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brygian
07-28-2014, 08:52 PM
Full Genomes Corporation has launched a new product - Y Prime, at $599. I read somewhere it has 90% the coverage of their full test which now costs $999. Does anybody have more detail on Y Prime and how it compares to the full test and to Big Y?

MfA
07-28-2014, 09:25 PM
Great blogpost about new Y Prime

http://cruwys.blogspot.co.uk/2014/07/full-genomes-launches-y-prime-new-y.html

brygian
07-28-2014, 10:06 PM
This test directly challenges Big Y. Hopefully the competition will drive prices down. I will order from the first who offers a price under $400 :)

brygian
07-28-2014, 10:30 PM
Great blogpost about new Y Prime

http://cruwys.blogspot.co.uk/2014/07/full-genomes-launches-y-prime-new-y.html


Testing will be performed by a U.S.-based sequencing facility.

Anybody knows which that facility is?

George Chandler
07-28-2014, 11:47 PM
This test directly challenges Big Y. Hopefully the competition will drive prices down. I will order from the first who offers a price under $400 :)

One thing to remember that you are getting a lot more coverage with Y Prime than Big Y. So even if the two products are priced similar you are getting more coverage with the Y Prime test. When comparing the my Full Y (elite) results with the Y Prime of another Chandler I tested it covered all of my Sanger verified SNP's. Of the 54 high quality raw SNP's located below DF13 in my Full Y results only 4 were negative in the other Chandler with two being Sanger verified (as I previously stated) and two which didn't pass Sanger verification. I'm not sure if the two which didn't pass Sanger testing were covered but even if they weren't that's pretty awesome.

One of the frustrations that people are having when trying to figure out the SNP lines are figuring out which SNP's aren't being covered by the Big Y test then having to go and test for them individually.

George

lgmayka
07-28-2014, 11:49 PM
Hopefully the competition will drive prices down.
It already has. FTDNA just announced a permanent price reduction on the Big Y, down to $595 (the price during the recent discount sale). Moreover, any leftover $100-off coupons are still valid.

A choice of vendors and products is certainly good for the consumer, and good for the industry in the longer term.

leonardo
07-29-2014, 12:12 AM
It already has. FTDNA just announced a permanent price reduction on the Big Y, down to $595 (the price during the recent discount sale). Moreover, any leftover $100-off coupons are still valid.

A choice of vendors and products is certainly good for the consumer, and good for the industry in the longer term.

"Do I hear $550, who wants to offer $550?!" The more reasonable the price, the more results we get. Competition is grand.

leonardo
07-29-2014, 12:19 AM
One thing to remember that you are getting a lot more coverage with Y Prime than Big Y. So even if the two products are priced similar you are getting more coverage with the Y Prime test. When comparing the my Full Y (elite) results with the Y Prime of another Chandler I tested it covered all of my Sanger verified SNP's. Of the 54 high quality raw SNP's located below DF13 in my Full Y results only 4 were negative in the other Chandler with two being Sanger verified (as I previously stated) and two which didn't pass Sanger verification. I'm not sure if the two which didn't pass Sanger testing were covered but even if they weren't that's pretty awesome.

One of the frustrations that people are having when trying to figure out the SNP lines are figuring out which SNP's aren't being covered by the Big Y test then having to go and test for them individually.

George
True. I was able to get the YFull analysis during the initial stages (i.e., for free) and that not only complemented but enhanced the Big Y results. Even at $49, it is well worth it. Is there a site where FGC and YFull share results, or a site where others can see the results from FGC, or are there experts who can access both, so the results can be inter-faced in the future?

Timothy
07-29-2014, 12:43 AM
Even for $100 less with a coupon, Big Y seems so obsolete now, compared to YPRIME!

morrisondna
07-29-2014, 01:48 AM
Even for $100 less with a coupon, Big Y seems so obsolete now, compared to YPRIME!

So, when comparing results to near matches who have already done Big Y, is YPRIME expected to cover the same regions as BigY plus more? Or would it better that a new participant order another Big Y just for compatibility reasons?

George Chandler
07-29-2014, 03:10 AM
"Do I hear $550, who wants to offer $550?!" The more reasonable the price, the more results we get. Competition is grand.

It is good to have competition but you have to ask yourself who has the better product? If you went to purchase a vehicle and the dealer won't drop the price..then another dealer shows up down the street offering a better price, warranty, better engine, more bells and whistles. Even if the first dealer drops their price you go with the better product. For me the better product is the Y Prime from FGC. There isn't anything wrong with Big Y testing but if I spend this kind of money I want the best cost benefit around.

George

lgmayka
07-29-2014, 03:43 AM
For me the better product is the Y Prime from FGC. There isn't anything wrong with Big Y testing but if I spend this kind of money I want the best cost benefit around.
To be fair, I must point out that FTDNA retains two perennial advantages, which in some cases may be conclusive:

1) FTDNA does not usually require a new DNA sample if the person has previously tested. In dealing with relatives and friends who were reluctant to "donate" even once, a second request strains social boundaries. And of course, if the "donor" is deceased...

2) FTDNA's Big Y results are at least somewhat integrated with those of their other DNA products.

George Chandler
07-29-2014, 03:50 AM
True. I was able to get the YFull analysis during the initial stages (i.e., for free) and that not only complemented but enhanced the Big Y results. Even at $49, it is well worth it. Is there a site where FGC and YFull share results, or a site where others can see the results from FGC, or are there experts who can access both, so the results can be inter-faced in the future?

