 > Y11151 - R30b1

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  8. #1205
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    Suddenly I received e-mail:
    "The following reports have been generated for your kit

    Neurology Test
    Pharmacogenetics Report (en_us)
    Scientific Fitness Report (en_us)
    Wellness & Lifestyle Report (en_us)
    Nutrigenomics & Lifestyle Report (en_us)"

    I'm not certain what this related to. I have bought their neurology analysis & one month of subscription which I canceled when not a single report was actually updated in the past. So perhaps they've just finally got around to that, or alternatively this is related to the new reports (Fitness etc.) although I haven't seen an announcement they were going to be rolled out to everybody for free.

    Checking my profile it appears my old BGI-seq SNP only results have been re-processed, too, and INDEL and CNV files have become available. In addition the FASTQ and BAM files are downloadable, and insterestingly there's a "DNA Explorer" allowing viewing the BAM file, which should require quite a bit of resources from them. I'm in the process of downloading those to see if they've used new pipeline etc. of course the old BGI-seq was 100bp PE only, so the longer structures probably suffer a bit.

    There's a lot to unpack in all those files (Both literally and figuratively), first observation is "Neurology Test" no longer has clipped-off-page texts as the original report I had. I believe the original report just dumped Genetics Home Reference public domain text for any variant they found, but this new report seems to only contain description for a few of the variants found, and I'm not sure how those are chosen. It's possible the description is now written by Dante Labs, and includes references to literature on some. The rsID's have now been lifted as main identifier, while the HGVS molecular codes are listed only for the few variants with a detailed description. Also the new report has only PDF, without the huge spreadsheet table with different (old) sources for the variant information.

    The new pharmacogenetics report states "This report is NOT intended for US persons. This report was not submitted for approval to the US Food and Drug Administration (FDA)." whereas the original one I received stated something along the lines of it being fully compliant, which I commented at the time was surely not correct. (There has, however, been significant question as to whether just simply leaving any drug brand-names out of a report, leaving generic/effective ingredient wouldd be compliant, as at least at the time FDA quidance seemed to suggest that was the issue).

    Overall with the reports I'm seeing few disclaimers about mis-interpreting the results. One main thing I'd like to note is that for *most* variants (but not all), harmful effects come with two copies, and the reports do not really address this. Clinically this is very complicated though, as all DNA reading methods are more likely to make an error on the number of variants than on the absence/presence of a variant, some compound heterozygotes (variants occurring on different locations of both copies of the same gene) and complex heterozygotes (variants on different genes on the same biological pathway) count, as well as structural variants could affect other copy of the gene. There are also many cases where variant in just one copy has full or partial effect; as well as two carriers of a variant could pass the condition to their children. Therefore it's never safe to say "You have only one copy, so no need to worry", but with the current reports I think people generally get the impression they have some condition when they have just one copy detected.

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  10. #1206
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    BAM file (which I didn't have download link to but received on USB stick originally), INDEL and CNV files look to have been re-processed with DRAGEN, but interestingly SNP-file that was only one downloadable before appears not to have changed. (The original BAM etc. had A at the end of the kit number, the new BAM and INDEL/CNV have just the number). Which is bit of a shame, as I was looking forward to comparing variant calls from GATK and DRAGEN. At least I have the DRAGEN BAM to compare now. The Broad Institute blog-post on DRAGEN-GATK project seems to suggest that DRAGEN primarily improves INDEL/CNV calling, so basing the reports on the old SNP calls may not be bad idea.

    Again I'm not sure what triggered this as "Scientific Fitness Report", "Welness & Lifestyle Report" and "Nutrigenoics & Lifestyle Report" can be ordered separately, but I have not ordered them. I have ordered the monthly report update, AI report and personal report, none which I've received, so it's possible they're just getting around to that. On the other hand these reports are included in the newly ordered genome sequences. So maybe they're just being added to old kits for free? Haven't seen any other reports of this yet.

