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Thread: Full Genomes Questions

  1. #11
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    Quote Originally Posted by Dibran View Post
    Hi all,

    So I plan on doing Full Genomes as my next test after I receive my LivingDNA results.

    I am quite the amateur at this sort of thing. Out of curiousity, which test should I order? Y Elite 2.1?

    Will it provide me with private/undiscovered SNPs? And fully tested SNPs?

    Or should I order the whole genome sequencing 30 times?
    Dibran, here for a comparison are the results as posted at Yfull for my BigY & Y-elite. The FGC results took almost a year to complete. FTDNA had my DNA sample and was able to post results in 16 days. Some people say the wait for FGC is worth it. If I had to do it over, I would eliminate the Y-elite and go with WGS. For now the BigY would have been enough for my purposes. Being in good standing with a FTDNA administrator would be beneficial for participating and posting to a project with outside results.

    http://www.yfull.com/share/yreport/b...bb8a3b2bf1dc1/
    http://www.yfull.com/share/yreport/7...cdd5ff405c75d/

  2. #12
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    I'm getting so many different opinions I really don't know where to start. As I understand yelite 2.1 practically covers the whole genome. Yet some are saying it's useless. But 30x or long read is a little less than economical to purchase.

  3. #13
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    Quote Originally Posted by Dibran View Post
    I'm getting so many different opinions I really don't know where to start.
    Here's another option: 15x Whole Genome NGS from Yseq. But as far as I can tell, Full Genomes offers more for less.
    Last edited by lgmayka; 05-17-2017 at 01:49 PM.

  4. #14
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    Quote Originally Posted by Dibran View Post
    I'm getting so many different opinions I really don't know where to start. As I understand yelite 2.1 practically covers the whole genome. Yet some are saying it's useless. But 30x or long read is a little less than economical to purchase.
    Y Elite is testing solely the Y chromosome.

  5. #15
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    Quote Originally Posted by lgmayka View Post
    Here's another option: 15x Whole Genome NGS from Yseq. But as far as I can tell, Full Genomes offers more for less.
    Thats a little too expensive. Especially since FGC includes the MtDNA line too.

  6. #16
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    Quote Originally Posted by AntG View Post
    Y Elite is testing solely the Y chromosome.
    So fgc 20x would test mtdna and ydna?

  7. #17
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    Quote Originally Posted by Dibran View Post
    Is it possible that my 23 result is wrong since they don't test everything? Or do I most definitely belong to R-M417.
    It is not possible that you are negative for Page7 which is the phylogenetic equivalent to M417 and is tested by 23andme. Both YFull and ISOGG have them as phylogenetic equivalents. 23andme tests enough SNPs that define R, R1, R1a, and R1a1a that your placement is unquestionable. The 23andme new experience uses just one of the phylogenetic equivalents for each subclade even if it is one of the SNPs that they don't test.

    Below is what they do test for R, R1, R1a, R1a1a, and R1a1a1. You can cross reference these with your results using the rsid at https://you.23andme.com/tools/data/ to find out if you are positive or negative for each SNP them paste the positive SNPs one at a time into https://www.yfull.com/search-snp-in-tree/ to see their placement -

    Code:
    SNP	# rsid	Mutation
    
    F82/M620	rs2078144	G->A
    CTS3229/M672/PF6036/YSC0001265	rs9786223	A->C
    CTS3622/PF6037	rs11799067	C->G
    CTS5815/M696	rs9785771	C->T
    P229/PF6019	rs9786915	G->C
    M207/Page37/UTY2	rs2032658	A->G
    P224/PF6050	rs17307398	C->T
    P285	rs17249974	C->A
    P227	rs4481791	G->C
    P280	rs891407	C->G
    P232	rs9786261	G->A
    L144/S175	rs9306842	A->T
    M306/PF6147/S1	rs1558843	C->A
    P294/PF6112	rs1005041	G->C
    P242/PF6113	rs7067478	G->A
    P238/PF6115	rs9785717	G->A
    P231	rs9786465	A->G
    M173/P241/Page29	rs2032624	A->C
    P225	rs17307070	G->T
    P286/PF6136	rs1118473	C->T
    P236	rs9785959	C->G
    P234	rs9786197	T->C
    P233	rs9786232	T->G
    L63/M511/PF6203	rs17307677	T->C
    M56	i3000072	A->T
    M157.1	i3000033	A->C
    M204	rs2032655	T->G
    M87	rs2032644	T->C
    P98	i4000236	C->T
    PK5	i4000244	C->T
    M515	rs17221601	T->A
    M514/PF6240	rs17315926	C->T
    M198/PF6238	i3000048	C->T
    M17	rs3908	4G->3G
    Page7	rs34297606	C->T
    Page68	rs34351054	C->T
    M458/PF6241	i5053615	A->G

    Quote Originally Posted by Dibran View Post
    I read here in the forums this guy was assigned to F by 23andme and H by Genio 2.0.
    That was because 23andme does not test for SNPs between F and H-M69 and they did not have enough confidence in the positive H-M69 result that they gave to some people so the stepped him back one tested SNP to haplogroup F. However both 23andme and Geno 2.0 showed him to be positive for H-M69 and YSEQ tested him positive for H-M370 which is a phylogenetic equivalent to H-M69.