Right now there are comparison spreadsheets which identify and name the SNP's comparing them with other kits. Everyone would like the nice webpage comparison but if you give me the choice of information and low price or higher cost for a fancy web page I will take the information and the lower price. If FGC is working on that then you would have to ask them directly. What is really good is that you can actually contact them and get a quick response to your questions. That's part of what I call the "warranty service". I know some people here have been very satisfied with the YFull webpage but I haven't felt the need myself to participate.

George

George Chandler
07-29-2014, 03:59 AM
To be fair, I must point out that FTDNA retains two perennial advantages, which in some cases may be conclusive:

1) FTDNA does not usually require a new DNA sample if the person has previously tested. In dealing with relatives and friends who were reluctant to "donate" even once, a second request strains social boundaries. And of course, if the "donor" is deceased...

2) FTDNA's Big Y results are at least somewhat integrated with those of their other DNA products.

I've seen some who have been required to provide a sample and other who haven't. It is integrated into the FTDNA personal page for sure.

My position isn't to say they are a bad company or that Big Y is a bad product but from what I've seen the Y Prime is just a better product. The 9919 group has been waiting and testing for SNP's below L21 for years and found nothing besides DF13. Spending money to test WTY and getting no results so when FGC comes along and offers a product like this for the price and answers my email questions promptly they have my business. I wish this FGC test was around a while ago because you get SNP's STR's and MtDNA all in one test. One thing that frustrates many is that the SNP was only recently updated and was really far out of date. Now to be fair I know that with new SNP's being discovered all the time it's hard to keep up but I think FTDNA IMHO has invested more time in STR's, Family Finder and MtDNA than SNP's.

George

lgmayka
07-29-2014, 09:59 AM
What is really good is that you can actually contact them and get a quick response to your questions. That's part of what I call the "warranty service".
That would definitely be an advantage. At FTDNA, we used to be able to ask highly technical questions of Thomas Krahn, and he would answer. No more.

lgmayka
07-29-2014, 10:01 AM
I wish this FGC test was around a while ago because you get SNP's STR's and MtDNA all in one test.
YFull provides this for Big Y BAM files. I encourage everyone to add YFull's $49 analysis to the effective price of the Big Y.

George Chandler
07-29-2014, 02:53 PM
That would definitely be an advantage. At FTDNA, we used to be able to ask highly technical questions of Thomas Krahn, and he would answer. No more.

I remember those days when you could send an email regarding a technical problem or STR question and get a reply within a couple of days. Now you get a ticket number and with any luck you might get a reply with a month. Customer service needs to grow with a company and unfortunately they lost that.

I found that FGC provided a very get analysis service for the Big Y results as well for one of our kits which is always another option.

brygian
07-29-2014, 03:04 PM
Today I asked FGC whether Y Prime and Y Elite cover the so far known SNPs under CTS9219 (http://www.anthrogenica.com/showthread.php?1096-From-R-L150-to-R-CTS7822&p=45133&viewfull=1#post45133) and this is their reply:


I expect that all of these should be covered by the Y Elite test.
There may be a handful not covered by the Y Prime test. I just checked our coverage estimates based on our pilot results for one of the samples (Sample 1 here: http://goo.gl/pcq6FE ) and all 18 of the sites in the first branch of your diagram (7065166 through 23098285) were considered callable. Granted, there could be some variation from sample-to-sample.

Muircheartaigh
07-29-2014, 03:10 PM
YFull provides this for Big Y BAM files. I encourage everyone to add YFull's $49 analysis to the effective price of the Big Y.

You get a more comprehensive analysis of your Big Y results from FGC than you do from Yfull for the same price. They provide multiple files including comparisons with a dynamic database of more than 1500 people and a separate comparison with your closest matches in their system. The results are more or less chronological so you can see SNPs above or below your known terminal SNP. The analysis is in Excel which allows you to copy/paste the results to other spreadsheet, and filter sort etc.

It's hard to understand why FTDNA don't provide a comparable analysis. Perhaps the FGC Prime Y will make them wake up.

FGC Corp
07-29-2014, 08:17 PM
It already has. FTDNA just announced a permanent price reduction on the Big Y, down to $595 (the price during the recent discount sale). Moreover, any leftover $100-off coupons are still valid.

A choice of vendors and products is certainly good for the consumer, and good for the industry in the longer term.

Our price for the Y Prime is now $589.

leonardo
07-29-2014, 11:17 PM
It is good to have competition but you have to ask yourself who has the better product? If you went to purchase a vehicle and the dealer won't drop the price..then another dealer shows up down the street offering a better price, warranty, better engine, more bells and whistles. Even if the first dealer drops their price you go with the better product. For me the better product is the Y Prime from FGC. There isn't anything wrong with Big Y testing but if I spend this kind of money I want the best cost benefit around.

George
Still, there may be some who will make there decision based upon, say $100 (if they have the coupon, for example). I know I had a hard justifying the expense, and I was in the initial batch for $495. Fortunately there was another within my subclade who tested with FGC and submitted his results to YFull. So, in the end, the more who test the better, especially if the FTDNA participants submit theirs for further analysis.

FGC Corp
07-30-2014, 12:08 AM
You get a more comprehensive analysis of your Big Y results from FGC than you do from Yfull for the same price. They provide multiple files including comparisons with a dynamic database of more than 1500 people and a separate comparison with your closest matches in their system. The results are more or less chronological so you can see SNPs above or below your known terminal SNP. The analysis is in Excel which allows you to copy/paste the results to other spreadsheet, and filter sort etc.

It's hard to understand why FTDNA don't provide a comparable analysis. Perhaps the FGC Prime Y will make them wake up.

