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Dibran
05-12-2017, 03:20 PM
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?

RobertCasey
05-13-2017, 03:53 AM
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?

The YElite2.1 is a little less than WGS 30X but close to the same price. For one of our YElite2.1 tests, they switched it to the WGS 30X queue. Ordering more reads for WGS has a very questionable return. The only other option is way too expensive which is the WGS Long Read which is 20M base pairs vs. YElite2.1 at 13M base pairs - but $2,950 is obviously not as cost effective.

Once you order, you will still have to order 67 YSTR markers from FTDNA as well - in order to join projects and get your YElite2.1 test analyzed. If you turn out to be haplogroup R1b, upload your results to the Big Tree. FGC is quite slow, so you have to be patient. I ordered YElite1.0 around three years ago.

Dibran
05-17-2017, 04:02 AM
The YElite2.1 is a little less than WGS 30X but close to the same price. For one of our YElite2.1 tests, they switched it to the WGS 30X queue. Ordering more reads for WGS has a very questionable return. The only other option is way too expensive which is the WGS Long Read which is 20M base pairs vs. YElite2.1 at 13M base pairs - but $2,950 is obviously not as cost effective.


Once you order, you will still have to order 67 YSTR markers from FTDNA as well - in order to join projects and get your YElite2.1 test analyzed. If you turn out to be haplogroup R1b, upload your results to the Big Tree. FGC is quite slow, so you have to be patient. I ordered YElite1.0 around three years ago.

Why would I turn out to be R1b? Is it possible to be assigned to the wrong haplogroup?

I mean I have heard some cases where people were assigned a different haplogroup in different tests. I took my first test with 23andme and they said I was R-M417. Though as I understand it, it's impossible to be assigned the wrong haplogroup. Only the wrong subclade.

Couldn't I just post my FGC results on the forum instead of ordering another expensive test through ftdna?

Francisco
05-17-2017, 04:17 AM
Yep, is better to just get the FullGenome info and then go to GEDmatch (https://gedmatch.com) and Yfull (https://yfull.com), where for free and for only 49u$s you will get a perfect Haplogroup, race/origin clarification, STR reads, and also you can share info in "Haplogroups private project groups".
FTDNA has only the project groups as a positive thing, and only cause they where first and have more members, but the DNA analysis there is at most mediocre (67STR? give me a break) and costly (they want you to pay a little for some good for nothing test, then a littler more for something better, then more for something normal, then more for something good like Big Y and then more -for mithocondrial and autosomal that are not included, as are NOT included the STR in the Big Y test).
Is impossible to have a bad assignment of the Haplogroup with a Y Elite / WGS 30x. You will have more data than enough to make it correct, you will have even "new private markers" that no one has tested yet, and you will open a path for the others in your Haplogroup to refine it (and you will wait for those others to make a new deep test, Y Elite or Big Y, to confirm your private markers)

Dibran
05-17-2017, 04:22 AM
Yep, is better to just get the FullGenome info and then go to GEDmatch (https://gedmatch.com) and Yfull (https://yfull.com), where for free and for only 49u$s you will get a perfect Haplogroup, race/origin clarification, STR reads, and also you can share info in "Haplogroups private project groups".
FTDNA has only the project groups as a positive thing, and only cause they where first and have more members, but the DNA analysis there is at most mediocre (67STR? give me a break) and costly (they want you to pay a little for some good for nothing test, then a littler more for something better, then more for something normal, then more for something good like Big Y and then more -for mithocondrial and autosomal that are not included, as are NOT included the STR in the Big Y test).
Is impossible to have a bad assignment of the Haplogroup with a Y Elite / WGS 30x. You will have more data than enough to make it correct, you will have even "new private markers" that no one has tested yet, and you will open a path for the others in your Haplogroup to refine it (and you will wait for those others to make a new deep test, Y Elite or Big Y, to confirm your private markers)

Is it possible that my 23 result is wrong since they don't test everything? Or do I most definitely belong to R-M417.

I read here in the forums this guy was assigned to F by 23andme and H by Genio 2.0.

Dibran
05-17-2017, 04:25 AM
Cool. I didn't know FGC provides raw data for gedmatch. That's awesome.

RobertCasey
05-17-2017, 04:51 AM
Why would I turn out to be R1b? Is it possible to be assigned to the wrong haplogroup?

I mean I have heard some cases where people were assigned a different haplogroup in different tests. I took my first test with 23andme and they said I was R-M417. Though as I understand it, it's impossible to be assigned the wrong haplogroup. Only the wrong subclade.

Couldn't I just post my FGC results on the forum instead of ordering another expensive test through ftdna?

You did not post your R-M417 (R1a) status in your original post - so I was giving you broad generic advice that included possible R1b results. Sorry, I did not notice the R-M417 result under your name tag.

