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Thread: YSEQ's new 15x WGS

  1. #11
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    How does the 15xWGS test compare with Fullgenome's GenomeGuide 15X test?
    Price wise, it's $899 vs $795 but I don't understand enough about the testing to say anything beyond that.

  2. #12
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    The main test is identical. Both are using Illumina X10 to perform the sequencing. The servicing labs are different but that should not impact things.

    The main difference is YSEQ is validating 10 of your singleton variants with Sanger sequencing. This is a convenient way to make them available for close STR matches to try. This can be more cost effective than a second NGS test. The drawback is many of this can turn up negative in the match. Some feel this is a wasted investment.

  3. #13
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    Quote Originally Posted by JamesKane View Post
    The main test is identical. Both are using Illumina X10 to perform the sequencing. The servicing labs are different but that should not impact things.

    The main difference is YSEQ is validating 10 of your singleton variants with Sanger sequencing. This is a convenient way to make them available for close STR matches to try. This can be more cost effective than a second NGS test. The drawback is many of this can turn up negative in the match. Some feel this is a wasted investment.
    The other item is that there are going to be useful variants that Sanger sequencing cannot be used for. One may get 10 potential Sanger tests but those may not be useful for your close STR matches. You will still need to get BigY or WGS results to work on the variants from regions not accessible to Sanger.

  4. #14
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    Post WGS Product Change Details for 2018...

    Quote Originally Posted by RobertCasey View Post
    Of course, all these NGS/WGS tests will be replaced in 12 to 18 months when WGS tests have much longer read lengths (think 500) with 50X to 100X coverage. These new WGS test will easily read all 111 YSTR markers, be near the limits of what can be read on the YCHR and would include the atDNA data. So this test will be around $500 to $750 which will include 111 YSTRs (plus 300 more YSTRs), a far superior Big Y (35 % more) and a better atDNA test (not sure how much larger atDNA tests would help vs. IT costs to analyze). However, with no databases for these tests, their future is remains problematic. I am super surprised that you and others have done such a good job of feeding files into the Big Tree which is a database of sorts. Expanding Alex's Big Tree scope from R-P312 to all of the genome is a big step though as they leadership beyond P312 is more distributed in nature. Also, Alex's charts are missing branches discovered by missing VCF files not shared, has most of the FGC files though, missing all the individual YSNP testing from YSEQ and will be missing all the private YSNPs being included in FTDNA SNP packs. But we are getting slowly getting there. The tests are moving faster than the quality of the tools and databases though.
    Robert et al- Assuming IT assets manage to close some of these gaps in the next year or two, which in a cloud-IoT driven world they will be trying hard as an industry at least from a capacity and power standpoint to do, your projection of a major WGS quality results crossover point being reached sometime in 2018 leads to me to ask two questions:

    1.) Seems like someone patient who does not currently have high resolution Y results would be well advised to wait till next year before dropping $700+ in any of the products on the market in 2017. More or less true?

    2.) Can you describe for an WGS labwork newbie who is technology terminology proficient, what specific underlying technology in WGS testing do you expect to see hitting the market in 2018 which will bring "much longer read lengths (think 500) with 50X to 100X coverage"...I am guessing it is a new generation of silicon from one or more specific vendors?

    Thanks for any insight you or others in this space can offer...

  5. #15
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    There are several changes in the wings:

    1) The Whole Genome Sequencing (WGS) testing will come down faster than Next Generation Sequencing (NGS) testing for two reasons: a) NGS testing requires YDNA enrichment (filters out YDNA from atDNA); b) WGS is far more main stream in medical industry - so this technology go down faster due to medical testing using this technology in large quantities.