We have had three priorities from the beginning:

1. The best Y chromosome data currently achievable
2. The most comprehensive Y chromosome analyses feasible, given our size
3. The most affordable Y chromosome product of its type that is achievable

Those provide the best information that we can deliver, in our estimation. Our website will be upgraded in time.

Dr_McNinja
08-21-2014, 10:06 PM
Does Yfull take FGC results or only FTDNA Big Y?

lgmayka
08-21-2014, 11:38 PM
Does Yfull take FGC results or only FTDNA Big Y?
YFull's order form (http://yfull.com/order/) makes clear that they do accept FullGenomes BAM files.

haleaton
08-22-2014, 04:25 AM
YFull's order form (http://yfull.com/order/) makes clear that they do accept FullGenomes BAM files.

They analyzed my Full Genomes BGI BAM file. However several months ago they did have a software issue which precluded analyzing another BAM file from the same person in that case my Big Y BAM--but it had nothing to do with the type of file. They may have corrected this. They really are excellent programmers in addition to DNA analysis.

GailT
08-22-2014, 01:41 PM
So, when comparing results to near matches who have already done Big Y, is YPRIME expected to cover the same regions as BigY plus more? Or would it better that a new participant order another Big Y just for compatibility reasons?

I tested both FGC FullY and FTDNA BigY. FullY identified 50 high reliability SNPs compared to 25 in BigY, so BigY had 50% of the coverage compared to FullY.

Full Y identified 24 of the BiGY SNPs as high reliability and 1 as medium reliability. If YPrime has 90% of the coverage of BigY, it should identify 45 high reliability SNPs compared to 25 in BigY in my case, so I would expect YPrime to identify almost all of the BiGY SNPs.

I don't see the FTDNA webtools as a benefit at this point because they are not accurate or precise in identifying close matches. Perhaps they will get there in the future, but I wish FTDNA would hire FGC and Thomas to do their data analysis. At present, you should plan on having FGC or YFull analyse all of your BiGY BAM files, unless you have the expertise to do that analysis yourself.

Emmerson
08-22-2014, 02:29 PM
I tested both FGC FullY and FTDNA BigY. FullY identified 50 high reliability SNPs compared to 25 in BigY, so BigY had 50% of the coverage compared to FullY.


Gail,

Since you are a Goddess (http://en.wikipedia.org/wiki/Goddess) of human mtDNA, why didn't you use the FGC BAM file or YFull to look at the full mtDNA and compare it to your full mtDNA results from FTDNA?

It can be done and the mtDNA analysis is a free extra from FGC. YFULL also provides this NGS analysis service. FTDNA does not provide a NGS mtDNA analysis service as they continue to milk customers for their standalone $199 full mtDNA test (https://www.familytreedna.com/mt-dna-compare.aspx?).

The ISOGG page for FGC says "Approx. 99% coverage of the mtDNA sequence" (http://www.isogg.org/wiki/Full_Genomes_Corporation) Actually it is more like 99.999% coverage.

Ian Logan, Ann Turner and other Senior Genetic Genealogists are familiar with using a BAM file to do this .... and thought you would like to also.

Persons such as Roberta Estes (a biased person as she is a contractor for FTDNA) badmouths using a FTDNA or FGC BAM file to do a full mtDNA analysis. Wonder why ... perhaps FTDNA is afraid of losing their lucrative full mtDNA profit margins.

Estes and Mittelman at FTDNA say BAM mtDNA analysis is only trivial "incidental findings" (http://dna-explained.com/2014/04/01/mitochondrial-dna-results-from-the-big-y-test/) That's pure hogwash because others, including my own YFULL mtDNA analysis, found ALL mutations and correctly identified my Haplogroup just as my FTDNA full mtDNA analysis had 2 years previously when this FTDNA mtDNA test cost around $300.

I hope you will check all this out and report back your observations and findings about using NGS testing for mtDNA analysis.

Emmerson

GailT
08-22-2014, 03:44 PM
I can only report mtDNA results for my FGC and BigY kits, so I can't evaluate how reliable they are for mtDNA in general.

FGC analyzed my mtDNA results for both the FullY and BigY, and they both correctly identified me as U5a2a1 and both also identified my 2 extra unique coding region mutations at markers 3196 and 6434. However, FullY did not report the base at two markers - instead they reported a double question mark instead of a single question mark, so it seems they correctly flagged these two markers as potentially different from the RSRS but were not confident in assigning a base at those markers. BigY results were reported relative to the Yoruba reference so I had to convert to rCRS and RSRS. The BigY mtDNA results did not report my U5 mutations at markers 16192 and 16294.

So I would say that neither was 100% reliable, and if you want absolute confidence, you should test the full sequence at FTDNA. Also, FTDNA has an excellent database and good matching algorithm for mtDNA.

If you are not interested in looking for matches, and you simply want a very good estimate of your haplogroup and subclade, then FGC or BigY is probably good enough. Of course, this is based on a sample size of one, so I don't know how often they might miss important mutations.

Emmerson
08-22-2014, 04:30 PM
I can only report mtDNA results for my FGC and BigY kits, so I can't evaluate how reliable they are for mtDNA in general. So I would say that neither was 100% reliable, and if you want absolute confidence, you should test the full sequence at FTDNA. Also, FTDNA has an excellent database and good matching algorithm for mtDNA.