YSNPs by themselves are not not very good since they have one YSNP mutation per three generations - not exactly the granularity required for any kind of genealogical brick wall projects. Even though most of the 67 markers are already included in the YElite2.1 test, it will not be able to read five or six YSTRs included in FTDNA's 111 marker test due to a smaller read length of 250. Also, you are buying access to the FTDNA database which is critical since nobody is currently collecting the YSTRs inside of NGS tests to date.

GEDMATCH does not currently accept VCF files or BAM files from NGS tests, they only allow you to upload your terminal YSNP manually to date. YFULL is a better option for R1a since they are a Russian based company that covers R1a and haplogroup I the best (but does cost around $50). For R1b, the best source is BigTree (which is free).

For the 500 YSTRs reported in the NGS test - there is no quality control information on how to properly use these YSTRs that have no academic reviews. Some are probably unstable, mutation rates are extremely important and a public database is needed to track results. Once the NGS read length goes over 500 to 1,000, this should provide enough read length to determine all 111 markers in the FTDNA YSTR test. We only know the mutation rates of around 150 YSTRs from academic studies to date (and these have known issues).

MacUalraig
05-17-2017, 07:39 AM
Couldn't I just post my FGC results on the forum instead of ordering another expensive test through ftdna?

Any person leading a research project should help you irrespective of who you tested with IMHO. I tested at FGC and YSEQ but add FTDNA customers to my charts, wthout demanding they take further tests. If you are at YFull you are already able to do both SNP and STR matching. However in my experience through running a YFull haplogroup project most people aren't particularly interested in the rankings of the STR matches since the SNP matching exceeds it in accuracy/reliability. It's more of a curiousity these days. If you have a YFull kit number that is visible on their tree you can add it to your signature here.

lgmayka
05-17-2017, 08:29 AM
I read here in the forums this guy was assigned to F by 23andme and H by Genio 2.0.
That's because the haplogroup definitions changed slightly--the one European clade of F was moved to H-P96 (https://yfull.com/tree/H-P96/). 23andMe still uses the old haplogroup definitions.

Cofgene
05-17-2017, 09:59 AM
You did not post your R-M417 (R1a) status in your original post - so I was giving you broad generic advice that included possible R1b results. Sorry, I did not notice the R-M417 result under your name tag.

YSNPs by themselves are not not very good since they have one YSNP mutation per three generations - not exactly the granularity required for any kind of genealogical brick wall projects. Even though most of the 67 markers are already included in the YElite2.1 test, it will not be able to read five or six YSTRs included in FTDNA's 111 marker test due to a smaller read length of 250. Also, you are buying access to the FTDNA database which is critical since nobody is currently collecting the YSTRs inside of NGS tests to date.

GEDMATCH does not currently accept VCF files or BAM files from NGS tests, they only allow you to upload your terminal YSNP manually to date. YFULL is a better option for R1a since they are a Russian based company that covers R1a and haplogroup I the best (but does cost around $50). For R1b, the best source is BigTree (which is free).

For the 500 YSTRs reported in the NGS test - there is no quality control information on how to properly use these YSTRs that have no academic reviews. Some are probably unstable, mutation rates are extremely important and a public database is needed to track results. Once the NGS read length goes over 500 to 1,000, this should provide enough read length to determine all 111 markers in the FTDNA YSTR test. We only know the mutation rates of around 150 YSTRs from academic studies to date (and these have known issues).

WGS results at 20x+ coverage will provide a variant every 2 generations. I will agree with others that at this time it is best to go with a WGS result over and Elite 2.1 or BigY since that will provide you an entry point into looking at other genealogically useful changes (CNV's, microdeletions, ....) present on other chromosomes. Also if you have the extra money one could order a "long read" whole genome which would provide true next generation results and much more coverage of the y-chromosome.

Amerijoe
05-17-2017, 11:45 AM
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/bee44e70102cb6b417fbb8a3b2bf1dc1/
http://www.yfull.com/share/yreport/7bb3a9bfc7a37dd3d50cdd5ff405c75d/

Dibran
05-17-2017, 12:46 PM
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.

lgmayka
05-17-2017, 01:46 PM
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 (https://www.yseq.net/product_info.php?products_id=42468). But as far as I can tell, Full Genomes offers more for less.

AntG
05-17-2017, 01:47 PM
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.

Dibran
05-17-2017, 01:51 PM
Here's another option: 15x Whole Genome NGS from Yseq (https://www.yseq.net/product_info.php?products_id=42468). 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.

Dibran
05-17-2017, 01:52 PM
Y Elite is testing solely the Y chromosome.

So fgc 20x would test mtdna and ydna?