    Quote Originally Posted by lgmayka View Post
    That's because the haplogroup definitions changed slightly--the one European clade of F was moved to H-P96.
    No, the 23andme mutation mapper already had M69 in haplogroup H and that person is positive for M69 and not just with 23andme but also with Geno 2.0. The person he is talking about was not positive for P69 which 23andme old experience has as haplogroup F3.

    Quote Originally Posted by lgmayka View Post
    23andMe still uses the old haplogroup definitions.
    Only for the people that are still in the old experience. As of Nov 15 2016 Everyone in the new experience is now just given the farthest downstream SNP out of the SNPs tested by 23andme and are considered by them to be an accurate result. It looks like Dibran is on the new experience due to his haplogroup placement.
    Last edited by ArmandoR1b; 05-17-2017 at 02:53 PM.

  8. #18
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    Quote Originally Posted by Dibran View Post
    I'm getting so many different opinions I really don't know where to start. As I understand yelite 2.1 practically covers the whole genome. Yet some are saying it's useless. But 30x or long read is a little less than economical to purchase.
    Here is a post from Full Genomes on the expected coverage of their tests:

    Average Callable Loci (Y chromosome)
    30x 14,558,001
    20x: 13,888,138
    15x: 13,241,107 (approx) <-- new data
    10x 8,046,540
    4x 1,050,996
    2x: 349,397

    Y Elite 2.1:
    14,000,000 (approx)


    This chart indicates that YElite 2.1 is somewhere between 20X and 30X WGS test. A more recent post states that the Long Read version is around 20,000,000 callable loci but remains at $2,950. To me, the 20 X test is probably the most cost effective WGS test as the costs pretty much track the number of reads. So going from 20X to 30X gives you 5 % more data but costs 50 % more. To me, the WGS 20X and YElite2.1 are pretty much a wash from a YCHR discovery perspective. The long read is much better test for sure but again, not very cost effective. The long read gives you 43 % more coverage but costs 381 % more.

    At least the choice between Big Y and YElite2.1 is much more of clear tradeoff: BigY is around 10,000,000 and YElite2.1 is around 14,000,000. So for 35 % more, you get 40 % more coverage. But in reality, YElite2.1 is not hitting the 14,000,000 mark and is closer to 13,800,000 to 13,900,000 since many of their calls are not producing YSNPs that are consistently reliable. Most have been seeing around a 35 % increase in good YSNPs of YElite2.1 over Big Y. So, upgrading from Big Y to YElite2.1 is very cost effective. You pay 35 % more but get 35 % more.

    Covering the whole genome is really not that important. This is primarily a YSNP discovery test. You do get the atDNA tests (value $80) but that is not very much. A bigger issue is that YElite2.1 also produces more YSTR calls since the read length is 250 vs. Big Y's 150. YElite2.1 only misses three or four of FTDNA's 111 markers but the Big Y misses ten to twelve markers of the 111 marker test. It is believed that 500 to 1,000 read length would catch all of FTDNA's 111 markers. There is no published data on how well the WGS tests do on YSTR calls.
    Last edited by RobertCasey; 05-17-2017 at 03:10 PM.

  9. #19
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    Quote Originally Posted by Dibran View Post
    So fgc 20x would test mtdna and ydna?
    mtDNA has almost no genealogical value but it is useful for the haplotree of womankind. The problem is that mtDNA is only 16,000 base pairs of content. YElite2.1 is 13,800,000 base pairs - which includes YSTRs. mtDNA is not really worth any discussion in my opinion. YElite2.1 no longer provides mtDNA in order to get the costs closer to Big Y. WGS does - you really do not need mtDNA for genealogical research.

    Again, you need to test 67 markers at FTDNA as well. If you do not, people will not know that you exist. All YDNA research is based on 67 markers first and then YSNP testing. Your WGS/NGS will be used by the YDNA community since this research is done by YFULL for R1a. But unless you pay $50 to get added to the YFULL database, people will not know that you have tested. Posting on forums is not how YSNP research is conducted. So, you still have to pay $50 to YFULL to get your YSNP results put into a public database and you have to order 67 YSTR markers from FTDNA (not 111) to get your YDNA analyzed for genealogical purposes. If these extra costs are an issue, order the Big Y, 67 markers and YFULL.

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  11. #20
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    Quote Originally Posted by RobertCasey View Post
    mtDNA has almost no genealogical value but it is useful for the haplotree of womankind. The problem is that mtDNA is only 16,000 base pairs of content. YElite2.1 is 13,800,000 base pairs - which includes YSTRs. mtDNA is not really worth any discussion in my opinion. YElite2.1 no longer provides mtDNA in order to get the costs closer to Big Y. WGS does - you really do not need mtDNA for genealogical research.
    We still provide the mtDNA data with Y Elite 2.1. Note that the coverage estimates I provided are a little conservative. We do a little better with both Y Elite and the 20x WGS in some instances.

    The other point here is that there are project discounts and payment plans available so there is room for further discounts in certain instances.

    Also, there's no added cost associated with the mtDNA. That is additional data that always comes with the capture. Cost-saving isn't the reason why mtDNA wouldn't be provided.
    Last edited by FGC Corp; 05-17-2017 at 04:11 PM.
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