Gail,

There are "others", such as Mark Jost (http://archiver.rootsweb.ancestry.com/th/read/genealogy-dna/2014-06/1403530283), who have used their FGC BAM files, to get on genbank (https://m.google.com/app/basic/stream/z13adnphrnblfpaju04cexug3qa2up4gg1w?cbp=fkgx6o2j30 no&partnerid=operamini1104&sview=27&cid=5&soc-app=115&soc-platform=1&spath=/app/basic/%2BY-strOrg/posts&sparm=cbp%3Dgxkat4gqv5uv%26partnerid%3Doperamini11 04%26sview%3D27%26cid%3D5%26soc-app%3D115%26soc-platform%3D1%26spath%3D/app/basic/%252BFelixChandrakumar/posts%26sparm%3Dcbp%253D1kmupxu9k9qwb%2526partneri d%253Doperamini1104%2526sview%253D27%2526cid%253D5 %2526soc-app%253D115%2526soc-platform%253D1%2526spath%253D/app/basic/%25252BFelixChandrakumar/posts%2526sparm%253Dcbp%25253D1lyb38u9lzb3i%252526 partnerid%25253Doperamini1104%252526sview%25253D27 %252526cid%25253D5%252526soc-app%25253D115%252526soc-platform%25253D1%252526stct%25253DEgkIyPPrjNfGvAIo qIDSs4GvvQIwlI7O_r6vvQI4AUAC%252526spath%25253D/app/basic/s/%2525252523Software/related%252526sparm%25253Dcbp%2525253D1e453ul5rygo p%25252526partnerid%2525253Doperamini1104%25252526 sview%2525253D28%25252526sri%2525253D0%25252526spa th%2525253D/app/basic/s/%252525252523Download/related%25252526sparm%2525253Dcbp%252525253D5quq0x sxpy2i%2525252526partnerid%252525253Doperamini1104 %2525252526sview%252525253D28%2525252526sri%252525 253D0) ... so is that type of reliability good enough for you? ... I am sure it is for 99%+ of Senior Genetic Genealogists.

Remember, in regards to "looking" for mtDNA matches, FTDNA is not the only game in town.

You failed to mention that one can search for mtDNA matches for FREE on FTDNA. (https://www.familytreedna.com/public/u5b/default.aspx?section=mtresults) And, also on this FTDNA run site. (http://www.mtdnacommunity.org/)

One can search for mtDNA matches for FREE on genbank. (http://www.ianlogan.co.uk/mtDNA.htm)

One can search for mtDNA matches for FREE on mitosearch. (http://www.mitosearch.org/search_start.asp?uid=)

One can search for mtDNA matches for FREE on mitomap (https://www.mitomap.org/bin/view.pl/Main/SearchAllele).

Contrary to what you said, and with all due respect to you, I think that the proper analysis of a NGS BAM file from FTDNA or FGC via YFULL or others will not miss "any" mtDNA mutation.

Emmerson

lgmayka
08-22-2014, 05:32 PM
There are "others", such as Mark Jost, who have used theirFGC BAM files, to get on genbank ... so is that type of reliability good enough for you?
Genbank itself does not verify the lab quality of submissions. Ian Logan regularly posts news of Genbank mtDNA submissions, and he often comments on the mistakes and omissions he sees.

... I am sure it is for 99%+ of Senior Genetic Genealogists.
The mtDNA results from the Big Y generally have neither the accuracy nor the completeness necessary for genealogical purposes. They are, however, generally good enough for ancestry and anthropology.


You failed to mention that one can search for mtDNA matches for FREE on FTDNA. (https://www.familytreedna.com/public/u5b/default.aspx?section=mtresults)
Only those customers who choose to join that project are listed on its web page.


And, also on this FTDNA run site. (http://www.mtdnacommunity.org/)
I suspect that an even smaller percentage of FTDNA customers use that site.


One can search for mtDNA matches for FREE on genbank. (http://www.ianlogan.co.uk/mtDNA.htm)
Only a small fraction of FTDNA customers submit their sequences to Genbank.

One can search for mtDNA matches for FREE on mitosearch. (http://www.mitosearch.org/search_start.asp?uid=)
Or to mitosearch.

Etc.


Contrary to what you said, and with all due respect to you, I think that the proper analysis of a NGS BAM file from FTDNA or FGC via YFULL or others will not miss "any" mtDNA mutation.
Yes, it does--or at least, it certainly may. Here is the statistical summary that YFull provided for my BAM file with respect to mtDNA:

ChrM BAM file size: 365.87 Kb
Length coverage: 16512 bp (99.66%)
Min depth coverage: 1X
Max depth coverage: 2186X
Mean depth coverage: 42.97X
Median depth coverage: 21X
One reading position!: 43
No call: 57 bp

The last number is the most crucial. YFull was unable to call the result on 57 base pairs of the mtDNA sequence. FGC examined the same BAM file, and listed 65 '?' as well as 12 '??'.

I do not blame FTDNA, YFull, or FGC for this. Rather, I accept that mtDNA sequencing is not the primary purpose of the Big Y.

GailT
08-22-2014, 06:06 PM
Genbank itself does not verify the lab quality of submissions. Ian Logan regularly posts news of Genbank mtDNA submissions, and he often comments on the mistakes and omissions he sees.

For my primary interest (anthropology) I think the FullY and BigY mtDNA results are good enough for submission to GenBank, but perhaps not good enough for use in phylogenetic tree building, at least in some cases. There are several thousand sequences in GenBank that rely on lower coverage NGS and that sometimes have large numbers of no calls, or more rarely, obvious mistakes. The Schoenberg NGS samples, and the recent Li et al. and Raule et al. samples have lower quality results than FTDNA NGS, which has very high coverage. I will use all of these samples, unless they have a large number of no calls, but I'll discount results that seem to have missing mutations that should be present.



I do not blame FTDNA, YFull, or FGC for this. Rather, I accept that mtDNA sequencing is not the primary purpose of the Big Y.

