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Thread: YSEQ's new 15x WGS

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    YSEQ's new 15x WGS

    This seems like a well made all-around product with having more emphasize on Y-DNA but you'll receive complete mtDNA sequence, and autosomal file in 23andMe format.

    https://www.yseq.net/product_info.php?products_id=42468


    This WGS test is specifically designed for genealogy researchers and includes:
    • Full Mitochondrial Genome (Fasta file & haplogroup)
    • Annotation of all Y-SNP names and Y haplogroup information from Ybrowse.org
    • Separate VCF files for derived and novel Y-SNPs
    • User friendly autosomal allele files that can be immediately uploaded to genealogy tools like GedMatch
    • All raw data (FastQ, BAM, VCF etc.) supplied for free download or on SD card by mail
    • FREE Sanger sequencing confirmation of up to 10 novel Y-SNPs (for well prepared submission to the ISOGG tree)
    • Turn around time less than 3 months (after sample arrival)
    Last edited by MfA; 01-10-2017 at 10:03 AM.
    E-M84>FGC18389>FGC18413>FGC18401>FGC18422>Y99171 tMRCA 2550ybp

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    Yes it's an intriguing development and I wish Thomas well with it. As I understand it he was sort of working with FGC though, doing their DNA extraction??
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
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    It is a little disappointing that they chose 15X coverage - wish it was 30X or 50X (but that would push it to the $1,000 range which would turn off many). Also, does anyone know the read length ? Probably 150 which is another issue. Also, there is no mention if relevant list of YSNPs will be entered into their database as well as the YSTR values. Both FGC and YSEQ are really missing the advantage of a robust database to match the genetic data being provided. They need to partner with some IT people and charge for this service. Of course FTDNA does a minimal job of YSNPs for their database as well and fail to even analyze the YSTRs at all. I guess that you have to enter the market with one test to see the level of interest. Delivery time could be a real plus for YSEQ over FGC.

    Wish they would have stuck to their core business of YSNP testing and introduced Mass Array SNP packs with a lot more branches and private YSNPs (without all the equivalent YSNPs that have minimal value compared to private YSNPs). This would obviously boost the YSNP sales as well which are suffering due to their SNP panel test orders declining. They should also lighten up on testing YSNPs found in unstable areas but have consistent test results - another FTDNA advantage.

    Do not get me wrong, I regularly encourage YSEQ testing for the L226 and the Casey projects. Under L226, YSEQ has been discovering branches at 10 % of the cost of yet more Big Y tests. It is really hard to convince a lot of people to test with YSEQ or FGC though. All three FGC tests under L226 are for Casey men only to date.

    I am really surprised how much success that L226 has had with the L226 SNP pack that includes 50 private YSNPs. Not only has this test revealed another seven branches under L226, but my charting of L226 using signatures has increased from 50 % to 75 % and has been more useful than just a few more Big Y tests. The Mass Array is having some substantial reliability issues (more than expected) but it remains a super useful test. Also, FTDNA's insistence on posting private YSNPs in the L226 SNP as branches really is misleading and confusing which detracts from a fine test.
    Last edited by RobertCasey; 01-10-2017 at 04:35 PM.

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    I think it is actually a good move. They can learn a lot from it. I understand why they specifically offer it to Genealogical Researchers. A matching system would be nice but they are a small team.

    Hopefully this also shakes things up a bit with the bigger companies. Competition is healthy.

    Look forward to hear about the first results.
     
    Paternal Y-DNA: R-DF27>Z220>S21184>FGC13557+, DYS487=Null, MDKA: Arnoldus Otten, d. 1721 Schinnen, Netherlands (FTDNA: N126593)
    Paternal mtDNA: U5a2c4, MDKA: Maria de Baur, d 1761, Sittard, Netherlands
    Paternal grandmother Y-DNA: R-U106>Z18>S17721+, MDKA: Adriaan Petri Brouwers, Oosterhout, Netherlands
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    Quote Originally Posted by RobertCasey View Post
    It is a little disappointing that they chose 15X coverage - wish it was 30X or 50X (but that would push it to the $1,000 range which would turn off many). Also, does anyone know the read length ? Probably 150 which is another issue. Also, there is no mention if relevant list of YSNPs will be entered into their database as well as the YSTR values. Both FGC and YSEQ are really missing the advantage of a robust database to match the genetic data being provided. They need to partner with some IT people and charge for this service. Of course FTDNA does a minimal job of YSNPs for their database as well and fail to even analyze the YSTRs at all. I guess that you have to enter the market with one test to see the level of interest. Delivery time could be a real plus for YSEQ over FGC.

    Wish they would have stuck to their core business of YSNP testing and introduced Mass Array SNP packs with a lot more branches and private YSNPs (without all the equivalent YSNPs that have minimal value compared to private YSNPs). This would obviously boost the YSNP sales as well which are suffering due to their SNP panel test orders declining. They should also lighten up on testing YSNPs found in unstable areas but have consistent test results - another FTDNA advantage.

    Do not get me wrong, I regularly encourage YSEQ testing for the L226 and the Casey projects. Under L226, YSEQ has been discovering branches at 10 % of the cost of yet more Big Y tests. It is really hard to convince a lot of people to test with YSEQ or FGC though. All three FGC tests under L226 are for Casey men only to date.

