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Thread: Dante Labs (WGS)

  1. #41
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    Quote Originally Posted by karwiso View Post
    In the beginning of the 10th week I received results of my WES analysis. I have got an email that reports are available for the test.
    I was able to download a VCF, which is aligned to GRCh37 and contains two files - one for SNPs and one for INDELS.
    Right now I am trying to use them with Promethease, and I have uploaded uncompressed VCF for SNPs to GEDmatch.com
    Wellness and longevity report report is very strange. It is some file from sequencing.com, but I see the information as not useful. It is produced by the Genome viewer App at sequencing.com and contains a lot of statistics about reads, aminoacids and so on. I have not seen any 100-pages report about my traits or disease risks and protections. It would be an complete abracadabra for a general average user. I haven't been able to find any direct useful health information there.
    I've contacted the customer service about alignment to GRCh37 and they have answered that FASTQ files are provided for customers and the files could be aligned to any genome reference. That is nice. I have not seen any FASTQ or BAM files for direct download from the page. I will wait with contacting the customer service for the files because I am waiting for my WGS and have more samples from my relatives. I want to see how WGS results are and which reports are provided then.
    If you are planning to test WES for possible disease risks, than you have probably to use some third party service or have a bio/medical-analyst to interpret your test results.
    After the contact with some genealogist I can say that WES is not recommended for genealogical purposes. I write more when I have got my WGS results.

    Well, the current price for WGS and WES is a hard competition compared to other services around or above 1000$, another good point is European market and very fast delivery with DHL. The customer service is friendly and responsive. They still need to improve their reports and FASTQ and BAM files should be available for download directly from the account, at least for a limited time, hm... 30 days after the completion and upon a later request. The Wellness and Longevity report is of an inferior quality so far and should be improved.

    PS Some part referred as Quality in Number of effects:
    Quality:

    Min 30
    Max 20,628
    Mean 2,159.85
    Median 1,092

    If it is about number of reads than it is superior I think.

    The report from Promethease was a lot more informative than Promethease based on the analysis of the data from AncestryDNA.
    Thank you Karwiso for your excellent update - Can I ask you why you get both WGS and WES tests?

    I am still waiting for my results for my WGS but it should not be long now. I am interested hearing how you get on with the WGS tests and in particular the usability for genealogical purposes.

    Best regards

    Johannes

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  3. #42
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    Quote Originally Posted by karwiso View Post
    After the contact with some genealogist I can say that WES is not recommended for genealogical purposes. I write more when I have got my WGS results.
    For those who haven't seen it, this is what gedmatch says about exome date:

    "About the close 'Exome' matches

    Are you puzzled by the new, very close, match you are seeing with somebody. Does it have "Exome" in the name? Even if it does not say "Exome", there are a few "Exome" kits on Genesis. Exome kits are different than the "genealogy" kits we are used to dealing with. The exome regions of the chromosome have much less difference from one individual to the next. Because of that, they appear as close matches to more people.

    We apologize for the "false match". We plan to provide some means of differentiating these "exome matches" from the real thing, but it will take a while to get it in place."

    So I'm not sure how much investigation of exome-exome comparisons has been carried out, contrasted with standard matching between the same people?
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019, Chronomics Jan 2020, Sano Genetics Feb 2020, Nebula Genomics June 2020)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A------ (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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  5. #43
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    Quote Originally Posted by karwiso View Post
    Wellness and longevity report report is very strange. It is some file from sequencing.com, but I see the information as not useful. It is produced by the Genome viewer App at sequencing.com and contains a lot of statistics about reads, aminoacids and so on. I have not seen any 100-pages report about my traits or disease risks and protections. It would be an complete abracadabra for a general average user. I haven't been able to find any direct useful health information there.
    Sounds like you are looking at or were given the wrong report. There is a sample on their site

    https://s3.amazonaws.com/dantelabswe...ugust+2017.pdf

    for the health report. What you are describing sounds like the genome overview report which is cool if you like data like I do but not particularly useful.

    https://s3.amazonaws.com/dantelabswe...ple+Report.zip
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019, Chronomics Jan 2020, Sano Genetics Feb 2020, Nebula Genomics June 2020)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A------ (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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  7. #44
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    Quote Originally Posted by jenssonjoi View Post
    Thank you Karwiso for your excellent update - Can I ask you why you get both WGS and WES tests?

    I am still waiting for my results for my WGS but it should not be long now. I am interested hearing how you get on with the WGS tests and in particular the usability for genealogical purposes.

    Best regards

    Johannes
    Hi! I ordered WES first because it was cheaper than WGS and because WES has more coverage (100x). Some of my relatives are interested in health risks and I have ordered both tests for them.
    WES could probably be used for genealogy. I have uploaded VCF to GEDmatch Genesis and now it has been analysed. I see overlaps from 16 000 to 62 000 with other kits, mostly FGC, Gencove, Genes for God, (imputed) VCFs from dna.land, much less are 23andme, FTDNA and Ancestry. I match myself 64 cM in total with Ancestry results and 104 cM in total with MyHeritage results, no match on me with Living DNA kit. So, if the genealogy is the goal, then any cheaper autosomal test will do better than WES.

    I expect my WGS in two weeks. I ordered it a bit later than WES. For most of my relatives I have ordered only WGS.

    Best regards.

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  9. #45
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    Some genealogically useful Y SNPs are inside genes anyway. M222, the world's most famous SNP*, is in the USP9Y gene.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019, Chronomics Jan 2020, Sano Genetics Feb 2020, Nebula Genomics June 2020)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  11. #46
    Quote Originally Posted by jenssonjoi View Post
    RBTISR

    Did you get your results back from Dante Labs?
    Nope. I've been bugging them about it and was just told "We are completing the quality control on your sample. You are expected to receive the result by the end of next week."
    The end of next week will be 16 weeks since they received the sample.

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  13. #47
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    Quote Originally Posted by MacUalraig View Post
    Some genealogically useful Y SNPs are inside genes anyway. M222, the world's most famous SNP*, is in the USP9Y gene.
    Is that the gene stated as.....slow sperm swimmers?

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  15. #48
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    Quote Originally Posted by vettor View Post
    Is that the gene stated as.....slow sperm swimmers?
    Well, it seems they were quite productive, nonetheless.
    Last edited by gotten; 11-15-2017 at 01:10 AM.

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  17. #49
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    Joking apart, yes USP9Y is involved in sperm creation but M222 is benign ;-)
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019, Chronomics Jan 2020, Sano Genetics Feb 2020, Nebula Genomics June 2020)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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  19. #50
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    Update about my WES:
    It was probably some glitch in Dante Labs systems or it probably takes some days to get results from Wellness and Longevity App. Today I was able to access my health report.
    The report is 160 pages, but most of them are explanations about how to read the report and references to research.
    Effectively the report is 11-12 pages. The content and the appearance corresponds to the sample reports provided by Dante Labs. I think the report is easy-readable, the risk overviews are easy to understand and it is nice to have life style recommendations in order to prevent some possible conditions. I find Promethease report to be more detailed, but it is of course not so easy to browse compared to Wellness and Longevity App interpretation. I think the report is better suited for an average user that could be bored or scared by scientific or medical terminology and details. It would be more fun to read such report if it would contain some factoids and phenotype traits - it would be an more entertaining for a general audience and could be a good selling point (like ethnicity estimates in genealogical testing).
    After this amendment I think that the product corresponds to my expectations, but the access to FASTQ and BAM files should be improved (as I said before - at least possibility to download them during some limited period).

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