Exactly, it's a bonus, and for most people it might be all they need or want. It is useful for confirming a suspected mtDNA common ancestor, and for many people, that might be all they can do with mtDNA. But there will be cases where more accurate testing will be useful. If you can give me GenBank accession numbers for other results, I can check to see if they also had missed calls.

Emmerson
08-22-2014, 09:54 PM
For my primary interest (anthropology) I think the FullY and BigY mtDNA results are good enough for submission to GenBank ...

Quote Originally Posted by lgmayka
I do not blame FTDNA, YFull, or FGC for this. Rather, I accept that mtDNA sequencing is not the primary purpose of the Big Y.

GailT: Exactly, it's a bonus, and for most people it might be all they need or want.

et alii (Male Commentor) & et aliae (Gail),

When I was 18, the primary purpose of my car was not the facilitation of my personal transportation needs. The primary purpose of the car at that age was to facilitate my personal lustful s*xu*l urges with a bevy of congenial females. The transportation angle was a mere bonus.

Now some 50 years later at 68, the primary purposes of my car are varied and they do include trips to Walgreens for my bonus booster of Cialis and antioxidants that really work on my telomeres. (http://www.ucsf.edu/news/2013/09/108886/lifestyle-changes-may-lengthen-telomeres-measure-cell-aging)

My red convertible has the vanity licence plate of "JOY" on it. I use it for joy rides. For some 50 years, my cars (http://i117.photobucket.com/albums/o59/krefly/wienermobile.jpg) have aided me in my secondary and infrequent procreation efforts and my primary and frequent pleasuring efforts.

So, I would bet the majority of those taking ancestral DNA tests would see a NGS test WITH mtDNA analysis and interpretation as an added value versus a secondary item or a bonus item as has been bantered about. Such a mtDNA analysis does have a $200 value. So, please don't try your trivializing comments on something of obvious value. That might work better in explaining a trivial 'toy surprise' in a box of Cracker Jacks. (http://en.wikipedia.org/wiki/Cracker_Jack#Toys)

Certainly, it appears that FTDNA does want the mtDNA analysis in their BIG Y test to remain a secret, otherwise they are giving up $199 in profits from their regular full mtDNA test. In regards to FGC, who could promote the mtDNA analysis as part of their Y Elite or Y Prime tests, they don't have the marketing moxie to do it. But if FGC did, it would have the FTDNA boys down in Houston pulling their hair out and they would see that FGC is a scrappy competitor.

Another commentator here focuses only on BIG Y with a range of mtDNA no call rates. I think if he looked at FGC he would find a 'zero' to "six" no call rate which would equate to 99.99% mtDNA coverage for their NGS test.

I think the proper thing to do is to get about 50+ FGC and FTDNA BIG Y customers to analyze their NGS mtDNA results and let the crowd decide. On addition, if we see consistent higher no call rates on mtDNA with FTDNA .... then FTDNA is obviously taking overt steps to do thus and tamp down the use of BIG Y for mtDNA analysis.

Emmerson

lgmayka
08-23-2014, 02:55 AM
I think the proper thing to do is to get about 50+ FGC and/or FTDNA BIG Y customers to analyze their NGS mtDNA results and let the crowd decide.
I surveyed all of the Big Y mtDNA statistics to which I have personal access. Here are their no-call counts, in base pairs:
879
228
0
297
57
7
0
197
51
5
2

As one can see, the no-call count varies widely. Some customers actually get a complete mtDNA scan (0 no-calls); others get a very incomplete result. (The no-call count of 879 was for my uncle.)

Ann Turner
08-23-2014, 02:13 PM
Like Larry, I've seen a range of mtDNA results, although I don't have exact numbers at hand. Some are good enough to submit to GenBank, which does accept next generation sequencing results with some "N" bases (the code for aNy base, or more accurately, not determined). Others shouldn't make the cut for GenBank but might still be sufficient to estimate a haplogroup. For genealogical purposes, there might be too many no-calls to use the standard matching rules for searching a database, but one could still gain benefit from seeing if two results are consistent or inconsistent with a common ancestor.

Emmerson
08-23-2014, 03:13 PM
In an earlier posting I made comments comparing NGS mtDNA coverage depth and completeness between the weaker FTDNA BIG Y mtDNA results versus the stronger FGC mtDNA results.

As with FGC's YDNA stronger completeness, there is also FGC's mtDNA stronger completeness in a $589 Comprehensive NGS Uniparental DNA test.

Here is some meat on the bone to support these claims and assertions.

With a FGC NGS test I had a strong 99.97% mtDNA completeness. There were No Calls on 5 bp and these bp are usually not phylogeny relevant. The FGC mtDNA results matched my earlier $300+ full mtDNA results from FTDNA on a non NGS test.

In addition to my strong FGC mtDNA completeness results, one should also consider mtDNA expert comments from Ian Logan on the quality of Mark Jost’s mtDNA data from FGC. Jost is one of the first citizen scientists to submit their NGS mtDNA results to GenBank.

Logan made these comments on Jost's results:
"First, let me go back to have a fresh look at Mark Jost's results
to work out just how good (or poor) they might be.

Typical H11a2a sequence
ANON: HQ843503 FTDNA H11a2a 09-JAN-2011
T195C A263G 315.1C A750G T961G A1438G A4769G T8448C A8860G G13759A
A14587G A15326G T16140C A16293G T16311C

JOST:
KJ831815(Dutch) FGC H11a2a 21-JUN-2014
T152C T195C A263G T310N C317N A523N C524N A750G T961G A1438G
A4769G T8448C A8860G C12014T G13759A A14587G A15326G T16092C T16140C
T16195N
A16293G T16311C (+ 16568N 16569N)

- So Jost has all the mutations expected of a typical H11a2a, together
with his 'private' mutation C12014T - that he already was aware of.
- FGC gives 7 N's so its base determination is 99.96% accurate
- The poly-C area 309-315 is not fully assigned
- The coding area mutations are 9 (FTDNA) against 10 (FGC)
- and there are a couple of HVR1 & 2 mutations that might be extra,
T195C & T16092C
However, apart from these minor points, the FGC sequencing is good.
And there are no serious 'extra' mutations, and the FGC sequence fits in
perfectly with the known phylogenetic tree."