ArmandoR1b
05-17-2017, 02:45 PM
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 (https://isogg.org/tree/ISOGG_HapgrpR.html) 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 -



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




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.


That's because the haplogroup definitions changed slightly--the one European clade of F was moved to H-P96 (https://yfull.com/tree/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.


23andMe still uses the old haplogroup definitions.
Only for the people that are still in the old experience. As of Nov 15 2016 (https://blog.23andme.com/ancestry/updates-to-23andme-paternal-haplogroup-assignments/) 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.

RobertCasey
05-17-2017, 02:59 PM
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.

RobertCasey
05-17-2017, 03:26 PM
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.

FGC Corp
05-17-2017, 03:45 PM
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.

FGC Corp
05-17-2017, 05:33 PM
To me, the WGS 20X and YElite2.1 are pretty much a wash from a YCHR discovery perspective.

I agree. For SNP discovery Y Elite and the 20x WGS are equivalent.

Dibran
05-17-2017, 07:21 PM
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.

There are payment plans?!?! Could you send me information on how I would go about it? If I can do a payment plan for WGS 20x or yelite 2.1i would love to. Discounts wouldn't hurt either. Lol.

FGC Corp
05-17-2017, 07:59 PM
There are payment plans?!?! Could you send me information on how I would go about it? If I can do a payment plan for WGS 20x or yelite 2.1i would love to. Discounts wouldn't hurt either. Lol.

Yes, and you can address questions to:
sales [at] fullgenomes.com

Dibran
05-17-2017, 10:58 PM
Yes, and you can address questions to:
sales [at] fullgenomes.com

Thank you kindly!!

FGC Corp
05-18-2017, 12:15 AM
Thank you kindly!!

Question answered.

Francisco
05-18-2017, 12:50 AM
Man, Whole genome 20/30x is the best. You will get the raw data to also have health info: FGC will say that "they donīt endorse any health information, nor provide it, nor give medical advise at all", but only because thatīs "the law" in USA and they must say it. You will have the raw genetical data and with it you can visit third party webs or use third party programs to known about your hereditary Health traits (of course, if you want that).
A Big Y/Y elite is only for the genealogical matter. For a couple hundred bucks more you will get a genetical diagnosis ("but FGC will not endorse any health genetical data", you know)

sktibo
08-16-2017, 03:52 PM
Hi, I just want to ask a question here to clarify something I'm curious about:

Do they do autosomal full genome sequencing? if so what are the results transferable to?
I think this is a yes, but I just wanted to clarify. Thanks!

FGC Corp
08-18-2017, 12:16 AM
Hi, I just want to ask a question here to clarify something I'm curious about:

Do they do autosomal full genome sequencing? if so what are the results transferable to?
I think this is a yes, but I just wanted to clarify. Thanks!

Yes, we do. It is whole genome sequencing. Results can be transferred to Promethease, Gedmatch, or researchers/geneticists.

sktibo
08-19-2017, 09:43 PM
Yes, we do. It is whole genome sequencing. Results can be transferred to Promethease, Gedmatch, or researchers/geneticists.

Thank you. I'm starting to think about autosomal full genome sequencing as it is something I would very much like to have one day; although I'm not going to be able to do it anytime soon, seeing as I've tested with just about every major company available I think I will most likely get it done eventually. I'm curious about the differences between 2x, 15x, 20x, 30x, and Long Read. They all sequence your entire autosomal and X chromosomes as I understand it.. but there is still a difference in accuracy? About how long does it take to complete these tests also?
Sorry for the basic questions but I have just begun to look into whole genome sequencing, so I know next to nothing about it

FGC Corp
08-20-2017, 06:42 PM
Thank you. I'm starting to think about autosomal full genome sequencing as it is something I would very much like to have one day; although I'm not going to be able to do it anytime soon, seeing as I've tested with just about every major company available I think I will most likely get it done eventually. I'm curious about the differences between 2x, 15x, 20x, 30x, and Long Read. They all sequence your entire autosomal and X chromosomes as I understand it.. but there is still a difference in accuracy? About how long does it take to complete these tests also?
Sorry for the basic questions but I have just begun to look into whole genome sequencing, so I know next to nothing about it

We recommend 15x or better for ancestry testing. 30x or better is the standard for people who to use their results with third parties for health interpretation.

sktibo
08-20-2017, 08:41 PM
We recommend 15x or better for ancestry testing. 30x or better is the standard for people who to use their results with third parties for health interpretation.

I really appreciate you taking the time to inform me about your product via this message board, that is absolutely fantastic. Now I have my goal set for what I want and I know who to test with in the future, and what test to get. Thanks again!

pauleug
04-19-2019, 02:57 AM
Yes, interesting