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warwick
03-25-2013, 01:51 PM
Hello,

I'm doing a Phase III pilot of our Y Chromosome sequencing via my organization, Full Genomes, Inc. (Per the prior approval of admins I'm announcing it here). We can take a limited number of additional orders as we get going:

You receive:

1. Full Y chromosome sequence
2. 400-600 STRs
3. 9000 snps
4. 14 gigabytes of data
5. the full mtdna sequence can also be produced though we are doing quality control on this in the beta phase

Cost: (not cheap) $1250 raw data (including .bam files); $1350 with interpretation (to yield STRs and SNPs).

Time: 6-8 weeks for data to be analyzed
Total time from order: about 12 weeks (in the pilot phase).

Samples are collected via standard saliva sample collection kits and then analyzed via BGI in Hong Kong.

Emails may be sent to this address (temporarily):
[email protected]ail.com

(typo corrected)

Cofgene
03-25-2013, 04:55 PM
Note that the value of this effort comes with several individuals at specific y-tree branch points participate. This allows any new y-SNPs to be localized to sections of the y-tree.

introvert
03-26-2013, 07:57 AM
Hello!

Thanks for your interesting post. Bit of a newcomer here. I would like to understand what sort of deal this is, relative to getting testing done at some other lab, such as FTDNA.

For example, how much would need to be spent to get an equivalent test made at FTDNA?
Is the beta test described above even available at other labs?
What would be a nice test to do after this test, to get data on mitochondrial and autosomal DNA?

Thank you!

Ann Turner
03-26-2013, 03:55 PM
Justin, I haven't seen you post this elsewhere. Is that deliberate, to avoid being overwhelmed with queries?

warwick
03-26-2013, 04:04 PM
Justin, I haven't seen you post this elsewhere. Is that deliberate, to avoid being overwhelmed with queries?

Yes, though at the current price I don't think we'll be overwhelmed, plus qc has to be done as we proceed.

warwick
03-26-2013, 04:05 PM
Hello!

Thanks for your interesting post. Bit of a newcomer here. I would like to understand what sort of deal this is, relative to getting testing done at some other lab, such as FTDNA.

For example, how much would need to be spent to get an equivalent test made at FTDNA?
Is the beta test described above even available at other labs?
What would be a nice test to do after this test, to get data on mitochondrial and autosomal DNA?

Thank you!


"equivalent test made at FTDNA?"

There is no full Y chromosome test at FTDNA.

"beta test described above even available at other labs?"

Not to my knowledge.

"autosomal DNA?"

A microarray test for autosomal data is relatively straightforward to do.

warwick
03-27-2013, 08:05 PM
Hello,

I'm doing a Phase III pilot of our Y Chromosome sequencing via my organization, Full Genomes, Inc. (Per the prior approval of admins I'm announcing it here). We can take a limited number of additional orders as we get going:

You receive:

1. Full Y chromosome sequence
2. 400-600 STRs
3. 9000 snps-------------> correction > 1000 SNPs
4. 14 gigabytes of data
5. the full mtdna sequence can also be produced though we are doing quality control on this in the beta phase

Cost: (not cheap) $1250 raw data (including .bam files); $1350 with interpretation (to yield STRs and SNPs).

Time: 6-8 weeks for data to be analyzed
Total time from order: about 12 weeks (in the pilot phase).

Samples are collected via standard saliva sample collection kits and then sequenced via external collaborators..

Emails may be sent to this address (temporarily):
[email protected]

(typo corrected)

Corrections above.

AndersP
05-02-2013, 12:54 PM
3. 9000 snps
4. 14 gigabytes of data

How come you get only 9000 SNP and as much as 14 GB of data? You can store info about 9000 SNP far more efficiently... ;)

Clinton P
05-02-2013, 01:19 PM
How come you get only 9000 SNP and as much as 14 GB of data? You can store info about 9000 SNP far more efficiently... ;)

See here (http://fullgenomes.com/) for full details.

Clinton P

MJost
05-02-2013, 02:27 PM
For the introductory price, are we to assume that this price includes an interpretation (to yield STRs and SNPs)?

MJost

Clinton P
05-02-2013, 03:23 PM
For the introductory price, are we to assume that this price includes an interpretation (to yield STRs and SNPs)?

MJost




Cost: (not cheap) $1250 raw data (including .bam files); $1350 with interpretation (to yield STRs and SNPs).



I think the price may have changed slightly from the phase III price.

Clinton P

Cofgene
05-02-2013, 05:05 PM
How come you get only 9000 SNP and as much as 14 GB of data? You can store info about 9000 SNP far more efficiently... ;)

Eventually someone will mine the low quality or low coverage sections present in the raw data. But for now annotating and keeping track of the SNPs will be enough work. Tick-tock. Almost time for my 14GBs of ACGT to show up.

MJost
05-02-2013, 05:36 PM
Eventually someone will mine the low quality or low coverage sections present in the raw data. But for now annotating and keeping track of the SNPs will be enough work. Tick-tock. Almost time for my 14GBs of ACGT to show up.

I look forward to your results. One question will be how long will it take to get enough guys to take the same test and parse out the new snps in everones main terminal Haplogroup.

MJost

Cofgene
05-02-2013, 11:41 PM
I look forward to your results. One question will be how long will it take to get enough guys to take the same test and parse out the new snps in everones main terminal Haplogroup.

MJost

This definitely comes from coordination within a haplogroup research project. Within the R-U106 project there are at least 7 of us being tested. The results are across a number of the descendant branches. The U106 results will also be compared to at least one P312* individual who is in the queue. We will be able to bucket some of the of the new snps between specific points on the tree based upon who has tested. For my results I will compare against Justin L. since we are both branch out below the null425 R-Z326 cluster. Right now we share Z319+, CTS2509+. It will take some work to determine which new SNPs are downstream of Z319 and which one is the terminal branch point before we move into our 'private' SNPs including my L188. My results are important for figuring out whether a specific downstream Z-series SNP is reliable. Justin's result for that SNP has us scratching our heads.

MJost
05-03-2013, 12:00 AM
It sounds exciting. Have you had any L21's in the que? I might be interested in a few months.

MJost

David
05-03-2013, 06:37 PM
It sounds exciting. Have you had any L21's in the que? I might be interested in a few months.

MJost
Me -- L21+ ... DF5+ CTS3655+ L627+
My sample headed off to Hong Kong yesterday, so several months away from results.

--david

MJost
05-03-2013, 07:27 PM
David,

Nice. Thing inside L21 is you might be able find a couple of SNPs that tie a few BIG10 SNPs together back to DF13.

MJost

GailT
05-03-2013, 10:31 PM
I hope that we will be able to assign accurate age estimates to each branch point in the y tree by counting the number of SNPs between each node. Any thoughts on whether this will give us good age estimates?

David
05-04-2013, 05:58 PM
David,

Nice. Thing inside L21 is you might be able find a couple of SNPs that tie a few BIG10 SNPs together back to DF13.

MJost
That's what I'm hoping for. It is starting to get rather expensive to add new SNPs under DF13 due to the crowded field there.

--david

haleaton
05-17-2013, 03:17 PM
There is no full Y chromosome test at FTDNA.



Looking at the FTDNA's parent company's website, www.genebygene.com, they do have a division "DNA DTC is the RUO division of Gene By Gene and a sister division of Family Tree DNA which pioneered the concept of direct to consumer DNA tests in the field of genetic genealogy." RUO means "Research Use Only" which indicates "the whole genome does not include any analysis or interpretation." "DNA DTC provides sample preparation, QC and sequencing. Customers are provided with their raw data as a fast queue file."
The cost is $6, 995.

warwick
05-17-2013, 09:31 PM
Looking at the FTDNA's parent company's website, www.genebygene.com, they do have a division "DNA DTC is the RUO division of Gene By Gene and a sister division of Family Tree DNA which pioneered the concept of direct to consumer DNA tests in the field of genetic genealogy." RUO means "Research Use Only" which indicates "the whole genome does not include any analysis or interpretation." "DNA DTC provides sample preparation, QC and sequencing. Customers are provided with their raw data as a fast queue file."
The cost is $6, 995.

That's not a competitive price quite candidly for a full genome sequence.

Rory Cain
05-20-2013, 12:26 AM
It sounds exciting. Have you had any L21's in the que? I might be interested in a few months.

MJost

Me too. Also DF5+ like David Reynolds, but L658+ instead of CTS3655+. Plus a M222+ guy, all good for comparative purposes. Whatever number of new SNPs downstream of DF5 this might deliver for David & I, some of those are likely to be singletons, at least for the present, while others are likely to be held in common by both David & I. Those new SNPs held in common would, after investigation, add further increments to the DF5 sub-clade. We might also be able to change the "haircomb" pattern of SNPs clustered immediately downstream of DF5 into more of a "tree-fork" pattern. Perhaps ditto immediately downstream of DF21 as David was hoping.

Rory

R.Rocca
05-20-2013, 11:15 AM
Have any of the Phase II results come in yet?

warwick
05-20-2013, 11:36 AM
Have any of the Phase II results come in yet?

We're averaging an 8 week turnaround time; I will send everyone an email and confirm our expected data delivery date.

warwick
05-25-2013, 01:16 AM
Demo of the results from the pilot (my results included):
https://www.fullgenomes.com/demo

haleaton
05-25-2013, 02:44 AM
Demo of the results from the pilot (my results included):
https://www.fullgenomes.com/demo
Thanks! For the private SNPs will you be calling out singletons based on reference sequence 37? I was confused by "no call," if it meant there was no conclusive data at the location in the bam file desipite 50x tries or the result was negative against the reference sequence? How does the raw data differ from Sanger sequencing in that it gives you every value at a location if there is coverage and a good read.

Cofgene
05-25-2013, 09:39 AM
Demo of the results from the pilot (my results included):
https://www.fullgenomes.com/demo

Looking at Justin's results they move him down into the Z319/CTS2509 level under Z326. Seems to be missing a called result for Z324. It should be negative. The Z81+ result doesn't seem to agree with Greg M.'s genome mining results. So is Z81 going to turn out to be unreliable?

The format is such that it will be easy to do a diff in Excel to highlight where I differ from Justin below the Z319 branching point.

GTC
05-25-2013, 02:19 PM
So, what about the advertised "full Y chromosome" data? Is that delivered in another phase of the process?

warwick
05-26-2013, 12:24 AM
So, what about the advertised "full Y chromosome" data? Is that delivered in another phase of the process?



User-friendly presentation of results is in development.

Ann Turner
05-26-2013, 12:35 AM
You got a lot more STRs than I would have predicted!

Of course, I was also pleasantly surprised to see mtDNA results as well. Some people who did the exome at 23andMe figured out their mtDNA results. The exome data seemed to work quite well except for the poly-C region leading up to 315.1C and around 16189C, possibly because of length heteroplasmies.

What are DYR markers?

warwick
05-26-2013, 01:49 AM
You got a lot more STRs than I would have predicted!

Of course, I was also pleasantly surprised to see mtDNA results as well. Some people who did the exome at 23andMe figured out their mtDNA results. The exome data seemed to work quite well except for the poly-C region leading up to 315.1C and around 16189C, possibly because of length heteroplasmies.

What are DYR markers?

I will double-check on the DYR and report back here.

Pretty good work for a grad student still in school, eh?

GTC
05-26-2013, 03:07 AM
User-friendly presentation of results is in development.

Thanks for that.

haleaton
05-30-2013, 06:41 PM
Thanks! For the private SNPs will you be calling out singletons based on reference sequence 37? I was confused by "no call," if it meant there was no conclusive data at the location in the bam file desipite 50x tries or the result was negative against the reference sequence? How does the raw data differ from Sanger sequencing in that it gives you every value at a location if there is coverage and a good read.