Dr_McNinja
08-23-2014, 03:42 PM
I ordered a Y Prime test and I've also got my results from a mt Full Sequence FTDNA test on Genebank, I can have Ian see how well they match whenever that's done. Y Prime is supposed to have a quicker turnaround than the old FGC test I think.

Dr_McNinja
08-24-2014, 02:52 AM
They say 4 months for results, so I don't know if that's any better than the original test.

Timothy
09-03-2014, 04:28 AM
I don't understand the FGC Home page. They don't have a list of what they offer. Last month YPrime was offered for sale, this month it's not. Right now, only the Full Y at it's newly discounted price of $850 is offered. It's like YPrime doesn't even exist any more. Does it? They also don't "advertise" that they do 3rd party analysis. What else do they offer that they're not telling the buying public about?

VinceT
09-03-2014, 08:34 AM
They're running a shoe-string operation thanks to market dominance of FTDNA's BigY, and AFAIK haven't been able to contract technical expertise to update their web-site as consequence, and are now looking for a volunteer web guru.

Last I heard (July 29), the price for Y-Prime was reduced to $589 US, and can be ordered via the coupon code "YPRIME". Contact sales[at]fullgenomes[dot]com for further info.

Vince T.

jbarry6899
09-03-2014, 11:50 AM
Unconfirmed information, based on posting from another board, suggested that FGC had suspended YPRIME because the domestic lab could not meet its quality standards. Haven't seen anything official.

FGC Corp
09-03-2014, 04:04 PM
Unconfirmed information, based on posting from another board, suggested that FGC had suspended YPRIME because the domestic lab could not meet its quality standards. Haven't seen anything official.

That's correct. Y Prime has been temporarily suspended pending confirmation of another supplier though we can fulfill all previous orders via our existing supplier, i.e. BGI.

To clarify, we are not using the previously designated supplier for the Y Prime test any longer, although their quality was good. They are no longer providing non-clinical genetic testing.

Timothy
09-03-2014, 06:37 PM
Y Prime has been temporarily suspended pending confirmation of another supplier though we can fulfill all previous orders via our existing supplier. To clarify, we are not using them as a supplier. Their quality was good.

I'm sorry to hear that, whatever you just said. The "clarify" actually made the response confusing. You're looking for another supplier, but current orders (including mine) can be filled by the "existing supplier". But you're not using them (the formerly designated YPRIME supplier?) although their quality was good. So is that a price issue or an ability to meet demand issue? Is the "existing supplier" the original YPRIME supplier or the Chinese lab?

FGC Corp
09-03-2014, 06:53 PM
I'm sorry to hear that, whatever you just said. The "clarify" actually made the response confusing. You're looking for another supplier, but current orders (including mine) can be filled by the "existing supplier". But you're not using them (the formerly designated YPRIME supplier?) although their quality was good. So is that a price issue or an ability to meet demand issue? Is the "existing supplier" the original YPRIME supplier or the Chinese lab?

If possible we will use the new supplier for existing YPrime orders, otherwise we will use BGI.

George Chandler
09-03-2014, 09:39 PM
I tested both FGC FullY and FTDNA BigY. FullY identified 50 high reliability SNPs compared to 25 in BigY, so BigY had 50% of the coverage compared to FullY.

Full Y identified 24 of the BiGY SNPs as high reliability and 1 as medium reliability. If YPrime has 90% of the coverage of BigY, it should identify 45 high reliability SNPs compared to 25 in BigY in my case, so I would expect YPrime to identify almost all of the BiGY SNPs.

I don't see the FTDNA webtools as a benefit at this point because they are not accurate or precise in identifying close matches. Perhaps they will get there in the future, but I wish FTDNA would hire FGC and Thomas to do their data analysis. At present, you should plan on having FGC or YFull analyse all of your BiGY BAM files, unless you have the expertise to do that analysis yourself.

Hi Gail,
No YPrime had greater than 90% coverage of the Full Y testing done through BGI not 90% the Big Y testing. In my testing the YPrime capture was greater than 95% of the BGI Full Y results. It was a really good sequencing company in my opinion.

George

FGC Corp
09-03-2014, 09:53 PM
Put differently:

Y Elite: sequenced by BGI
Y Prime: sequenced by either a new provider or BGI

Timothy
09-04-2014, 09:10 AM
.... YPrime had greater than 90% coverage of the Full Y testing done through BGI .... In my testing the YPrime capture was greater than 95% of the BGI Full Y results. It was a really good sequencing company in my opinion. George

It was the price point and glowing reviews by George Chandler and Debra Cruwys regarding the high capture rate that sold me on YPrime.

I'm not a technical person, so it causes me to wonder what is done differently between the 2 tests that gets results so close and yet at such a significantly lower price, and if a different company will now be doing YPrime, how would that affect the capture rate. Also, now, the Y Elite price has dropped from $1,250 to $999 (when YPrime was launched) to $850, narrowing the gap between the 2 tests.

Since the existing YPrime orders appear to be in a temporary limbo, I wonder if FGC would be willing to allow an upgrade and those who wish to do so could pay the difference and transition their original order from YPrime to Y Elite, which in my case would be going from $599 to $850, the difference an additional $251.

