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Thread: Full Y Chromosome Sequencing: Phase III Pilot

  1. #1481
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    R1b-FGC29071
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    U5a1b1g*

    Ireland England Netherlands Germany France
    The most recent numbers for callable loci on hg38 from chrY and chrY_KI270740v1_random are:
    Big Y - 8,573,969 (n: 376)
    Y Elite 1.0 - 12,703,898 (n: 28)
    Y Elite 2.0 - 13,503,380 (n: 7)

    For methodology I realign using the 1000 Genomes version of hg38 with BWA MEM and follow the GATK Best Practices guide. The samples are predominantly R-L21, but there are a few U106s and R1a's.

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  3. #1482
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    R1b U106 Z81

    Quote Originally Posted by JamesKane View Post
    The most recent numbers for callable loci on hg38 from chrY and chrY_KI270740v1_random are:
    Big Y - 8,573,969 (n: 376)
    Y Elite 1.0 - 12,703,898 (n: 28)
    Y Elite 2.0 - 13,503,380 (n: 7)

    For methodology I realign using the 1000 Genomes version of hg38 with BWA MEM and follow the GATK Best Practices guide. The samples are predominantly R-L21, but there are a few U106s and R1a's.
    I sent you a PM. I think we may be using slightly different settings. Vince T. also did an independent analysis using GATK but that was against hg37.
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  4. #1483
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    Quote Originally Posted by FGC Corp View Post
    I sent you a PM. I think we may be using slightly different settings. Vince T. also did an independent analysis using GATK but that was against hg37.
    In any case, we do find that using the hg38 yields more high quality SNPs than hg37.
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  5. #1484
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    Strategy update:

    We have two versions of 2.1:

    2.1a
    2.1b

    We use two different suppliers. This way we have a backup in case of supplier failure. We have two different designs, by two different companies, (each equivalent) in case the suppliers for the designs fail, and we switch to the other. Two different teams are available to do quality control and I have two different groups to handle kit shipping.

    I have briefed another team member on all aspects of our operations as well, in the event that I need a backup. Two different team members can now handle hg37 to hg38 conversions as well.

    Likewise, we have four options for high quality Y chromosome and ancestry data:
    Y Elite 2.1
    30x whole genome
    20x whole genome
    GenomeGuide

    Sample collection:
    1. Normal procedure: saliva samples
    2. We also accept blood samples (we have a lab to do QC now)
    3. We accept cheek scrub brush samples
    4. we accept samples from third party companies

    Customer feedback:
    Languages spoken by team members:
    English, French, Russian, Hebrew, Chinese, Arabic, and Spanish
    Last edited by FGC Corp; 03-21-2016 at 02:13 AM.
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  7. #1485
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    Quote Originally Posted by JamesKane View Post
    The most recent numbers for callable loci on hg38 from chrY and chrY_KI270740v1_random are:
    Big Y - 8,573,969 (n: 376)
    Y Elite 1.0 - 12,703,898 (n: 28)
    Y Elite 2.0 - 13,503,380 (n: 7)

    For methodology I realign using the 1000 Genomes version of hg38 with BWA MEM and follow the GATK Best Practices guide. The samples are predominantly R-L21, but there are a few U106s and R1a's.
    NOTE FOR ALL: I believe these numbers will be off by about 1,000,000 bases too few based on off-line discussion with FGC.

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  9. #1486
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    Results for Batch 9007 will be distributed this week.
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     bfcockburn (03-28-2016),  cairn (03-28-2016),  gotten (03-28-2016),  haleaton (03-29-2016),  JamesKane (03-28-2016),  MitchellSince1893 (03-28-2016),  morrisondna (03-31-2016)

  11. #1487
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    Thank you
    The Interpretation Results for Batch 9007 received, Waiting for Bam file.

  12. #1488
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    About, The Results for Batch 8001-8006.
    When you will be able to distribute it?
    Thank you for your efforts.

  13. #1489
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    R-DF27>FGC13557
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    H3-T152C!
    Y-DNA (M)
    R-U152>Y22447
    mtDNA (P)
    U5a2c4

    Netherlands Netherlands Limburg Germany Belgium Netherlands Noord-Brabant
    Quote Originally Posted by boaziz View Post
    About, The Results for Batch 8001-8006.
    When you will be able to distribute it?
    Thank you for your efforts.
    FGC now lists the expected delivery times on their Q&A: https://www.fullgenomes.com/qanda/
     
    Paternal Y-DNA: R-DF27>Z220>S21184>FGC13557>FGC43335, DYS487=Null, MDKA: Arnoldus Otten, d. 1721 Schinnen, NL (FTDNA: N126593)
    Paternal mtDNA: U5a2c4, MDKA: Maria de Baur, d 1761, Sittard, NL
    Paternal grandmother Y-DNA: R-U106>Z18>S17721+, MDKA: Adriaan Petri Brouwers, Oosterhout, NL
    Maternal Y-DNA: R-U152>Y22447+, MDKA: Göttgens, confirmed NPE (FGC: X5ZNK)
    Maternal mtDNA: H3-T152C!, MDKA: Helena Cuijpers, d. 1778 Spaubeek, NL
    Maternal grandmother Y-DNA: I-M253>Z74

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  15. #1490
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    Quote Originally Posted by boaziz View Post
    About, The Results for Batch 8001-8006.
    When you will be able to distribute it?
    Thank you for your efforts.
    We have a set of data (8002) that we are finishing now. Once we get those results, we will run 8001 and the others.
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