The SNP definitions were modified which makes more sense to correct "no calls" to ancestral:
Legend for Y-DNA SNPs:
+ derived
- ancestral
x controversial
? no call

This is a beta project, but it will be interesting if they also really do provide the private SNPS and provide definition for them.

warwick
05-31-2013, 06:56 PM
Our announcement on google communities genetic genealogy:
https://plus.google.com/105627236123531587497/posts/KLRPYPgBuq3

haleaton
05-31-2013, 08:11 PM
Our announcement on google communities genetic genealogy:
https://plus.google.com/105627236123531587497/posts/KLRPYPgBuq3

Thanks! The added MTDNA data brings to mind the question: Is FullGenomes, in addition to its own data reduction and great reports, providing to its customers all raw data generated by BGI in the orignal format and sent to Full Genomes Corp?" So for example do they also actually provide autosomal data but is not provided to customers? It always bothered me that FTDNA had a lot of snp-chip Y data from Family Finder which they never provided to the people who paid for it and could be used for population studies for those willing to make it public. When I looked at NGS testing in the US the requirement to have a US physician involved, which is not value added, made it cost prohibitive to genealogy hobbyists.

Other question not answered by demo data is how new, usually "Private" snps, will be reported maybe with "FGC" prefix? My main concerns, which happened with GENO 2.0, was that they did not immediately give out the SNP definitions at the same time as the data. I think it is okay to have duplicates, but only if the definition and reference sequence information is provided.

warwick
05-31-2013, 09:17 PM
Thanks! The added MTDNA data brings to mind the question: Is FullGenomes, in addition to its own data reduction and great reports, providing to its customers all raw data generated by BGI in the orignal format and sent to Full Genomes Corp?" So for example do they also actually provide autosomal data but is not provided to customers? It always bothered me that FTDNA had a lot of snp-chip Y data from Family Finder which they never provided to the people who paid for it and could be used for population studies for those willing to make it public. When I looked at NGS testing in the US the requirement to have a US physician involved, which is not value added, made it cost prohibitive to genealogy hobbyists.

Other question not answered by demo data is how new, usually "Private" snps, will be reported maybe with "FGC" prefix? My main concerns, which happened with GENO 2.0, was that they did not immediately give out the SNP definitions at the same time as the data. I think it is okay to have duplicates, but only if the definition and reference sequence information is provided.

Anyone who wants the raw data will get it. The sequencing test we use only produces Y DNA and mtdna, i.e. no autosomal results.

People are getting raw and snp results in tandem, as far as analytical speed permits.

RobertCasey
06-03-2013, 05:55 PM
There are now seven R-L21 Full Genome orders: DF49/M222+, DF21/L658+ (Rory Cain), DF21/L627+ (David Reynolds), DF21/S190+, DF41/CTS2501+ (240201), DF49/M222 (David Wilson) and myself Z253/L226+ (77349). Anyone else out there who has ordered this test under R-L21.

David Reynolds, are you going to be consolidating the results in addition to the Nat Geo and WTY results ? If not, I would be glad to assist.

MJost
06-11-2013, 04:31 AM
My order is in and maybe some results by my birthday.

MJost

RobertCasey
06-11-2013, 02:38 PM
My order is in and maybe some results by my birthday.
MJost
Up to nine known L21 tests in the queue now:
DF13** (M Jost - 148326), DF21/L658+ (Rory Cain), DF21/L627+ (David Reynolds), DF21/S190+, DF41/CTS2501+ (240201), DF49/M222 (David Wilson), DF49/M222 (2nd), DF49/Z2963 with M222- (159309) and myself (Robert Casey) Z253/L226+ (77349). If you know kits numbers or other L21 submissions, let me know. With seven in U106 (previous post), we are covering R-M269 pretty fast. Does anyone know the status of P312 without major branches included ? I also have a P312,DF27,Z196- line (my mother's line which has been determined to be a 1765 NPE line via genetics).

MJost
06-12-2013, 09:03 PM
It really would be a huge advantage if there was at least one or more tester(s) from each of the remaining major DF13 subclades such as L251, L255, L513, L1335, etc AND one or two more DF13**'s which would surely reveal several SNP(s) that tie several of the DF13 subclades to a common ancestor node, including someone from the 1130-A2 variety as well.

MJost
06-12-2013, 09:09 PM
If I would have read my L21 Yahoo emails first I would have seen theses posts on more orders.

Taylor 258447 DF13>L1335>L1065*

Ken M. also mentioned someone from the Z251 subclade ordered but he didnt say who.

MJost

MJost
06-12-2013, 09:18 PM
Of the DF13*'s we really need some of the larger varieties to jump in and test.

MJost

RobertCasey
06-12-2013, 09:20 PM
I now have ten R-L21 FG tests in the queue now. I know that we should send our XCEL spreadsheets to David Reynolds to be added to his Nat Geo and WTY summaries - but not sure where we should send the raw data files for the 1000 genomes type people to squeeze more out of our tests. Do not know if David will assist us with that as well or if we should attempt to find out who would the focal point for raw reports for R-L21. It is critical that we get our raw data files to those who read the raw files. Hopefully they will not just pick the older and broader SNPs as I am interested in SNPs under L226.

VinceT
06-13-2013, 06:09 AM
Does anyone know the status of P312 without major branches included ?
Goldenhind (R-P312**) is expecting his data around the end of this month.

GoldenHind
06-13-2013, 06:21 PM
Goldenhind (R-P312**) is expecting his data around the end of this month.

It would be very helpful if other P312** individuals were to join in.

VinceT
06-15-2013, 05:36 AM
Indeed! It would be most helpful if several other P312**, U106**, and even L11** men would brave the plunge!

kenmunn
06-15-2013, 09:01 PM
If I would have read my L21 Yahoo emails first I would have seen theses posts on more orders.

Taylor 258447 DF13>L1335>L1065*

Ken M. also mentioned someone from the Z251 subclade ordered but he didnt say who.

MJost

for kit #
139697

MJost
06-17-2013, 02:12 PM
Up to nine known L21 tests in the queue now:
DF13** (M Jost - 148326), DF21/L658+ (Rory Cain), DF21/L627+ (David Reynolds), DF21/S190+, DF41/CTS2501+ (240201), DF49/M222 (David Wilson), DF49/M222 (2nd), DF49/Z2963 with M222- (159309) and myself (Robert Casey) Z253/L226+ (77349). If you know kits numbers or other L21 submissions, let me know. With seven in U106 (previous post), we are covering R-M269 pretty fast. Does anyone know the status of P312 without major branches included ? I also have a P312,DF27,Z196- line (my mother's line which has been determined to be a 1765 NPE line via genetics).


with these two testing we have 11 L21's in the pipe line.

Taylor 258447 DF13>L1335>L1065*
and
139697 Godwin DF13>Z251+ (Geno2 tested)

Charles Moore said over on the U106 board that there are at least ten guys test FullY:

"Justin Loe, Vince Tilroe, Wayne Kaufman, Charles Moore, Dave Wooten, Mikhail Rogov, Philippe Creuly, and Dave Pacek have all publicly identified themselves as participants. I know about at least two others."

MJost

MJost
06-17-2013, 04:35 PM
There is at least one in P312 - Goldenhind (R-P312**). Anyone else in this Clade?

MJost

GoldenHind
06-17-2013, 06:56 PM
Not that I am aware of. There are currently only 35 of us who have been so identified, though there are undoubtedly a lot more out there who haven't tested yet for DF27 or DF19.

However, unless I really am descended from someone from Mars, my results should give us at least one new subclade beneath P312. I am convinced there are at least two or three P312 subclades which haven't yet been publically identified.

MJost
06-17-2013, 07:07 PM
I would assume that some would be HG I guys as well.

We are filling in quite nicely to get a big overall picture of each major subclade.

MJost

MJost
06-18-2013, 02:04 PM
I heard through the grape vine, there will be around a larger number of kits submitting shortly for testing.

MJost

emmental
06-18-2013, 04:53 PM
Ten days ago they had about 35 kits and were waiting for a few more to batch and send out shortly. I guess now its even shorterly. Can't wait. I'm guessing the 8 weeks average turn around time begins when they ship a batch. Mid August?

MJost
06-18-2013, 05:03 PM
I understand they are waiting for one redo sample to arrive before the batch is shipped. Mine kit arrived today to be sent out to be processed.

MJost

MJost
06-18-2013, 05:05 PM
Emmental are you in for U152 testing?

MJost

emmental
06-18-2013, 06:19 PM
Yes. Mine arrived three weeks ago. As far as I know it hasn't gone out yet.

Rich posted a list of the U152 group on the U152 thread. As far as I know its still current.

The updated list...

Kit No. MDKA U152 Grouping Phase
125963 Jonas Eaton, b. 1637, Staple, Canterbury, England L2+ Z49- Z367- Phase III
E11688 Portonarius De Portonariis, Monteveglio, Bologna, Italy L2+ Z49- Z367- Phase III
37207 Johannes Crauss b. 4 Nov 1751, Ronshausen, Hesse, Germany L2+ (Z49 and Z367 not tested) Phase III
N90341 Pietro Rocca, b. 1559, Agira, Sicily, Italy L2+ Z49- Z367- Phase III
10814 Brantly Duncan b. 1821, SC, d. 1864, GA U152* (L2- Z36- Z56- DYS492=12) Phase III
204013 Jacob Musselman b c1698, to Bucks Co, PA c1724 (Switzerland) Z36+ Z54- Z143- CTS188- L671- ???
195362 Theodricus de Rocourt ±1550-1583, Liège-Hasselt Z36+ Z54- Z143- CTS188- L671- ???

Clinton P
06-19-2013, 08:30 AM
If anyone is thinking about taking the comprehensive Y-DNA test, and is holding back, then now may be the time to act.

According to the FullGenomes website....

“The Early Bird Special of $1,299 USD offer ends on June 30th, 2013”

Clinton P

MJost
06-19-2013, 12:55 PM
Yes. Mine arrived three weeks ago. As far as I know it hasn't gone out yet.

Rich posted a list of the U152 group on the U152 thread. As far as I know its still current.

Thanks for posting the list of U152's.

As I understand there are now 40 or more kits ready.

MJost

Andrew Lancaster
06-19-2013, 02:19 PM
If anyone is thinking about taking the comprehensive Y-DNA test, and is holding back, then now may be the time to act.

According to the FullGenomes website....

“The Early Bird Special of $1,299 USD offer ends on June 30th, 2013”

Clinton P

I am thinking about it, but it would be nice to see a batch completed and the results being processed successfully. As I understand it only a few kits have had results so far? And have they had full results?

It might be handy to get a kind of update for dummies to also help us visualise how this works in practice.

Regards
Andrew

Calamus
06-19-2013, 11:00 PM
I just ordered this test. (I1-L813/CTS9346)

Any other I1's thinking about taking this test?

LarryWalker
06-20-2013, 04:36 AM
Robert, Mark, & David;

A second DF41+ (who wants his name with-held for now) told me a few days ago that he has also ordered. That will give us me in 41-1426C* and him in 41-1426C-A with lots of GD.

Cheers,
Larry 240201

MJost
06-20-2013, 01:11 PM
It really would be a huge advantage if there was at least one or more tester(s) from each of the remaining major DF13 subclades such as L251, L255, L513, L1335, etc AND one or two more DF13**'s which would surely reveal several SNP(s) that tie several of the DF13 subclades to a common ancestor node, including someone from the 1130-A2 variety as well.

So L255, L513 are left for testing as a L251 and L1335 have now placed an order.