I'm also curious as to whether others are thinking along these same lines, or am I being overly cautious regarding what will now be an unknown as to the quality of the YPrime results, given that the test will be done by a different company, and not the original one whose "quality was good" and was "a really good sequencing company". Or, is everyone using the same sequencers and same procedures, so it's really still comparing apples to apples.

FGC Corp
09-04-2014, 03:59 PM
It was the price point and glowing reviews by George Chandler and Debra Cruwys regarding the high capture rate that sold me on YPrime.

I'm not a technical person, so it causes me to wonder what is done differently between the 2 tests that gets results so close and yet at such a significantly lower price, and if a different company will now be doing YPrime, how would that affect the capture rate. Also, now, the Y Elite price has dropped from $1,250 to $999 (when YPrime was launched) to $850, narrowing the gap between the 2 tests.

Since the existing YPrime orders appear to be in a temporary limbo, I wonder if FGC would be willing to allow an upgrade and those who wish to do so could pay the difference and transition their original order from YPrime to Y Elite, which in my case would be going from $599 to $850, the difference an additional $251.

I'm also curious as to whether others are thinking along these same lines, or am I being overly cautious regarding what will now be an unknown as to the quality of the YPrime results, given that the test will be done by a different company, and not the original one whose "quality was good" and was "a really good sequencing company". Or, is everyone using the same sequencers and same procedures, so it's really still comparing apples to apples.

Everyone uses the same Illumina technology so the provider doesn't effect the results substantially. Providers do effect prices of course.

Dr_McNinja
09-04-2014, 04:25 PM
It was the price point and glowing reviews by George Chandler and Debra Cruwys regarding the high capture rate that sold me on YPrime.

I'm not a technical person, so it causes me to wonder what is done differently between the 2 tests that gets results so close and yet at such a significantly lower price, and if a different company will now be doing YPrime, how would that affect the capture rate. Also, now, the Y Elite price has dropped from $1,250 to $999 (when YPrime was launched) to $850, narrowing the gap between the 2 tests.

Since the existing YPrime orders appear to be in a temporary limbo, I wonder if FGC would be willing to allow an upgrade and those who wish to do so could pay the difference and transition their original order from YPrime to Y Elite, which in my case would be going from $599 to $850, the difference an additional $251.

I'm also curious as to whether others are thinking along these same lines, or am I being overly cautious regarding what will now be an unknown as to the quality of the YPrime results, given that the test will be done by a different company, and not the original one whose "quality was good" and was "a really good sequencing company". Or, is everyone using the same sequencers and same procedures, so it's really still comparing apples to apples.I sent my kit in the other day and I was thinking along similar lines as you. FGC seems to be assuring us that the results will be legit and as advertised. I'd be happy with BGI doing the test (they're the best, right?) of course but if they go with a new provider I hope they meet that standard. I planned to get next generation Y-sequencing test for my uncle in several months so my choice will depend on how my experience with FGC plays out.

FGC Corp
09-04-2014, 04:26 PM
I sent my kit in the other day and I was thinking along similar lines as you. FGC seems to be assuring us that the results will be legit and as advertised. I'd be happy with BGI doing the test (they're the best, right?) of course but if they go with a new provider I hope they meet that standard.

We just are investigating faster providers. BGI is sequencing tens of thousands of samples from across the world so they can be delayed in delivering results.

Overall, though BGI has been our most reliable partner.

Dr_McNinja
09-04-2014, 04:29 PM
FGC Corp, will you be letting current Y Prime kit owners know where/when their kit is going to end up? If it's going to BGI or a domestic lab within the States and an ETA on results?

FGC Corp
09-04-2014, 04:31 PM
FGC Corp, will you be letting current Y Prime kit owners know where/when their kit is going to end up? If it's going to BGI or a domestic lab within the States and an ETA on results?

I'm working on this new provider and we'll keep you posted.

Emmerson
09-10-2014, 09:10 PM
FTDNA Whate Paper on BIGY: https://www.familytreedna.com/learn/wp-content/uploads/2014/08/BIG_Y_WhitePager.pdf

It would be good for FGC Customers, if FGC could produce a new FGC White Paper and show how they are better than BIGY.

FGC has several customers who have taken a FGC test as well as a BIGY test and they can select about 3 of these customers and include in their FGC White Paper.

VinceT
09-11-2014, 12:27 AM
From the "WhitePager" [sic] linked above:


Conclusion

BigY covers approximately 20 million bases of the non-combining MSY regions of
the Y chromosome, which overlaps with 85% of the Gold standard region and >75% of
other SNP Chip based genotyping technologies. After using our cost effective NGS
instruments, HiSeq 2000 and 2500, to sequence and then performing in-depth
downstream analysis with Arpeggi Engine, it is possible to provide genotypes in
approximately 10.31 million bases on average with confidence. The calls made by Arpeggi
Engine have proven to be comparable to calls made by others, such as the 1000
Genomes project.
Discovery of novel variants in samples will eventually assist refinement of the human
evolutionary tree, thus improving our understanding of human genealogy.

Bolded phrase is an outright lie. BigY is incapable of ChrY coverage exceeding more than 13 million bases (by design), of which only 8 million to 11 million are reliably mapped.

Emmerson
09-11-2014, 04:12 PM
VINCEE (sic): "Bolded phrase is an outright lie. BigY is incapable of ChrY coverage exceeding more than 13 million bases (by design), of which only 8 million to 11 million are reliably mapped."

So if BIGY has inferior Y coverage, other than price, why is the FTDNA BIGY test vastly outselling anything which FGC Offers?