    You can download a sample of the standard reports, at least if you give your e-mail for marketing (The link to download is sent to your e-mail), so I'm not sure if it would be fruitful for me to review those reports further. Like everything in this world, they could still use some work, though at least customers can also use third party services like SNPedia/Promethease, Varsome, Genetics Home Reference, Google Scholar, OMIM etc. which I encourage to use in conjunction with any report. Also there's some fancy new tools I should keep track of but can never remember the URL, like there is a whole genome browser-side VCF viewer which allows you to filter for variants associated with given conditions, but I can't find it just now...

    There's consistent problem with over-promising in genetic analysis currently though, for example almost all of those intepretations are summarized as "People with your genetic profile are likely...". While they don't list references, many of these claims appear to be based on ridiculously small sample-sizes with selection bias and unknown environmental factors. ("Israeli elite endurance athletes" etc.), where the variant or variants in question are found to explain only small faction of the variance in the trait. Typically just a single variant is considered, while other variants not considered or discovered (to say nothing of environmental factors) could have larger effect. Admittedly, if every intepretation has to read, SNPedia-like, "This variant has been found associated with a small change in benefit from endurance training among some ethnicities and regions, assuming no other difference" or something like that would be lot less sexy and overall incomprehesible. I think on the long run only overall genetic literacy will help, and people rely on a lot more flaky sources for their fitness advice, for example. Many services have for example been trying to put "confidence" on each analysis alongside the effect size, and increasing larger studies will help to improve confidence.

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  12. #1207
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    Quote Originally Posted by karwiso View Post
    I am testing for genealogical pursposes, not medical. If we consider discounted prices, you get more bang for the buck with WGS compared to tests at FTDNA, Ancestry and so on. With WGS one gets exome, autosomal, mt-DNA and Y-chromosome. If we count all tests as FF, mtDNA-full, Y67/Y111 plus BigY, then WGS is the way to go. There is only question how we could use WGS for genealogy - the results could not be easily shared and compared yet.
    So, two years later from this reply, did you guys figure out if WGS is a solid option to get BigY, full-mtDNA and solid autosomal coverage for genealogical purposes?
    Recent ancestry: 2/4 Central Moldova (Orhei district), 1/4 Southern Moldova (Cahul district), 1/4 Northern Moldova (Briceni district)
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  13. #1208
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    Quote Originally Posted by Dorkymon View Post
    So, two years later from this reply, did you guys figure out if WGS is a solid option to get BigY, full-mtDNA and solid autosomal coverage for genealogical purposes?
    It seems to be so. Especially with Nebula if the results can be transferred to FTDNA. I haven't still heard any experiences with this option.

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  15. #1209
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    Quote Originally Posted by teepean47 View Post
    It seems to be so. Especially with Nebula if the results can be transferred to FTDNA. I haven't still heard any experiences with this option.
    Was anybody able to transfer Nabula WGS results to FTDNA so far?

  16. #1210
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    Indian - Punjabi Jatt
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    Y-DNA (P)
    R2-SK2142 > Y1383*
    mtDNA (M)
    U7a3a5a
    Y-DNA (M)
    R1b-Z2109 > Y84821
    mtDNA (P)
    M5a1a (185G)

    England United Kingdom India Punjab India
    Quote Originally Posted by Jatt1 View Post
    Was anybody able to transfer Nabula WGS results to FTDNA so far?
    FTDNA customer support mentioned to noman that they're planning on releasing more information regarding this at a later date (COVID-19 has probably delayed this).
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-SK2142 > Y1383* - M5a1a (185G)
    * Maternal Uncle: R1b-Z2109 > Y84821 - U7a3a5a
    * MGMs MGF: R1a-Z93 > Y7 - ?

    Friends Haplos:
    * North Moroccan Berber: E-M35 > M81 - R0
    * Han Chinese: O-M117 > F1531 - M7e
    * Gujarati Lohana: T-M70 > Y11151 - R30b1

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