Anyone from these two thinking about sticking the toe into the new waters? How about a DF63 and L21** Guy


MJost

RobertCasey
06-20-2013, 04:36 PM
Got an email from another Z253 Full Genomes tester who is Z253+ and Z2534*, 233265. So this will help isolate downstream L226 SNPs from Z2534* downstream SNPs. Need a Z253 * or L554, PF825 or L1308 person to separate Z2534 downstream SNPs for Z253* SNPs. Also, since L226 is the largest terminal under Z253, we need a second L226 submission (genetically isolated from my 77349 YSTR pattern). Also, L1066 is turning out to a pretty large terminal SNP and is approaching the same size as L226 which may be another good candidate (or its father Z2185). L1066 has multiple fingerprints and is pretty broad while L226 is a single fingerprint but is well tested over the last few years. We really need two L1006/Z2185 testers. These tests would round out Z253 testing for the first round.

We really need a DF13** person to really discover some broad new SNPs as well as to isolate all the big "ten" or whatever the number is these days for DF13 sons. This would probably be the most important test from R-L21 research point of view since there are so many people that do not fit into the big ten DF13 SNPs.

MJost
06-24-2013, 09:22 PM
MikeW reports that a R1b-L513** man, Reid 228772 has now ordered the Full Y which will really help bridge the SNP gap between the IntraClade Coalescence Age of around 2,637 ybp (oldest most common ancestor node possible for these 247 Hts) to that of 8,108 L21 guys with a Intraclade Founder's Modal Age of 4,253 ybp.

This is leaving someone who is currently a L21*, DF63, L255 or a large DF13* variety that could help test the waters. Due date by June 30th.

MJost

MJost
06-24-2013, 09:26 PM
Just read a post by Justin that he has just sent 60 samples to the lab today for sequencing. I am now in the excited column.

MJost

LarryWalker
06-24-2013, 10:11 PM
On what list or thread? I thought I was checking them all:(

MJost
06-24-2013, 11:02 PM
I think this was from a small private group.

MJost

MJost
06-25-2013, 04:16 PM
Here is the self reporting list that I am aware Still another 25 or so not known from the 60 kits sent to the lab.

P312 - Goldenhind (R-P312**)

These are the 15 known L21 tests in the queue now:

DF13** MJost (148326),
DF21/L658+ (Rory Cain),
DF21/L627+ (David Reynolds),
DF21/S190+, Unknown
DF41/CTS2501+ Walker (240201),
DF41+ (name with-held for now in 41-1426C-A Variety,
DF49/M222 David Wilson (8999)
DF49/M222, Unknown
DF49/Z2963/M222- Trainor (159309),
Z253/L226+ Robert Casey (77349),
L1335>L1065*, Taylor 258447,
L1335/L1065, Iles, 107327,
Z251+ Munn 139697 (Geno2 tested),
Z253+ and Z2534*, Mathieu LE GALL - Brittany, Bretagne (233265),
L513**, Reid 228772


Rich posted a list of seven from the U152 group on the U152 thread and was reposted on Anthrogenica.

U152 Grouping Phase Kit No. MDKA
L2+ Z49- Z367- Phase III 125963 Jonas Eaton, b. 1637, Staple, Canterbury, England
L2+ Z49- Z367- Phase III E11688 Portonarius De Portonariis, Monteveglio, Bologna, Italy
L2+ (Z49 and Z367 not tested) Phase III 37207 Johannes Crauss b. 4 Nov 1751, Ronshausen, Hesse, Germany
L2+ Z49- Z367- Phase III N90341 Pietro Rocca, b. 1559, Agira, Sicily, Italy
U152* (L2- Z36- Z56- DYS492=12) Phase III 10814 Brantly Duncan b. 1821, SC, d. 1864, GA
Z36+ Z54- Z143- CTS188- L671- ??? 204013 Jacob Musselman b c1698, to Bucks Co, PA c1724 (Switzerland)
Z36+ Z54- Z143- CTS188- L671- ??? 195362 Theodricus de Rocourt ±1550-1583, Liège-Hasselt


Charles Moore said over on the U106 board that there are at least ten guys test FullY:

"Justin Loe, Vince Tilroe, Wayne Kaufman, Charles Moore, Dave Wooten, Mikhail Rogov, Philippe Creuly, and Dave Pacek have all publicly identified themselves as participants. I know about at least two others."

HG I
(I1-L813/CTS9346) (?Torgeir Gjermundson 37525)

MJost

RobertCasey
06-25-2013, 04:24 PM
I have one more for L21:

DF49/DF23-, Bill Harrison, 129036

MJost
06-25-2013, 04:34 PM
Outstanding!

This group of L21's should uncover alot of interconnections in the subclades, I would expect, and also into DF13**'s

MJost

seferhabahir
06-26-2013, 12:45 AM
Z251+ Munn 139697 (Geno2 tested)

MJost

I think I may take the plunge and order before the discount ends this weekend, so there will be two Z251 people testing. I am a GD of 32 from Kit 139697 at 111 markers, and as large as 41 for yet another Z251. Maybe this will uncover an elusive Baltic Cluster SNP or two between Z251 and L583. Pretty sure there is one (or more).

MJost
06-26-2013, 03:12 AM
I think I may take the plunge and order before the discount ends this weekend, so there will be two Z251 people testing. I am a GD of 32 from Kit 139697 at 111 markers, and as large as 41 for yet another Z251. Maybe this will uncover an elusive Baltic Cluster SNP or two between Z251 and L583. Pretty sure there is one (or more).


Your approx. tmrca's =1,632 @ 32 And 41 = 2,091 or so half the age of L21. So I would really consider the opportunity to see the tree results inside your subclade.

MJost

Telfermagne
06-26-2013, 04:29 PM
I might be able to do FullY after August 16th, gettin' a decent payday then. Figure the more R-P312** testing the better.

seferhabahir
06-27-2013, 03:26 AM
I think I may take the plunge and order before the discount ends this weekend, so there will be two Z251 people testing. I am a GD of 32 from Kit 139697 at 111 markers, and as large as 41 for yet another Z251. Maybe this will uncover an elusive Baltic Cluster SNP or two between Z251 and L583. Pretty sure there is one (or more).

Ordered, so now there will be (at least) two Z251 people. I'm FTDNA kit 193834 (Yurzditsky).

MJost
06-27-2013, 01:35 PM
We are getting nice coverage of the L21 branch. Here is the update list

P312 - Goldenhind (R-P312**)

These are the 18 known L21 tests in the queue now:

DF13** MJost (148326),
DF13* Edgecombe (186947),
DF21/L658 Rory Cain,
DF21/L627 David Reynolds,
DF21/S190 Alex Williamson (196041),
DF21 (21-5909-A, L1336-) Maher, (N3362),
DF41/CTS2501 Walker (240201),
DF41 (41-1426C-A Variety) Name with-held,
DF49/M222 David Wilson (8999),
DF49/M222 Unknown,
DF49/Z2963 (M222-)Trainor (159309),
DF49 (DF23-) Bill Harrison (129036),
L1335/L1065* Taylor (258447),
L1335/L1065 Iles, (107327),
Z251+ Munn (139697) (Geno2 tested),
Z251/L583 Yurzditsky, (193834),
Z253/L226 Robert Casey (77349),
Z253/Z2534* Mathieu LE GALL - Brittany, Bretagne (233265),
L513**, Reid (228772)

seferhabahir
06-27-2013, 04:52 PM
We are getting nice coverage of the L21 branch.

And add DF13*, Edgecombe, 186947

MJost
06-27-2013, 05:07 PM
And add DF13*, Edgecombe, 186947

I am so glad we have a DF13* guy! Thanks for the info.

MJost

GoldenHind
06-27-2013, 05:07 PM
I might be able to do FullY after August 16th, gettin' a decent payday then. Figure the more R-P312** testing the better.

That is fantastic news! Comparing your results to mine would certainly give us at least one, and possibly two or more new (or at least not yet publicly identified) SNPs below P312.

seferhabahir
06-28-2013, 01:29 AM
I am so glad we have a DF13* guy! Thanks for the info.

MJost

And another one, Smith N55408 DF13**

Getting to be quite a list.

MJost
06-28-2013, 02:01 AM
I cant check right now but what is his gd from me?

Mjost

seferhabahir
06-28-2013, 04:44 AM
I cant check right now but what is his gd from me?

Mjost

Looks like it is 36

MJost
06-29-2013, 02:47 PM
Posting a nice link to a diagram created by Thomas Krahn

Symbolic Map of the Yq11 Palindromic Region (Version 3)

http://www.dna-fingerprint.com/static/PalindromicRegion-V3.pdf

MJost

corner
06-30-2013, 06:53 PM
Here is the self reporting list that I am aware Still another 25 or so not known from the 60 kits sent to the lab.

P312 - Goldenhind (R-P312**)

These are the 15 known L21 tests in the queue now:

DF13** MJost (148326),
DF21/L658+ (Rory Cain),
DF21/L627+ (David Reynolds),
DF21/S190+, Unknown
DF41/CTS2501+ Walker (240201),
DF41+ (name with-held for now in 41-1426C-A Variety,
DF49/M222 David Wilson (8999)
DF49/M222, Unknown
DF49/Z2963/M222- Trainor (159309),
Z253/L226+ Robert Casey (77349),
L1335>L1065*, Taylor 258447,
L1335/L1065, Iles, 107327,
Z251+ Munn 139697 (Geno2 tested),
Z253+ and Z2534*, Mathieu LE GALL - Brittany, Bretagne (233265),
L513**, Reid 228772


Rich posted a list of seven from the U152 group on the U152 thread and was reposted on Anthrogenica.

U152 Grouping Phase Kit No. MDKA
L2+ Z49- Z367- Phase III 125963 Jonas Eaton, b. 1637, Staple, Canterbury, England
L2+ Z49- Z367- Phase III E11688 Portonarius De Portonariis, Monteveglio, Bologna, Italy
L2+ (Z49 and Z367 not tested) Phase III 37207 Johannes Crauss b. 4 Nov 1751, Ronshausen, Hesse, Germany
L2+ Z49- Z367- Phase III N90341 Pietro Rocca, b. 1559, Agira, Sicily, Italy
U152* (L2- Z36- Z56- DYS492=12) Phase III 10814 Brantly Duncan b. 1821, SC, d. 1864, GA
Z36+ Z54- Z143- CTS188- L671- ??? 204013 Jacob Musselman b c1698, to Bucks Co, PA c1724 (Switzerland)
Z36+ Z54- Z143- CTS188- L671- ??? 195362 Theodricus de Rocourt ±1550-1583, Liège-Hasselt


Charles Moore said over on the U106 board that there are at least ten guys test FullY:

"Justin Loe, Vince Tilroe, Wayne Kaufman, Charles Moore, Dave Wooten, Mikhail Rogov, Philippe Creuly, and Dave Pacek have all publicly identified themselves as participants. I know about at least two others."

HG I
(I1-L813/CTS9346) (?Torgeir Gjermundson 37525)

MJost
Bob Dickinson, kit 134765, who matches DF27* (Z196-, L617-, Z225-, Z229-, L194-, L1231-, DF84-, DF83-, DF81-, DF79-) 'Rox2', has ordered the FullY.

seferhabahir
07-01-2013, 01:44 AM
Bob Dickinson, kit 134765, who matches DF27* (Z196-, L617-, Z225-, Z229-, L194-, L1231-, DF84-, DF83-, DF81-, DF79-) 'Rox2', has ordered the FullY.

Also now Holladay, kit 117117, DF49/DF23-

MJost
07-01-2013, 02:10 AM
Looks like it is 36

I could have sworn that I replied to you. Thanks for checking Barnard. I checked and Smith and Edgecombe are closer together than I am to them in GD's but not to far off. Smith and I have tested negative for all or most major subclade SNPs.