Dr_McNinja
09-11-2014, 04:20 PM
VINCEE (sic): "Bolded phrase is an outright lie. BigY is incapable of ChrY coverage exceeding more than 13 million bases (by design), of which only 8 million to 11 million are reliably mapped."

So if BIGY has inferior Y coverage, other than price, why is the FTDNA BIGY test vastly outselling anything which FGC Offers?Because it's implemented within their website which has a large customer database and has been selling many other products for years now.

FGC Corp
09-11-2014, 08:26 PM
FTDNA Whate Paper on BIGY: https://www.familytreedna.com/learn/wp-content/uploads/2014/08/BIG_Y_WhitePager.pdf

It would be good for FGC Customers, if FGC could produce a new FGC White Paper and show how they are better than BIGY.

FGC has several customers who have taken a FGC test as well as a BIGY test and they can select about 3 of these customers and include in their FGC White Paper.

Greg put together a white paper in Nov 2013 which was later updated in Feb 2014 and which has been validated by consumer comparisons later. We distributed on our Facebook group already:
https://www.facebook.com/groups/fullgenomesY/

VinceT
09-12-2014, 12:22 AM
VINCEE (sic): "Bolded phrase is an outright lie. BigY is incapable of ChrY coverage exceeding more than 13 million bases (by design), of which only 8 million to 11 million are reliably mapped."

So if BIGY has inferior Y coverage, other than price, why is the FTDNA BIGY test vastly outselling anything which FGC Offers?
They have an established and growing market share / customer base, a pretty good web-space ecosystem, and prohibit their volunteer surname/geographic/haplogroup project admins from using the project messaging system for advertising test options offered by competitors.

Also, price!

FGC Corp
09-12-2014, 01:17 AM
They have an established and growing market share / customer base, a pretty good web-space ecosystem, and prohibit their volunteer surname/geographic/haplogroup project admins from using the project messaging system for advertising test options offered by competitors.

Also, price!

We haven't done too badly as a small team of volunteers competing against a multimillion dollar company that has sold a million tests.

Milestones:

1. First direct-to-consumer next generation Y chromosome test.
2. First direct-to-consumer whole genome test using xTen under $2000.
3. Sophisticated Y chromosome analysis tool

All accomplished by a very small team.

Emmerson
09-12-2014, 01:17 AM
...........

FGC Corp
09-12-2014, 01:21 AM
(4) poor leadership abilities to offer new price competitive products and to build a worthy management team.[/I]

It's easy to criticize. We did this with limited volunteer resources. Bad form.

Muircheartaigh
09-12-2014, 02:49 AM
Thanks Vince, I would also add some other tangible and intangible factors. (1) Small size of FGC and reliance on a handful of hobbyists and volunteers, (2) Lack of financial resources - borrowing power - equity capital to advertise - do PR - build buzz, (3) a poorly maintained website versus YFULL or FTDNA, (4) poor leadership abilities to offer new price competitive products and to build a worthy management team, (5) slower than normal times for customers to obtain test results after spending a $1000 or more, (6) the FGC 'company' is more hobbyist oriented than business oriented.

Have you done it, and if so are you satisfied with the results? If not don't knock what you haven't tried.

Ray Murta FGC Full y and ftdna Big Y

TigerMW
09-12-2014, 12:10 PM
Thanks Vince, I would also add some other tangible and intangible factors. (1) Small size of FGC and reliance on a handful of hobbyists and volunteers, (2) Lack of financial resources - borrowing power - equity capital to advertise - do PR - build buzz, (3) a poorly maintained website versus YFULL or FTDNA, (4) poor leadership abilities to offer new price competitive products and to build a worthy management team, (5) slower than normal times for customers to obtain test results after spending a $1000 or more, (6) the FGC 'company' is more hobbyist oriented than business oriented.

Emmerson, I'm posting as a moderator. It's okay to be critical and "leadership" could be considered a generic term rather than directed at an individual, but let us not tread on anything close to a personal attack.

I think the topic is Y Prime anyway. We've strayed a bit and need to focus on the topic.

TigerMW
09-12-2014, 12:22 PM
We just are investigating faster providers. BGI is sequencing tens of thousands of samples from across the world so they can be delayed in delivering results.

Overall, though BGI has been our most reliable partner.

I know you have been, but please continue to consider having an option with a lab in a country that does a little better at respecting international trade norms and individual rights. I think it would help.

I think the BGI lab is in Shenzhen but even in Hong Kong the recent news is not good.
http://www.cnn.com/2014/08/31/world/asia/hong-kong-elections/

I recognize we can't enforce western ideals everywhere, but this does have implications on customer rights to privacy with effective legal recourse.

Eldon
09-13-2014, 05:29 PM
I certainly share your political and human rights view points but is that really at risk by using BGI? It is my understanding that the only info FGC sends to the lab is the kit number. I too would prefer that they use a domestic lab but with only a kit number I fail to see how customer privacy could be violated.

FGC Corp
09-20-2014, 01:56 AM
I know you have been, but please continue to consider having an option with a lab in a country that does a little better at respecting international trade norms and individual rights. I think it would help.

I think the BGI lab is in Shenzhen but even in Hong Kong the recent news is not good.
http://www.cnn.com/2014/08/31/world/asia/hong-kong-elections/

We've been working on a US lab and may have some good news in that department in the next weeks.

I recognize we can't enforce western ideals everywhere, but this does have implications on customer rights to privacy with effective legal recourse.

We may be able to use a US lab in the next weeks.

FGC Corp
10-23-2015, 06:01 PM
This thread refers to a product that has been phased out, and the material in it is no longer up-to-date.