    2) The future increase read length of the WGS/NGS will probably increase in the near future. Big Y is 150 base pairs and Elite2.1 is 250 base pairs. Longer read lengths not only reveals more YSNPs but also increases the capability to read more YSTRs. At 1,000 base pairs, I think that would be enough to read all 111 markers of the FTDNA test as well as revealing few more longer YSTR structures as well. With all 67 markers being read (or 111 markers), you would no longer need to take a redundant YSTR test at FTDNA. This would reduce the perceived costs of WGS/NGS tests by $269 (67) or $359 (111) plus give us another 300 or so new YSTRs to investigate. With the Big Y going on sale for only $395 over the next week, these savings could bring down the cost of WGS/NGS. However, we would have to manually track these YSTRs - but we already have to manually track the YSNPs from Big Ys already. There is a 1,000,000 read length available today for $2,950 (that will only catch a few orders at that price). Remember the WGS was $10,000,000 only ten or so years ago. Help desk and IT support is probably already around 50 % of the costs these days, so testing costs is not the only issue.

    3) Waiting for technology to come down just does not make sense. Do you wait for new PCs to drop in prices - no you should purchase what you need when you need it. You can also wait for others to compile your genealogy for you. You can either be proactive and drive innovation/discovery or take a more passive role and let others make the significant strides now vs. later. YDNA testing is not inexpensive - but neither are Ancestry.com subscription fees for genealogical databases or your "family history" trips where travel expenses can add up. If you want to save your funds - wait for sales like tomorrow when the Big Y is reduced to $395 from the regular $575 price tag.

  6. The Following User Says Thank You to RobertCasey For This Useful Post:

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  7. #16
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    You can choose 15x, 30x, or 50x on the WGS on YSEQ currently. The cost goes up of course.

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    Excellent product but (for the wgs) without adequate interpretation and databases its useless. But considering you get FF, mtdna and bigY data for this price,it is a bargain.
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  9. #18
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    Quote Originally Posted by Afshar View Post
    Excellent product but (for the wgs) without adequate interpretation and databases its useless. But considering you get FF, mtdna and bigY data for this price,it is a bargain.
    It is better than that in terms of Y sequencing coverage as it captures the regions FGC sequence but BigY doesn't.
    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) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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    FBIMatch: A828783 (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

  10. #19
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    My FGC WGS 15x shows the statistic at YFull (Y chromosome):
    Length coverage: 22547120 bp (87.89%)
    Mean depth coverage: 13.08X
    Median depth coverage: 6X

    I don't have detail statistics, but it looks like this mean about 50 % coverage with depth 4 - 5 or better. For less than 4 reads there are too many error.

    In comparison with typical Big Y

    Length coverage: 14043329 bp (54.74%)
    Mean depth coverage: 61.07X
    Median depth coverage: 35X

    It looks like the reliable coverage is almost the same.

    Elite 1.0 is much better:

    Length coverage: 22959696 bp (89.50%)
    Mean depth coverage: 76.85X
    Median depth coverage: 37X
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

  11. The Following 2 Users Say Thank You to Petr For This Useful Post:

     Oleg (Rus) (11-25-2017),  Robert McBride (10-27-2017)

  12. #20
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    Quote Originally Posted by Petr View Post
    My FGC WGS 15x shows the statistic at YFull (Y chromosome):
    Length coverage: 22547120 bp (87.89%)
    Mean depth coverage: 13.08X
    Median depth coverage: 6X

    I don't have detail statistics, but it looks like this mean about 50 % coverage with depth 4 - 5 or better. For less than 4 reads there are too many error.

    In comparison with typical Big Y

    Length coverage: 14043329 bp (54.74%)
    Mean depth coverage: 61.07X
    Median depth coverage: 35X

    It looks like the reliable coverage is almost the same.

    Elite 1.0 is much better:

    Length coverage: 22959696 bp (89.50%)
    Mean depth coverage: 76.85X
    Median depth coverage: 37X
    Thanks for posting the stats. It does depend though on whether you are making a general comparison or whether you have a particular interest/need in the extended areas. And whether you are mostly looking for new variants (particularly in a previously unexplored group) or mainly comparing with a previous sample.
    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) - further WGS tests pending ;-)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
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    FBIMatch: A828783 (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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