MJost

warwick
07-10-2013, 04:19 PM
The total number of samples that are currently at BGI undergoing analysis is 103. This has been delayed such that our expected delivery time is closer to 16-20 weeks rather than 8-10. Overall, though, I have confidence in high quality results.

MJost
07-10-2013, 04:28 PM
Justin, thanks for the updates. It calms the soul!
:biggrin1:
MJost

Acque agitate
07-10-2013, 10:29 PM
Warwick, a little question.
the delivery time is 16-20 weeks for new samples or also applies to samples of Phase 3 ?
From the information that I have received, samples of Phase 3 should be delivered by July 2013. The deadline has been postponed to the end of August 2013 ?

In any case, I prefer to get good results rather than results hasty.

Thanks

lgmayka
07-10-2013, 10:40 PM
The total number of samples that are currently at BGI undergoing analysis is 103.
I assume you are referring only to those submitted by FullGenomes? BGI should currently be finishing up with the first set of samples from their cognitive genomics study (https://www.cog-genomics.org/). My account on that site says: "We estimate that we'll have results for you sometime in July."

warwick
07-11-2013, 03:16 PM
I assume you are referring only to those submitted by FullGenomes? BGI should currently be finishing up with the first set of samples from their cognitive genomics study (https://www.cog-genomics.org/). My account on that site says: "We estimate that we'll have results for you sometime in July."

Yes, the 103 samples only refers to the Y chromosome samples we have submitted.

R.Rocca
07-27-2013, 05:36 PM
Any updates on Phase III results and when they will start to appear?

warwick
07-28-2013, 04:16 AM
Any updates on Phase III results and when they will start to appear?

We're still waiting for sequencing results. In my estimation our timeline is closer to 20 weeks at this point than our previous estimate of 8 weeks. Mid-September likely will be the time for the next set of results to arrive. There are faster alternative suppliers which we are also pursuing.

Essentially, we'll not be dependent on one supplier in the future.

Erik_Maher
08-02-2013, 01:28 AM
Just out of curiosity, does anyone know if there are members of the "North-South" cluster with {437=14, 448=18, H4=10} among the P312* Full Genomes testers?
http://www.worldfamilies.net/forum/index.php?topic=9369

emmental
08-18-2013, 11:19 AM
We're still waiting for sequencing results. In my estimation our timeline is closer to 20 weeks at this point than our previous estimate of 8 weeks. Mid-September likely will be the time for the next set of results to arrive. There are faster alternative suppliers which we are also pursuing.

Essentially, we'll not be dependent on one supplier in the future.

Does anyone know if the mid-September target date is holding true for Phase III results? Is it possible that the early bird results will come in at the same time as Phase III?

Also, I noticed in the example SNP results that there is a series of "Y" SNPs. Are these the private SNPs which are being found? Is there an index which gives the mutations and positions for this "Y" series? Also, are the positions given in NCBI36 or GRCh37?

I'm getting antsy.

razyn
08-18-2013, 12:32 PM
Just out of curiosity, does anyone know if there are members of the "North-South" cluster with {437=14, 448=18, H4=10} among the P312* Full Genomes testers?
http://www.worldfamilies.net/forum/index.php?topic=9369

Erik, I just copied you on a post I made (about a Wales cluster you had suggested, under Z220+), but I'm not sure if you're on the Yahoo group discussing DF27 -- if not, you may have missed my mention of the fact that Hans van Vliet has had his full genome sequenced (by DNA-DTC, corporate partner of FTDNA -- not by the company that's doing just the Y chromosome). Anyway, Hans is in fact a member of the N/S cluster, and previously SNP tested Z220+, L484-. His 100 GB BAM file shows that he's Z210+, Z295+, CTS4065+ and as far as we know, that's his terminal SNP (of the ones that already have names). He probably has many other SNPs, but without any list of other locations to check, it's not obvious what would be phylogenetically informative.

warwick
08-18-2013, 01:20 PM
Does anyone know if the mid-September target date is holding true for Phase III results? Is it possible that the early bird results will come in at the same time as Phase III?

Also, I noticed in the example SNP results that there is a series of "Y" SNPs. Are these the private SNPs which are being found? Is there an index which gives the mutations and positions for this "Y" series? Also, are the positions given in NCBI36 or GRCh37?

I'm getting antsy.

We received a commitment that results would be ready by September 30 for all of the samples. For the next round of samples, we're using UCLA instead, to ensure a faster turnaround time.

R.Rocca
08-20-2013, 11:43 AM
We received a commitment that results would be ready by September 30 for all of the samples. For the next round of samples, we're using UCLA instead, to ensure a faster turnaround time.

That is excellent news. It looks like it will be an exciting Autumn.

Muircheartaigh
08-20-2013, 12:00 PM
We received a commitment that results would be ready by September 30 for all of the samples. For the next round of samples, we're using UCLA instead, to ensure a faster turnaround time.

Great news. How many samples will be included in the batches scheduled for completion September 30 and how will the results be made available (format etc.)

Celtarion
08-21-2013, 09:03 AM
Great news. How many samples will be included in the batches scheduled for completion September 30 and how will the results be made available (format etc.)

And how do we know which batch we are in? Will FGS update the profile for every single order?

Thanks :-)

warwick
08-21-2013, 02:48 PM
Great news. How many samples will be included in the batches scheduled for completion September 30 and how will the results be made available (format etc.)

93 samples are due by Sept 30. We'll be able to provide private SNP results, STR results as well as the raw data (the raw data would need to be delivered via USB drive). Greg Magoon has spent nearly 300 hours refining our tools.

Rory Cain
08-31-2013, 01:25 AM
And how do we know which batch we are in? Will FGS update the profile for every single order?

Thanks :-)

If you obtain a log-in, you will be able to see your order date and batch number. That's about all it shows at present. Unfortunately there is no information about how the batch number relates to the due dates under discussion, e.g. which batch number is expected in September?

warwick
08-31-2013, 02:05 AM
If you obtain a log-in, you will be able to see your order date and batch number. That's about all it shows at present. Unfortunately there is no information about how the batch number relates to the due dates under discussion, e.g. which batch number is expected in September?

Your kit was sent to BGI on June 24, 2013 along with others of Batch #4.

DebbieK
09-01-2013, 11:26 PM
Could someone clarify for me how many base pairs are sequenced in the Full Genomes test. I understand there are c. 60 million base pairs in the Y-chromosome but there are large areas that are beyond the reach of today's sequencing technology and which might never be sequenced. Am I right in thinking that this test sequences about 25 million base pairs?

I know that there were samples from haplogroups C, D and G in the beta-testing phase. Which haplogroups other than R1b1a2 and I1 are covered in Pilot Phase III?

warwick
09-01-2013, 11:34 PM
656

See above for description of full Y chromosome sequencing coverage.

warwick
09-01-2013, 11:37 PM
Could someone clarify for me how many base pairs are sequenced in the Full Genomes test. I understand there are c. 60 million base pairs in the Y-chromosome but there are large areas that are beyond the reach of today's sequencing technology and which might never be sequenced. Am I right in thinking that this test sequences about 25 million base pairs?

I know that there were samples from haplogroups C, D and G in the beta-testing phase. Which haplogroups other than R1b1a2 and I1 are covered in Pilot Phase III?

R1a1
J1
J2
E1b1
Q1b
R1b U152
R1b U106
N1c1
R1b M222

(among others)

George Chandler
09-02-2013, 02:22 AM
We received a commitment that results would be ready by September 30 for all of the samples. For the next round of samples, we're using UCLA instead, to ensure a faster turnaround time.

So just to be clear..all tests ordered now will not be tested by BGI but by UCLA instead?

warwick
09-02-2013, 02:24 AM
So just to be clear..all tests ordered now will not be tested by BGI but by UCLA instead?

We're going to beta-test UCLA and confirm their capabilities. Always better to have two horses in the race.

Muircheartaigh
09-02-2013, 02:06 PM
We're going to beta-test UCLA and confirm their capabilities. Always better to have two horses in the race.

When is the Beta-test scheduled to begin and what timescale for results? Will this consist of all Batch # 5 candidates?

warwick
09-02-2013, 03:28 PM
When is the Beta-test scheduled to begin and what timescale for results? Will this consist of all Batch # 5 candidates?

I'll begin the beta-test once the Roche chip is ready. The scale of the beta-test depends on two considerations:

#1 If BGI has provided us with high quality data by that point, that can restore our confidence in their capabilities
#2 My judgement based on UCLA's capabilities.

Note:
Y chromosome chip design is not a simple process so in the next phase we'll be using new chips and making judgements about the quality of the data as we proceed (i.e. which is better and more reliable).

greystones22
09-02-2013, 07:36 PM
Note:
Y chromosome chip design is not a simple process so in the next phase we'll be using new chips and making judgements about the quality of the data as we proceed (i.e. which is better and more reliable).

Out of interest, who makes the Y Chromosome capture chip for BGI?

greystones22
09-02-2013, 07:40 PM
656

See above for description of full Y chromosome sequencing coverage.

Thanks for posting the comparison. FGC is at 20Mb, so which regions of the Y are not covered by FGC/BGI currently??

warwick
09-03-2013, 03:03 PM
Thanks for posting the comparison. FGC is at 20Mb, so which regions of the Y are not covered by FGC/BGI currently??

There are non-sequenced regions of the Y chromosome. (i.e. highly repetitive non-mappable regions).

Incidentally, a very good expert on the Y is Dr. David Page of MIT. See:
http://wi.mit.edu/people/faculty/page

His papers are world-class and he is probably the #1 expert in the world on the Y chromosome.

JimT
09-04-2013, 09:24 PM
Bob Dickinson, kit 134765, who matches DF27* (Z196-, L617-, Z225-, Z229-, L194-, L1231-, DF84-, DF83-, DF81-, DF79-) 'Rox2', has ordered the FullY.

I'm another member of the Rox2 cluster who has just ordered the Full Y. I'm kit N3036 in the various R1b projects.

Jim Turner

warwick
09-07-2013, 03:45 PM
The remaining 7 samples of Batch 2 have been sequenced and we've done preliminary quality control, which shows the data to be good. We do not yet have data for the remaining 86 samples that we sent to BGI yet. However, it is good news that have received our results for those of Batch 2 and that quality is good.

Celtarion
09-08-2013, 11:18 PM
any new discoveries yet?

JimT
09-12-2013, 03:54 PM
I just checked the fullgenomes.com website and noticed that my kit has been changed from batch #5 to batch #99999999. What does that mean?

emmental
09-12-2013, 05:09 PM
My kit supposedly went to Hong Kong on June 24, but I never got a batch number. Just a status that says: Status: We're working on processing your order and will mail your kit soon. Then underneath it says: Your kit is currently being processed

Then I have this bar that is partially filled in yellow. It hasn't moved since it first appeared a couple of weeks ago. The site is "under construction" and I don't think anything on there really means anything.

ontheedge
09-12-2013, 06:50 PM
I posted this message on another forum but it seems to be appropriate here too:
Those of us who signed up for the misnamed ‘early bird’ sale in June may well not have any results by the end of September. I think I have just established that my kit has not even been batched yet, despite it being returned back in early July. However, there is a processing progress bar at around 25% when I login to the FG site, but I have no batch number. The FG website gives no useful individual information.
Apparently BGI are taking too long so kits may be sent in a couple of weeks time to UCLA instead. I gather that the UCLA option is only in beta stage at present. This is all very confusing, not to say frustrating. Anyone out there in a similar situation?

George Chandler
09-12-2013, 07:37 PM
Like any new company or process there is bound to be bumps and glitches. I'm just waiting for them to get worked out a bit before ordering (even though I really want to!). This is still the best way to go for those who are serious about discovering new SNP's.

