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Thread: Full Y Chromosome Sequencing: Phase III Pilot

  1. #1341
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    U152>PF6658>FGC5029
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    T2c1d-T152C!

    United States of America Scotland
    This is great!

    I have 2-3 Y-Elite orders I am working on for our project

    Tim

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  3. #1342
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    R1b U106 Z81

    We now offer a 20x Whole Genome for $1,200.
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  5. #1343
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    We're going to do a pilot 15x WGS for $895. Depending on results, we may make this a standard offering.

    GenomeGuide (15x): $895

    https://www.fullgenomes.com/purchases/21/?

    Upgrade costs:

    10x -> 15x = $170
    4x -> 15x = $500
    2x -> 15x = $615

    For those who want to dig deeper into the challenges of NGS:

    http://www.nature.com/ejhg/journal/v...g2014279a.html

    Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects
    Last edited by FGC Corp; 01-02-2016 at 03:34 AM.
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  7. #1344
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    New blog post on FGC:

    http://nextbigfuture.com/2016/01/who...g-for-330.html

    Note:
    The headline is not correct. Our WGS-4x is $395, not $330.
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  9. #1345
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    Item:

    Paper on whole genome coverage and coverage depth:
    See Fig 1.

    10x coverage and above covers 90% and above of the whole genome.

    http://www.nature.com/articles/srep00055#f3
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  11. #1346
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    Quote Originally Posted by FGC Corp View Post
    Item:

    Paper on whole genome coverage and coverage depth:
    See Fig 1.

    10x coverage and above covers 90% and above of the whole genome.

    http://www.nature.com/articles/srep00055#f3
    Great, I plan to upgrade my reads this year.
    Last edited by MacUalraig; 01-03-2016 at 11:44 AM. Reason: its already next year
    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: A828783 (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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  13. #1347
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    Quote Originally Posted by FGC Corp View Post
    New blog post on FGC:

    http://nextbigfuture.com/2016/01/who...g-for-330.html

    Note:
    The headline is not correct. Our WGS-4x is $395, not $330.
    Having read it twice I think they added the interpretation fee to the 2x cost 280+50=330 ?
    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: A828783 (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

  14. #1348
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    South Tyrol, Alps, Central Europe

    Austria Tirol Italy Trentino Alto Adige Germany Bayern Italy Veneto Switzerland France
    Quote Originally Posted by FGC Corp View Post
    Paper on whole genome coverage and coverage depth:
    See Fig 1.
    srep00055-f1.jpg
    Very useful chart to show the relationship of read-depth and sequence-coverage.
    Such data & charts from current NGS used by FGC tests (Illumina HiSeq X platform?) based on comprehensive sample-sets and up to 30x would be very useful.
    Looking at this chart it seems 3x has a great advantage over 2x; if this happens also for current NGS maybe offering 3x (and 6x instead of 2/4x) would be interesting?

    EDIT: most of the early studies (before 2013) surely had to work with read lengths of 70 bp or less, now 100-150 bp are standard, even 250 bp available (Y-Elite 2). I did not saw this NGS parameter included in comparisons regarding mapping and variant calling qualities. I wonder how much read length influences coverage length and variant (especially STR) detection.
    Last edited by ChrisR; 01-04-2016 at 11:35 AM.
    Particularly interested in: DNA/Admixture from Central Europe (Alps, Tyrol, Dolomites); Y-DNA J2a-PF5169, J2a-L210, R1a-M17, R1b-U106; mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects in which I work:Hidden Content , Hidden Content , J2a-PF5197, ISOGG Wiki, GenWiki (german)

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  16. #1349
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    J1c1i

    Czech Republic Austria Austrian Empire Bohemia Carinthia
    srep00055-f1.jpg
    Interesting, it looks like:
    1x - at least 1x coverage 49 %
    2x - at least 2x coverage 28 %
    3x - at least 3x coverage 32 %
    4x - at least 4x coverage 22 %
    5x - at least 5x coverage 18 %
    6x - at least 6x coverage 14 %
    7x - at least 7x coverage 12 %
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

  17. #1350
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    GenomeGuide 15x update:
    $895

    You receive:
    whole genome data including Y chromosome WGS results, and full mtDNA coverage. Although we do not provide medical reports, we can refer customers to third parties or customers can use available third party tools, such as Promethease.

    As mentioned earlier, these are our beta results for 1x coverage:

    Mapped Y coverage
    30x 22,856,938
    10x 22,025,697
    4x 17,678,170
    2x 13,755,442

    Average Callable Loci
    30x 14,558,001
    10x 8,046,540
    4x 1,050,996
    2x 349,397

    Y Elite 2.0:
    14,000,000 Callable Loci approximately on average

    Essentially:

    The customer receives:

    1. whole genome (equivalent SNPs to other companies ancestry tests can be extracted for ancestry analysis)
    2. comprehensive Y (though with somewhat less coverage than Y Elite)
    3. full mtDNA, 1000x coverage or more

    Note that the read length in the whole genome data is 150bp.
    Last edited by FGC Corp; 01-04-2016 at 08:30 PM.
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