    I am really surprised how much success that L226 has had with the L226 SNP pack that includes 50 private YSNPs. Not only has this test revealed another seven branches under L226, but my charting of L226 using signatures has increased from 50 % to 75 % and has been more useful than just a few more Big Y tests. The Mass Array is having some substantial reliability issues (more than expected) but it remains a super useful test. Also, FTDNA's insistence on posting private YSNPs in the L226 SNP as branches really is misleading and confusing which detracts from a fine test.
    Robert, do we have any assessments of confidence levels by read length. I was told 30x is questionable, particular given it is an average so many regions will be less than 30x. I haven't seen any good information on what the curve really looks like. Obviously there is a cost/times coverage curve but there is also a confidence/times coverage curve.

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    30x read depth is questionable for medical applications. For diagnosis of genetic conditions or personalized medicine a medical provider needs to be 99.999% or better sure the call is accurate. Much of this is because you are dealing with two copies of the autosomes. The reads are effectively split between them. With only 30x coverage thats only 15 reads per copy on average. This is why the current NCBI recommendation is 300x on the gene encoding regions.

    For genetic genealogy we only need 98% accuracy or so. This can be achieved with relatively small number of reads in areas like Poznik's Gold Regions. You want more reads for checking the consensus where the alignment algorithms like Burrow-Wheeler are challenged more. My comparison chart is already summarizing what can be accurately called with a few WGS read levels.

    15x coverage is actually performing surprisingly better than I thought for the Y chromosome. An average of 12 million loci have at least 4 reads with less than 10% chance of being incorrectly aligned for each. This compares with 9 million loci in a Big Y despite it averaging better than 55x read depth in the target regions. What the 15x WGS test doesn't give is assurances it is covering the same regions as Big Y. The two I've looked at have less than 6.5 million of the 8.5 million combBED bases covered.

    I'm working on generating histograms in an automated fashion to supplement the summaries, but keep getting distracted with other life priorities at the moment.
    Last edited by JamesKane; 01-13-2017 at 05:33 PM.

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    Quote Originally Posted by MacUalraig View Post
    Yes it's an intriguing development and I wish Thomas well with it. As I understand it he was sort of working with FGC though, doing their DNA extraction??
    Would this be any use to someone who has taken the Y Elite 2 test?

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    Quote Originally Posted by Eochaidh View Post
    Would this be any use to someone who has taken the Y Elite 2 test?
    If you are only interested in your Y DNA, there is no real benefit for a Y Elite tester to take a WGS. Your upgrade path will require something with 10k read lengths for anything appreciably better. The difference between Y Elite 2 and a 30x WGS is only 1 million callable bases in the best scenario and WGS doesn't have the same PCR stutter problems, which can make STR calls more accurate.

    If you haven't done autosomal testing, this is a very expensive 23andMe test you can put in Gedmatch until somebody builds a better mousetrap that does autosomal matching on WGS tests.

    I would consider this a pretty good deal for someone that hasn't done much testing on the sample donor though.

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    WGS wide autosomal matching will be the next big thing. I couldn't resist doing a WGS a couple of years ago, but as James says, doesn't really add anything to the Y you already did. Luckily one of the top autosomal experts who is looking at this is an autosomal match to me ;-)
    Last edited by MacUalraig; 01-14-2017 at 02:05 PM.
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    Quote Originally Posted by Mikewww View Post
    Robert, do we have any assessments of confidence levels by read length. I was told 30x is questionable, particular given it is an average so many regions will be less than 30x. I haven't seen any good information on what the curve really looks like. Obviously there is a cost/times coverage curve but there is also a confidence/times coverage curve.
    Here is quote on callable Loci based on various coverage from two to thirty that FGC stated:


    Average number of bases with at least 1x coverage: (on the Y chromosome)

    30x whole genome: 22,761,293
    10x whole genome: 22,025,697
    4x whole genome: 17,678,170
    2x whole genome: 13,755,442

    Callable Loci:
    30x whole genome: 14,644,185
    10x whole genome: 8,046,540
    4x whole genome: 1,050,996
    2x whole genome: 394,718

    Y Elite 1.0 by comparison:
    Average number of bases with at least 1x coverage: (on the Y chromosome):
    22,772,412

    Callable Loci: 14,000,000

    I would ignore all the 1X numbers and concentrate on callable Loci which is FGC's criteria for calling a YSNP.

    Here is another analysis of a 15X coverage:

    GenomeGuide 15x update:
    13.2 mb Callable Loci
    1000x+ mtDNA coverage
    98.7% autosomal SNP coverage (3.5 million SNPs+)


    Big Y is around 9,000,000 callable Loci, so the 15 X test would call a lot more than Big Y - but the calls would be very different parts of the Y chromosome. At 30X, it would be a clear winner. There is one big pro of this test over the Big Y: it would read areas that Big Y does not cover. There is one big con of this approach, it will be missing many of the Big Y reads. Probably having 30 % beyond Big Y and missing 15 % of Big Y. This has value in itself - like the old Walk the Y when they changed the area being scanned, there was a large jump of YSNPs being discovered.

    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.
    Last edited by RobertCasey; 01-14-2017 at 04:35 PM.

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