RobertCasey
09-12-2013, 08:58 PM
My kit (R-L226) was mailed on June 14, 2013. This is the only status that I have seen to date (my status is similar emmental):

Status: We're working on processing your order and will mail your kit soon. Then underneath it says: Your kit is currently being processed

Then I have this bar that is partially filled in yellow.

Also still very concerned on how we are going to test the deluge of new YSNPs found with these tests. Hopefully, FTDNA will continue to add new YSNPs per single order,
otherwise, we may need to find another source of individual testing. Since Thomas did primers for individual tests is no longer available, hopefully, these new Arpeggi guys will provide a solution.

Full Genomes responded earlier that they could refer us to another company (or be the go between) for individual or batch testing of newly discovered YSNPs. If no individual or group tests
become available, Full Genomes will be a hard sale for expanded testing. Also, manual tracking of Walk the Ys and manual analysis Nat Geo downloads to correct the faulty FTDNA Nat Geo transfer
process will be aggravated by Full Genomes manual tracking of YSNP test results.

MJost
09-12-2013, 09:49 PM
Well there are Citizen Scientists in the wild who have alot of experience in designing SNP primers. hopefully FtDNA allow the continuence of this practice of confirming and accepting these designer results, by ordering theses new primers and allowing their customers to continue using their existing DNA supplied samples in house. I would have to believe FtDNA would quicky continue the SNP confirmations as they have in the past in order to keep up with the knowledge for the own future Chipset design to enhance the beta Geno2 panels. Routing new DNA samples to a new 3rd party testing site is like having to moving to a new forum every few years.

FtDNA has a large informational dissemination lag.

MJost

GTC
09-13-2013, 12:23 AM
Well there are Citizen Scientists in the wild who have alot of experience in designing SNP primers. hopefully FtDNA allow the continuence of this practice of confirming and accepting these designer results, by ordering theses new primers and allowing their customers to continue using their existing DNA supplied samples in house.

I'm not too hopeful about that anymore. I believe that Thomas Krahn, with his dedication to SNP hunting, was key to that liaison process within FTDNA.


FtDNA has a large informational dissemination lag.

That's putting it mildly. I'd say that their customer communications are abysmally poor.

MJost
09-13-2013, 04:24 PM
As I understand it now, I will be paraphasing from various messages and posts:

103 samples only refers to the Y chromosome samples we have submitted.

The kits shipped June 24, 2013 are in Batch #4 for at total of 93 in batches 3-4, and are all due around Sept 30th. The remaining 7 samples of Batch 2 have been sequenced and we've done preliminary quality control, which shows the data to be good. Some of the batch #3 and #4 kits that have completed are now under QC after the initial run produced poor results by BGI when the quality of the first 38 sequenced was not good enough as Nimblegen switched to a liquid-based solution technology for the capture array, and for some reason the amount of data (reads) was much less than the original batch. BGI is attempted to correct this by a greater depth of sequencing. These 38 kits have been rerun and FG is awaiting data, and if those pass QC the remaining batch #4 kits are to be processed and sequenced. BGI is still sequencing these samples but due to unforeseen delays by BGI, not caused by Full Genomes Corporation the process has been slowed, and now is proving that BGI can complete the sequencing process within a reasonable time period. BGI will still be implementing the better technology (so accepting the delay is assumed warranted).

http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot&p=11994&viewfull=1#post11994

FG is pursuing is alternative suppliers in the future that will yield a faster turnaround time and they going to beta-test UCLA and confirm their capabilities.

AndyG and GregM have developed an approach for automated chrY phylogenetic tree construction based on whole genome sequencing results. In contrast to most typical approaches, this also allows "state reconstruction" for various points in the tree, so that they can automatically figure out where particular SNP and small INDEL variants are located on the tree using consisting of over 1250 male samples including a large number of "Phase III" 1000 Genomes Project (1kG) sample results along with a handful of samples from other sources. Greg Magoon has spent nearly 300 hours refining these tools.


My own Kit was ordered June 4 and I am still excited in my prospect of breaking my L21>DF13** with two other DF13*'er's and getting a big discovery of possible intermediate SNPs found under DF13 and its known subclades tying several of these younger clades to a older common yet unknown SNP, with maybe my own variety.

MJost
Waiting to do my Happy :dance:

ontheedge
09-13-2013, 05:23 PM
My own Kit was ordered June 4 and I am still excited in my prospect of breaking my L21>DF13** with two other DF13*'er's and getting a big discovery of possible intermediate SNPs found under DF13 and its known subclades tying several of these younger clades to a older common yet unknown SNP, with maybe my own variety.

MJost
Waiting to do my Happy :dance:

I’m one of the DF13* that you refer to, although I don’t think I’ve been batched yet and so don’t know when to expect results, either via BGI or UCLA. Do you know if you have been batched and what your ETA is?

MJost
09-13-2013, 07:06 PM
I’m one of the DF13* that you refer to, although I don’t think I’ve been batched yet and so don’t know when to expect results, either via BGI or UCLA. Do you know if you have been batched and what your ETA is?

I was in the Batch#4 that went in June 24th. My kit is held up due to the first 38 kits having QC issues and had to be reran. In other words, mine has not been tested yet it appears but is at the BGI lab due to waiting for 2nd run results to pass FGs review and satisfaction.

MJost

lgmayka
09-14-2013, 01:02 AM
Well, you are all now much better off than I am. My results from BGI Cognitive Genomics (https://www.cog-genomics.org/) were promised by May, then July. Their web site status still says July, which at this point probably means "before doomsday, if you're lucky."

An alternative possibility is that they have decided not to release results until their research papers are published. Hmm--that's actually about the same as "before doomsday, if you're lucky."

R.Rocca
09-14-2013, 01:29 AM
Well, you are all now much better off than I am. My results from BGI Cognitive Genomics (https://www.cog-genomics.org/) were promised by May, then July. Their web site status still says July, which at this point probably means "before doomsday, if you're lucky."

An alternative possibility is that they have decided not to release results until their research papers are published. Hmm--that's actually about the same as "before doomsday, if you're lucky."

They are already starting to release results, so that does not seem to be the case.

razyn
09-14-2013, 05:22 AM
They are already starting to release results, so that does not seem to be the case.

I tried just to say, woo hoo! But that wasn't ten characters. This is.

GoldenHind
09-14-2013, 03:36 PM
i was in the beta round of testing. After a rather long and frustrating wait, I have recently received my results. I am delighted to report the wait was well worth it. After years of fruitless SNP testing with FTDNA and a completely useless (from the Y viewpoint) Geno 2 test, my subclade (DF99) has at long last been identified. Not only that, but Greg M. was able to find two additional SNPs shared with one, but not another DF99 example in the 1KG data. The latter two do not even have names yet.

They also reported an additional 47 SNPs not currently found in any public database. Presumably most of these will turn out to be private, but some may yet turn out to be of wider significance. Unfortunately I am the sole DF99, or even P312** person who has signed up for this test to date, so there is no one to compare them to. When someone eventually does so, the results could well be even more impressive.

I also gather a large number of STRs are included in the data file, but since I am away from home for an extended period, I will have to wait until I return to open the file.

Muircheartaigh
09-14-2013, 08:37 PM
Congratulations Goldenhind. Brilliant news for all of us who wait in anticipation.

lgmayka
09-14-2013, 08:56 PM
They are already starting to release results, so that does not seem to be the case.
Cognitive Genomics participants are beginning to receive results? Great! But then I wonder why they haven't updated my status, which still says "July."

Are they giving Y chromosome results to customers in a separate file, or does each customer have to download the entire genome as a single file and then split out the Y chromosome himself?

Acque agitate
09-14-2013, 09:48 PM
Goldenhind, I don't understand, you were in the batch 2 or batch 3?

rms2
09-14-2013, 11:07 PM
i was in the beta round of testing. After a rather long and frustrating wait, I have recently received my results. I am delighted to report the wait was well worth it. After years of fruitless SNP testing with FTDNA and a completely useless (from the Y viewpoint) Geno 2 test, my subclade (DF99) has at long last been identified. Not only that, but Greg M. was able to find two additional SNPs shared with one, but not another DF99 example in the 1KG data. The latter two do not even have names yet.

They also reported an additional 47 SNPs not currently found in any public database. Presumably most of these will turn out to be private, but some may yet turn out to be of wider significance. Unfortunately I am the sole DF99, or even P312** person who has signed up for this test to date, so there is no one to compare them to. When someone eventually does so, the results could well be even more impressive.

I also gather a large number of STRs are included in the data file, but since I am away from home for an extended period, I will have to wait until I return to open the file.

Super news!

Hopefully more DF99+ results will start showing up somehow.

rms2
09-14-2013, 11:18 PM
. . . Unfortunately I am the sole DF99, or even P312** person who has signed up for this test to date, so there is no one to compare them to. . .


I guess you already know this, but apparently DF99 is included in BritainsDNA's new Chromo2 test, so you probably won't be the lone DF99+ for long.

R.Rocca
09-14-2013, 11:57 PM
Cognitive Genomics participants are beginning to receive results? Great! But then I wonder why they haven't updated my status, which still says "July."

Are they giving Y chromosome results to customers in a separate file, or does each customer have to download the entire genome as a single file and then split out the Y chromosome himself?

They are giving several files to customers, including mtDNA, one that compares against all known Y-SNPs and another that compares your results with that of other full sequences like 1000 Genomes samples and Personal Genomics. The full genome is sent out on a USB flash drive via mail.

Celtarion
09-15-2013, 01:14 PM
i was in the beta round of testing. After a rather long and frustrating wait, I have recently received my results. I am delighted to report the wait was well worth it. After years of fruitless SNP testing with FTDNA and a completely useless (from the Y viewpoint) Geno 2 test, my subclade (DF99) has at long last been identified. Not only that, but Greg M. was able to find two additional SNPs shared with one, but not another DF99 example in the 1KG data. The latter two do not even have names yet.

They also reported an additional 47 SNPs not currently found in any public database. Presumably most of these will turn out to be private, but some may yet turn out to be of wider significance. Unfortunately I am the sole DF99, or even P312** person who has signed up for this test to date, so there is no one to compare them to. When someone eventually does so, the results could well be even more impressive.

I also gather a large number of STRs are included in the data file, but since I am away from home for an extended period, I will have to wait until I return to open the file.

That's great news really!! Can't wait mine :-)

Cofgene
09-15-2013, 05:15 PM
They also reported an additional 47 SNPs not currently found in any public database. Presumably most of these will turn out to be private, but some may yet turn out to be of wider significance. Unfortunately I am the sole DF99, or even P312** person who has signed up for this test to date, so there is no one to compare them to. When someone eventually does so, the results could well be even more impressive.


A small number of these SNPs are probably upstream of P312. David Carlisle has a comparison program running where submitted files can be lined up and one can better see which new SNPs may not be private. Based upon the comparison order can place some of them between tester branch points on the haplogroup tree.

lgmayka
09-16-2013, 03:14 AM
They are giving several files to customers, including mtDNA, one that compares against all known Y-SNPs and another that compares your results with that of other full sequences like 1000 Genomes samples and Personal Genomics. The full genome is sent out on a USB flash drive via mail.
That all sounds great! Now if only they would update the status of my account, which still says "July."

Dubhthach
09-16-2013, 08:27 AM
I'm in Batch 5 myself, there are at least two other DF41ers who have ordered. Both in the 1426 cluster.

-Paul
(DF41+)

GoldenHind
09-16-2013, 09:17 AM
Goldenhind, I don't understand, you were in the batch 2 or batch 3?

I was in batch 2.

emmental
09-16-2013, 03:05 PM
This was just posted on FGC's Facebook page about 10:24 this morning:

We should receive the Batch #3 raw data shortly after this Wed Sept 18 with analyses to be done in the days that follow.

:beerchug:

I'm batch #4 -- but excited.

cilldara
09-16-2013, 04:14 PM
I can't wait to see people's results. It will be really interesting.

TigerMW
09-16-2013, 10:19 PM
I imagine a number of volunteers will work diligently comparing the raw results to see what novel SNPs turn up by subclade. Thank you, thank you, thank you!

Right now, that work has been done at the project level using different formats. I suggest that we develop a common or standard format that can incorporate results from FGC and the new Chromo offering as well Geno 2. Obviously there will have to be some transformations of data but I think this could be done by translation indices.

Even if we don't ever store the data from the different projects, if we at least use a standard format and have some controls in the process of storing the data we can eventually combine and analyze the data with automated tools.

Of course, at the rate computing technologies develop we may not need a data center anyway when the day comes to aggregate the data.

Celtarion
09-17-2013, 01:29 PM
Mike, do you know more or less how the data will be presented when each of us will receive their result? Will it be something such as a map, then new SNPs discovered, phylogenetic tree showing the new SNPs... Just curious to know :P

RobertCasey
09-17-2013, 03:01 PM
Mike, do you know more or less how the data will be presented when each of us will receive their result? Will it be something such as a map, then new SNPs discovered, phylogenetic tree showing the new SNPs... Just curious to know :P

We will get two reports: 1) XCEL spreadsheet that summarizes the test results for the known 24,000 YSNPs that FG has in their current database; 2) a second file that can be scanned by more advanced genetic analysis tools. These will be made available to those can analyze further for new mutations. Once discovered, these will be added to the FG database for future reports.

Remember, many of these newly discovered will be yet more duplicate SNPs (SNPs that 100 % track existing YSNPs) and many will be determined to be unstable (mutate too many times, found in areas that are later discovered to unreliable, etc.). So the list will be in a constant state of change. Some will be very private and genealogical YSNPs - hopefully, these will be included as well (but will never qualify for the ISOGG haplotree and will have to be tracked volunteers).

RobertCasey
09-17-2013, 03:04 PM
Right now, that work has been done at the project level using different formats. I suggest that we develop a common or standard format that can incorporate results from FGC and the new Chromo offering as well Geno 2. Obviously there will have to be some transformations of data but I think this could be done by translation indices.

Even if we don't ever store the data from the different projects, if we at least use a standard format and have some controls in the process of storing the data we can eventually combine and analyze the data with automated tools.

Of course, at the rate computing technologies develop we may not need a data center anyway when the day comes to aggre
gate the data.

I responded to your request for standardization in another thread:

http://www.anthrogenica.com/showthread.php?1329-Tracking-R1b-novel-SNPs-and-their-availability-incl-a-la-carte-ordering

warwick
09-18-2013, 02:53 PM
We will get two reports: 1) XCEL spreadsheet that summarizes the test results for the known 24,000 YSNPs that FG has in their current database; 2) a second file that can be scanned by more advanced genetic analysis tools. These will be made available to those can analyze further for new mutations. Once discovered, these will be added to the FG database for future reports.

Remember, many of these newly discovered will be yet more duplicate SNPs (SNPs that 100 % track existing YSNPs) and many will be determined to be unstable (mutate too many times, found in areas that are later discovered to unreliable, etc.). So the list will be in a constant state of change. Some will be very private and genealogical YSNPs - hopefully, these will be included as well (but will never qualify for the ISOGG haplotree and will have to be tracked volunteers).

You get more than the raw list of SNPs. You'll also get a report of your private SNPs as well as the SNPs shared or not shared with the others in your haplogroup, a report showing the SNPs shared with 1000k participants, and a haplogroup report.

Acque agitate
09-18-2013, 10:13 PM
I am part of III batch.
Today I received 3 emails from Full Genomes that activated my profile.
I think it is likely that the data will arrive shortly.

GailT
09-19-2013, 03:23 AM
I am part of III batch.
Today I received 3 emails from Full Genomes that activated my profile.
I think it is likely that the data will arrive shortly.

I received the same emails. There are options to share the results with another person, and to create an account to share kit results with multiple people at once.

lgmayka
09-19-2013, 01:47 PM
Cognitive Genomics participants are beginning to receive results? Great! But then I wonder why they haven't updated my status, which still says "July."
I have received a response from Cognitive Genomics.
---
Whole genome sequencing is complete, but proper postprocessing of the data is taking longer than we had anticipated.

More precisely, I inspected the files we could have returned in June, and found that they did not distinguish between high-confidence reference genome matches and no-calls. This is a common trait of research pipelines handling WGS data, but it would have made for highly incomplete reports from third-party personal genomics tools. We are currently working on fixing this, but I cannot yet give a reliable ETA (at this point, "July" is a placeholder for "I don't know yet").
The website will be updated as soon as I do have a reliable ETA, and you will receive an email when your data is about to be available for download.
---

haleaton
09-19-2013, 02:46 PM
For clarification, is the BGI Cognitive Genomics Full Genome (not just Y) project for volunteer people with good SAT scores et cetera trying to figure out why some people are good at math? Except perhaps for the lab and origins, is this separate from the Full Genomes Company and their own Y-DNA specific analyses being currently developed as a beta? I am in FGC Batch#3 but I missed the early history.

Clinton P
09-19-2013, 03:16 PM
Selected quotes from BGI Cognitive Genomics web site....

"BGI created the Cognitive Genomics Lab in 2011 with the goal of investigating the genetics of human cognition. Current projects include prosopagnosia ("face blindness") and general intelligence."

"Our volunteer study of prosopagnosia has not yet begun."

"If you qualify as a participant, we may send you DNA collection kits. After you return them, we will sequence your DNA, and the data will eventually be available to you in a format compatible with many 3rd party interpretational tools."

Clinton P

David
09-19-2013, 10:37 PM
A small number of these SNPs are probably upstream of P312. David Carlisle has a comparison program running where submitted files can be lined up and one can better see which new SNPs may not be private. Based upon the comparison order can place some of them between tester branch points on the haplogroup tree.

Given the number of P312+ publicly available whole genome sequences, any SNPs upstream of P312 should be recognized as such, rather than private.

--david

lgmayka
09-19-2013, 11:25 PM
For clarification, is the BGI Cognitive Genomics Full Genome (not just Y) project for volunteer people with good SAT scores et cetera trying to figure out why some people are good at math? Except perhaps for the lab and origins, is this separate from the Full Genomes Company and their own Y-DNA specific analyses being currently developed as a beta?
You are correct. The reason that I mention Cognitive Genomics in this thread is that it is using the same BGI lab that Full Genomes is/was using. One may give us a clue as to what is happening with the other.

GailT
09-20-2013, 03:35 AM
Given the number of P312+ publicly available whole genome sequences, any SNPs upstream of P312 should be recognized as such, rather than private.

--david

And we should also be able to identify all SNPs between P312 to U152, and from U152 to L2, etc. Hopefully we will get a good estimate of the number of generations between each of these groups.

Cofgene
09-20-2013, 10:27 AM
Given the number of P312+ publicly available whole genome sequences, any SNPs upstream of P312 should be recognized as such, rather than private.

--david

The coverage difference is what brings out new SNPs. Coverage both in terms of amount of the y that is sequenced and the number of reads at a given location. There are new upstream, of Z319 and also U106, SNP & INDELs present in my results.

GregRM
09-20-2013, 02:25 PM
The coverage difference is what brings out new SNPs. Coverage both in terms of amount of the y that is sequenced and the number of reads at a given location. There are new upstream, of Z319 and also U106, SNP & INDELs present in my results.

In the latest FGC reports, updated over the last few weeks, if the speculative "**" and "***" SNPs are excluded, then there should not be any SNPs classified as private that are upstream of U106 or P312. There could, however, be sporadic cases that are upstream of markers like Z319 that have only a handful of derived samples in the reference database, related to the issue that Cofgene brings up. If the more speculative variants are considered, then all bets are off...

R.Rocca
09-20-2013, 03:38 PM
In the latest FGC reports, updated over the last few weeks, if the speculative "**" and "***" SNPs are excluded, then there should not be any SNPs classified as private that are upstream of U106 or P312. There could, however, be sporadic cases that are upstream of markers like Z319 that have only a handful of derived samples in the reference database, related to the issue that Cofgene brings up. If the more speculative variants are considered, then all bets are off...

I'm sure there is also likely be some discussions around back migrations, which however rare, are bound to show up at some point.

razyn
09-20-2013, 06:44 PM
I'm sure there is also likely be some discussions around back migrations, which however rare, are bound to show up at some point.

Did you mean back mutations? Or the west-to-east migration thing? Not that one necessarily excludes the other, but they are at least different words.

R.Rocca
09-20-2013, 07:07 PM
Did you mean back mutations? Or the west-to-east migration thing? Not that one necessarily excludes the other, but they are at least different words.

Sorry, I meant mutations. A Freudian slip I guess :)

razyn
09-20-2013, 08:50 PM
I've been looking at an apparent back mutation (?) of GATAH4 in the DF27>Z196>Z220>Z295>CTS4065>L484 line. Somewhere around Z196, the modal shifts from 11 to 10, and that becomes more pronounced as the series becomes increasingly restricted; then right at the end of the line for my bunch (L484), it's back to 11. Either that's a remnant population, too tiny to affect the modal (otherwise, apparently, of long standing) at higher phylogenic levels; or it's a back mutation, approximately concurrent with our terminal SNP. Remnant doesn't seem very likely, given that we have all those other listed mutations.

Our instance of L484 has 13 other off-modals (in 111-marker comparisons with the rest of Z220). Several are on slowly mutating markers, and one that isn't (at DYS385ab) is multi-step, looks like a RecLOH. The total seems unusually high, for the relatively young age of the SNP indicated by variance, and I suspect some genetically interesting event or process is being reflected. But I have no idea what.

J Man
09-21-2013, 11:21 PM
I am curious to what you all think about this. Does this test actually sequence your whole entire Y-chromosome?...Also is it worth it?...Or should one wait for complete full genome sequencing?

MacUalraig
09-22-2013, 11:22 AM
Let's put it this way, I believe over 100 people have already ordered the test so yes it is regarded as extremely valuable. It sequences all the Y chromosome that can be sequenced ie minus the ultra repetitive bits which are too difficult. Should you wait for a complete genome? No IMHO, most of the rest is recombining. So the Y is the chromosome that is most important to do, unless you have a particular interest in the others. You get a full mitochondrial test thrown in with the Y order.

R.Rocca
09-22-2013, 02:20 PM
I am curious to what you all think about this. Does this test actually sequence your whole entire Y-chromosome?...Also is it worth it?...Or should one wait for complete full genome sequencing?

The best thing about the FG product is that it is of very high quality (50x compared to 4x for 1000 Genomes samples). The first commercially feasible $1000 full genome sequencing will likely be of low quality as high quality scans require a lot of data storage. I expect it to be many years before anyone can offer 50x coverage for the entire genome at a reasonable price. So, it really depends on how long you can wait, how much you want to spend, and what your expectation for quality is.

kenmunn
09-22-2013, 07:58 PM
The best thing about the FG product is that it is of very high quality (50x compared to 4x for 1000 Genomes samples). The first commercially feasible $1000 full genome sequencing will likely be of low quality as high quality scans require a lot of data storage. I expect it to be many years before anyone can offer 50x coverage for the entire genome at a reasonable price. So, it really depends on how long you can wait, how much you want to spend, and what your expectation for quality is.

Might I add: "And your age now and how long you expect to live". If you are not a youngster you may not live long enough to see a full genome at an equivalent price. In any case it seems you would not really have any more genealogical information, maybe just lower quality information covering a broader range.

J Man
09-22-2013, 08:54 PM
Okay thanks all! I think I am going to take the plunge and order it! :D

MJost
09-22-2013, 09:27 PM
Okay thanks all! I think I am going to take the plunge and order it! :D
I believe that there 20 HG J Kits in Full Genome testing.\\


Charles Moore said over on the U106 board that there are at least ten guys test FullY:

"Justin Loe (Phase1)

Vince Tilroe, Wayne Kaufman, Charles Moore, Dave Wooten, Mikhail Rogov, Philippe Creuly, and Dave Pacek (all Phase II) have all publicly identified themselves as participants. I know about at least two others."

HG G Phase1 Three Kits
HG I (I1-L813/CTS9346)
HG D D*
HG J: 20 Kits
HG Q:Five ordered, 3 are Q1b-L245, 1 - Q1b-M378, 1 - Q1a-L527
HG R1b=L21 atleast 21 kits ordered with eight major subclades along with three of us as DF13*'s

MJost

warwick
09-23-2013, 12:24 AM
I am launching the beta-test of UCLA Y chromosome sequencing as a limited pilot of their capabilities and quality control. Results may take 4-8 weeks. This limited pilot is less than 15 individuals. The reason for the limited beta is that we need to validate capabilities, turnaround time, data quality, and comparable coverage of the Y chromosome vs the BGI coverage.

warwick
09-23-2013, 06:25 PM
13 samples were just sent to UCLA for the beta test.

emmental
09-23-2013, 07:08 PM
Any updates on batches 3 & 4?

J Man
09-24-2013, 06:07 PM
Ordered mine up yesterday! Excited! :D

Muircheartaigh
09-24-2013, 08:04 PM
13 samples were just sent to UCLA for the beta test.

Any information of the haplogroups of the candidates?

rod
09-25-2013, 01:07 AM
Any information of the haplogroups of the candidates?

One is R1b-DF27.

snake86413
09-25-2013, 05:07 PM
U106 guys testing FG that I know of:

Vince Tilroe: U106>L199.1
Clinton Platt: U106>L217.1
Robert McMillan: U106>z156
Mikhail Rogov: U106>Z159
Dave Pacek: U106>L44
Charles Moore: U106>Z7>CTS10893
Benjamin Ellis: U106>Z7>CTS10893
Philippe Creuly: U106>Z9>Z8
Dan Woodruff: U106>Z9>Z8
Wayne Kaufman: U106>Z319>L188
Justin Loe: U106>Z319>Z81
Don Byars: U106>Z1>CTS7080

For a total of twelve.

Don Byars

RobertCasey
09-25-2013, 10:22 PM
Below is a summary of 24 known L21 submissions + one P312** submission:

Relevant SNPs FTDNA ID Surname

1 DF13* 186947 Edgecombe
2 DF13* N55408 Smith
3 DF13* 148326 Jost
4 DF21/L658 28714 Cain
5 DF21/L627 20437 Reynolds
6 DF21/S190 196041 Williamson
7 DF21* N3362 Maher
8 DF21/P314.2-/Z246- N36510 Fueston
9 DF49/DF23- 129036 Harrison
10 DF49/DF23- 117117 Holladay
11 DF49/M222 8999 Wilson
12 DF49/M222 (2nd) N7406 Donaldson
13 DF49/Z2961* 159039 Trainor
14 Z253/L226 77349 Casey
15 Z253/Z2534* 233265 Le Gall
16 Z253/Z2534- 205635 Murta
17 DF41 240201 Walker
18 DF41 (3rd) 176148 Duffy
19 DF41 (2nd) Unk Unk
20 Z251 139697 Munn
21 Z251/L583 193834 Yurzditsky
22 L513* 228772 Reid
23 L1335/L1065 107327 Iles
24 L1335/L1065 258447 Taylor

25 P312** Unk Goldenhind
(determine pre-L21 SNPs)

ontheedge
09-25-2013, 10:57 PM
I am Edgecombe DF13* on the above summary list. I've at last been allocated a batch number 5, although I still don't know when my sample will be sent and to where. I assume I am not part of the beta test for UCLA- at least I haven’t heard that to be the case. As it seems to be difficult to find out any specific information from FG, I wonder whether it would be useful to add the batch numbers and expected test result date (if known) to each submission so that collectively we can try to monitor the testing progress of this group?

VinceT
09-26-2013, 12:16 AM
I had been informed that "Anonymous: U106" is actually Clinton Platt: U106>L217.1

seferhabahir
09-26-2013, 03:42 AM
One is R1b-DF27.

How do you know? Do you have a list of whose tests were sent to UCLA?

warwick
09-26-2013, 03:49 AM
I am Edgecombe DF13* on the above summary list. I've at last been allocated a batch number 5, although I still don't know when my sample will be sent and to where. I assume I am not part of the beta test for UCLA- at least I haven’t heard that to be the case. As it seems to be difficult to find out any specific information from FG, I wonder whether it would be useful to add the batch numbers and expected test result date (if known) to each submission so that collectively we can try to monitor the testing progress of this group?

If you didn't an email from me you weren't in the UCLA beta test. Keep in mind that being in the UCLA beta is a beta, i.e. we can't be certain of the data quality from there. If I did send everyone to UCLA now, that would not be responsible since I can't be certain of the quality of the results for what we need.

Also, we (and me personally) have been disappointed by BGI's performance. I'm not going to send Batch #5 samples to BGI until at least Batch #3 data arrives and Greg and the team confirms its quality.

We need to balance the need to get data with the need to ensure that it is returned to us in a reasonable time frame and in good quality.

snake86413
09-26-2013, 03:52 AM
I had been informed that "Anonymous: U106" is actually Clinton Platt: U106>L217.1

Thanks, Vince. I have revised the U106 FG list.

rod
09-26-2013, 05:47 AM
How do you know? Do you have a list of whose tests were sent to UCLA?
I only know that I'm one of the thirteen.

Muircheartaigh
09-26-2013, 01:52 PM
If you didn't an email from me you weren't in the UCLA beta test. Keep in mind that being in the UCLA beta is a beta, i.e. we can't be certain of the data quality from there. If I did send everyone to UCLA now, that would not be responsible since I can't be certain of the quality of the results for what we need.

So to clarify the situation, if we were previously in Batch #5 and have not been notified that we are included in the 13 Beta samples sent to UCLA we remain in Batch #5

Also, we (and me personally) have been disappointed by BGI's performance. I'm not going to send Batch #5 samples to BGI until at least Batch #3 data arrives and Greg and the team confirms its quality.

We need to balance the need to get data with the need to ensure that it is returned to us in a reasonable time frame and in good quality.

That's fine with me. Quality results are more important than speedy results which don't provide for optimum, full and accurate analysis.

George Chandler
09-29-2013, 07:36 PM
Now that the test batch is off to UCLA will the next batches be going to BGI until the UCLA results come back, or will they be held until a decision can be made regarding which lab to use?

Thanks
George

warwick
09-29-2013, 10:43 PM
Now that the test batch is off to UCLA will the next batches be going to BGI until the UCLA results come back, or will they be held until a decision can be made regarding which lab to use?

Thanks
George

We're going to make our decision based on the quality of the results we receive from BGI in the next week as well as the quality of the UCLA tests. Keep in mind both are world-class genetic sequencing institutions. We will also base our judgement on the UCLA turnaround time.

Additionally, it is possible that the issues with BGI have been resolved, in which case they may remain our primary provider. This remains to be proven.

GTC
09-29-2013, 11:32 PM
Additionally, it is possible that the issues with BGI have been resolved, in which case they may remain our primary provider. This remains to be proven.

Been watching this pilot with some interest before committing.

What exactly are the BGI "issues" causing the protracted delay in results.

warwick
09-29-2013, 11:51 PM
Been watching this pilot with some interest before committing.

What exactly are the BGI "issues" causing the protracted delay in results.

BGI's supplier, Illumina, apparently did not provide them the supplies that they needed. There appears to be some dispute between the two companies, possibly related to attempts by Illumina to undercut BGI, which it sees as a competitor. I am not aware of the exact details here.

GTC
09-30-2013, 12:11 AM
Thanks for the info.

I seem to recall some time ago FTDNA having issues with Illumina over the quality of the chemicals they supplied causing batches to be delayed significantly.

Muircheartaigh
09-30-2013, 08:05 AM
BGI's supplier, Illumina, apparently did not provide them the supplies that they needed. There appears to be some dispute between the two companies, possibly related to attempts by Illumina to undercut BGI, which it sees as a competitor. I am not aware of the exact details here.

The RTT news item below from July probably relates to the problem but I also read somewhere that there were issues regarding Illumina objections to an attempted BGI take over of a Genome company in the States.

7/18/2013 2:14 PM ET
Complete Genomics, Inc., a subsidiary of BGI-Shenzhen, said Thursday that it has entered into a settlement agreement with Illumina, Inc. (ILMN: Quote) under which Illumina will dismiss with prejudice both lawsuits it had brought against Complete.

Complete will dismiss with prejudice all counterclaims. The parties have entered into mutual releases, and each party will bear its own litigation costs.

No payment is being made by either party to the other, and no licenses are being granted by either party to the other.

by RTT Staff Writer

warwick
10-01-2013, 04:38 PM
New article on FGC:
http://www.genomeweb.com/arrays/sequencing-ancestry-test-launch-startup-full-genomes-enters-array-dominated-mark

40 samples data now being analyzed.

MJost
10-01-2013, 05:05 PM
Since its a Pay site, what did it basically report?

MJost

warwick
10-01-2013, 05:09 PM
Since its a Pay site, what did it basically report?

MJost

The article reported on our service, that next generation sequencing is being used, and that other companies do not provide a comprehensive Y chromosome sequence. Our competitors, of course, were critical of the need for our product and stated that it appealed only to a small niche market.

I believe I cannot quote the article here without being in violation of its copyright.

MJost
10-01-2013, 05:12 PM
Thanks, I didnt wish to pay the big bucks to read it.

MJost

Kwheaton
10-01-2013, 06:54 PM
Thanks, I didnt wish to pay the big bucks to read it.

MJost

If you have a Google account you can put in the title in the Google search and the full article pops up for me.
"With Sequencing Ancestry Test Launch, Startup Full Genomes Enters Array-Dominated Market"

haleaton
10-01-2013, 07:06 PM
It popped up for me, so I will be happy to delete if they feel this violates fair use/

With Sequencing Ancestry Test Launch, Startup Full Genomes Enters Array-Dominated Market
September 30, 2013

By Justin Petrone
Ancestry testing, or genetic genealogy, is arguably the largest component of the direct-to-consumer genomics market, and is dominated by four companies and organizations with microarray-based offerings: 23andMe, Ancestry.com, Family Tree DNA, and National Geographic.

A new company, though, recently introduced a next-generation-sequencing-based service into the mix.

Since January, Full Genomes, a privately held Rockville, Md.-based firm, has been offering "comprehensive Y chromosome sequencing," for a price tag of $1,250.

As advertised on its website, the full Y sequencing service traces the "DNA you inherit from your father and his father and so on, back in time." Full Genomes provides information that allows customers to determine the SNPs and short tandem repeats they have in common with other family members, the company claims.

While the price of Full Genomes' service is about ten times that of current ancestry testing services — which in general cost between $99 and $199 — it provides information that the other DTC services do not provide, CEO Justin Loe told BioArray News.

He said that Full Genomes' product provides customers with between 300 and 400 short tandem repeats and about 28,000 SNPs, "of which 20 or more may be private to that individual."

Loe said that other ancestry-testing companies are providing "incomplete" coverage of the Y chromosome by relying on microarrays or microsatellite-based genotyping. But given the comprehensiveness of its test, Full Genomes aims to provide its customers with "essentially the last paternal line ancestry test that they will need."

Full Genomes' Y service offers 50x coverage with 100-base-pair reads. Loe said that the company outsources its sequencing to BGI or the University of California, Los Angeles. He confirmed that suppliers charge $1,000 for the raw data, and that the company has a margin of 25 percent for its services. Data is secured on Full Genomes' website and "accessed only by a small amount of people."

He declined to provide information on the company's investors or financing.

Loe acknowledged that Full Genomes' overall focus is "unexploited biotech markets and niches," noting that the firm has tried to woo foreign customers by making its website available in 10 languages. However, the company will compete more directly with established ancestry-testing services in the future.

According to Loe, the company is planning a sequencing-based autosomal DNA service. Existing providers of autosomal DNA testing enable customers to learn, in general, from what regions of the world their ancestors originated. Loe said that Full Genomes' autosomal DNA testing service would be "similar to, but with better coverage than the 23andMe-type microarray being marketed." Other potential genetic genealogy tests in the firm's pipeline include another Y chromosome sequencing service with lower coverage.

"Our first goal was to address this vacuum in the market in terms of Y chromosome testing for genealogy," said Loe, adding that the company aims to offer the market "products that are slightly different but of higher quality for genetic genealogy."

Full Genomes has separate technology development programs underway, Loe said. The firm's biotech R&D arm has a "distinct mission for medical testing" that would distinguish the company from others who rely on external parties to perform the sequencing component of their services. While this biotech program "has even better potential" than Full Genomes' genetic genealogy offerings, Loe declined to provide additional information, stating that the technology is being validated ahead of a filing with the US Patent and Trademark Office.

Evolving technologies

It is unclear to what extent sequencing may displace array or microsatellite-based genotyping in the ancestry-testing market, though some of the entrenched players have shown interest in applying the technology.

In August, Houston-based Gene by Gene, the parent company of Family Tree DNA, acquired Arpeggi, a provider of genome sequencing, data management, and computational analysis. Gene by Gene already offers exome sequencing services via a division it founded last year called DNA Traits. However, in April Gene by Gene CEO Bennett Greenspan told BioArray News that the firm had not seen any exome sequencing orders connected with genetic genealogy (BAN 4/9/2013).

David Mittelman, Gene by Gene's chief scientific officer, told BioArray News this week that his company is "actively looking into how to best capture the maximum information from the Y chromosome," and that the company's recent acquisition of Arpeggi has "shifted a lot of our attention to the best ways to exploit NGS to solve these sorts of problems."

He also noted that Gene by Gene offers a "pretty extensive catalog of SNP and STR tests," and that the firm offers 80X exome sequencing for $899, about $350 less than Full Genomes' 50X sequencing.

Other ancestry test providers seemed less interested in adding sequencing to their offerings. An Ancestry.com spokesperson declined to comment on Full Genomes' offering, saying that sequencing-based ancestry testing is "not a part of the market we have looked at much."

Spencer Wells, director of National Geographic's Genographic Project, seemed similarly unconcerned by Full Genomes' market entry.

"The market for this kind of testing is pretty tiny at the moment," Wells told BioArray News, adding that it "caters to a select group of people … interested in enough in their Y chromosome that they are willing to pay that much" for such a test.

Wells noted that the Genographic Project's chip contains 20,000 SNPs covering the Y chromosome, which he said is "plenty" to establish the Y-chromosome haplotype of an individual. While he said that sequencing-based Y testing will likely get bigger, it is not something that National Geographic is considering at this time.

The view from Mountain View, Calif., is somewhat different: 23andMe spokesperson Catherine Afarian said that the DTC firm has "always believed that our entire service will eventually move to full sequencing versus genotyping." She noted that 23andMe has "regularly done full sequencing as part of various research projects," and carried out an exome sequencing pilot program two years ago.

At the same time, she said that 23andMe's customer base has more than doubled since it lowered its price to $99 from $299 last December. While the firm will "continue to stay on top of evolving technologies," she said that "for now, genotyping remains the most effective and efficient technology platform for a consumer-facing service."

The way of the future?

One industry observer who is interested in sequencing-based ancestry testing is Doug McDonald, a professor of chemistry at the University of Illinois who offers biogeographical ancestry analysis to DTC customers who wish to have their raw data reanalyzed. He is also the data curator for the Clan Donald Y-Chromosome Project.

"I think they are the cat's meow," McDonald told BioArray News when asked for his opinion of sequencing-based ancestry tests. McDonald said that Clan Donald will likely organize sequencing-based ancestry tests for "at least 15 people" participating in the project. And if the price tag for sequencing-based ancestry-testing services drops below $1,000, Clan Donald may try to have as many as 100 participants sequenced, he added.

"We are somewhat unique, but this is finally allowing us to assign people to clan septs," he said. He added that once Clan Donald "figures things out" with regards to its lineage, "only a few chip-based SNPs will do the job" of allowing a participant to place himself on the clan's genetically reconstructed family tree.

Genetic genealogy consultant Roberta Estes said she was "very excited" about applying next-generation sequencing. Estes is the founder of DNAExplain, a company that helps ancestry-testing customers analyze and interpret their data results.

But Estes also told BioArray News that there is a need for a comparison database to aid in interpreting one's test results.

"I think [sequencing-based ancestry testing] would be much more useful if it were simply incorporated into an existing database," like Family Tree DNA's, Estes said. "I also think that until the price point falls to about half of [$1,250], there won't be enough people to take the test to create that comparative database, if that is being considered," she said.

Estes also raised questions about data privacy, noting that the SNPs and STRs that have been included on current array and microsatellite-based genotyping tests have been selected to minimize the risk of one's personal medical information becoming public.

Still, she said that tests such as Full Genomes' offering are the "way of the future," and that, by combining one's sequencing results with STR data, ancestry-testing companies will eventually be able to construct a "very personal" genetic story for their customers.

Justin Petrone is the editor of GenomeWeb's BioArray News and covers the microarray and biochip sector of the genomics market.

MJost
10-01-2013, 07:37 PM
Nice overall article with DNA personalities getting quoted.

MJost

MacUalraig
10-01-2013, 07:39 PM
Thanks for posting. Overall a good article, not sure why he had to leave in the misleading comparison between the 'cheaper' exome sequencing though.

Muircheartaigh
10-01-2013, 07:49 PM
It popped up for me, so I will be happy to delete if they feel this violates fair use/



Spencer Wells, director of National Geographic's Genographic Project, seemed similarly unconcerned by Full Genomes' market entry.

"The market for this kind of testing is pretty tiny at the moment," Wells told BioArray News, adding that it "caters to a select group of people … interested in enough in their Y chromosome that they are willing to pay that much" for such a test.

Wells noted that the Genographic Project's chip contains 20,000 SNPs covering the Y chromosome, which he said is "plenty" to establish the Y-chromosome haplotype of an individual. While he said that sequencing-based Y testing will likely get bigger, it is not something that National Geographic is considering at this time.

Ironic considering that NatGeo have piggy-backed on the 1KG project and Citizen Scientists discovered SNPs for their product, which incidentally will be 2 years behind the times next month as far as SNPs are concerned, and of course, they will NOT be incorporating SNPs discovered by the FGC process in their future products.

Clinton P
10-01-2013, 07:56 PM
"Wells noted that the Genographic Project's chip contains 20,000 SNPs covering the Y chromosome" ???

National Genographic could not predict my Haplogroup - L217 failed on the Geno2.0 chip.

Clinton P

Kwheaton
10-01-2013, 08:03 PM
I had to call FTDNA for another reason today. There was no information on when FTDNA would offer a Full Y although he did say it is actively being discussed and sounds like something along this line is on the way....but no time frame was given.

FTDNA needs to step up to the plate with the departure of the Krahns and the WTY with them. Full sequencing makes the most sense but it is too bad it isn't integrated into existing FTDNA Y projects and that Newly discovered SNPs aren't in the pipeline for near immediate testing like it was when the Krahns were there.

Our Wheaton L2 is poised to test the whole Y just wish we had a crystal ball. Any thoughts welcome....
Kelly

Clinton P
10-01-2013, 08:26 PM
I think that FamilyTreeDNA have had their day.
They've lost their best asset.
Their Y-Chromosome tree is obsolete.
Their IT department struggles at the best of times.
I suspect that they are now focusing on the medical aspects of genetics.

Clinton P

Scarlet Ibis
10-01-2013, 08:30 PM
I think that FamilyTreeDNA have had their day.
They've lost their best asset.
Their Y-Chromosome tree is obsolete.
Their IT department struggles at the best of times.
I suspect that they are now focusing on the medical aspects genetics.

Clinton P

Let's hope it's not permanent. Because honestly, it would be a loss to the genetic genealogy community.

MJost
10-01-2013, 08:32 PM
I opinion is base on testing and upgrading my testing over the years since 2008 is that sometimes it an opportunity cost in money and time. You can test a 50x today and get a reasonable amount of data on your Y SNPs and STRs, along with MtDNA. What would it cost to get everything mention tested to the hilt. tMuch closer t the cost of a FG test. If someone hasnt tested and feel they will extend out and test everything needed, then go for the full monte.

MJost

Kwheaton
10-01-2013, 08:47 PM
I appreciate the opinions. As I explained to the customer service rep I spoke with I have a big contributor who is 92 yrs. I believe we will go for the Whole Y very soon if for no other reason than I would like to find out as much as we can while he is still with us. Since this is a collaborative effort for our group I always feel like I am asking for money (which I feel awkward doing) but you never know what will turn up. Its always a gamble that nothing will come of it (as far as new SNPs or progress) and non-scientific types do not seem to understand that progresses science too! Finding something always seems more exciting than finding nothing but that's just how it goes....

Like Scarlet Ibis I hope for all of our sakes that FTDNA remains an active player---but I also worry about the direction it may be headed....but I have those concerns of all the companies-- that the long term lure of big pharma profits will lure their focus away from genetic genealogy and population genetics.

GTC
10-02-2013, 12:51 AM
I think that FamilyTreeDNA have had their day.
They've lost their best asset.
Their Y-Chromosome tree is obsolete.
Their IT department struggles at the best of times.
I suspect that they are now focusing on the medical aspects of genetics.

Clinton P

Although I think FTDNA has certainly lost its way, I'm not quite ready to write them off yet.

FTDNA's Achilles heel has been its IT effort coupled with an inability to communicate effectively with its customers.

Its existing IT infrastructure cannot support next generation testing. Dealing with "big data" is a very big technological challenge and way beyond the capabilities of their current IT department which, as shown by a recent run of snafus, cannot even cope with its current databases.

Gene by Gene's purchase of Arpeggi, Inc shows lots of promise, but whether that is to cover health or genealogy, or both, is yet to be seen.

snake86413
10-03-2013, 04:48 AM
The status of my DNA sample has been updated at Full Genomes. The status bar now shows about 80% complete. See the following:

"Donald Byars - 93T65 - Status: We sequenced your kit and are analyzing the results
Your kit is currently being processed. Batch #3."

Acque agitate
10-03-2013, 07:53 AM
I also belong to the III° batch. unfortunately my state is not yet changed:
"Status: We've sent your kit to the lab and will notify you when your results are available"

The status bar is still at about 50%.

I hope will change today or in the coming days.

warwick
10-03-2013, 04:51 PM
I also belong to the III° batch. unfortunately my state is not yet changed:
"Status: We've sent your kit to the lab and will notify you when your results are available"

The status bar is still at about 50%.

I hope will change today or in the coming days.

22 of 29 from Batch #3 were sequenced and 18 of 56 from Batch #4 were sequenced. There will be another round of data delivery, hopefully within the next three weeks.

parasar
10-03-2013, 07:16 PM
22 of 29 from Batch #3 were sequenced and 18 of 56 from Batch #4 were sequenced. There will be another round of data delivery, hopefully within the next three weeks.

Any R1a1 among these?

cilldara
10-03-2013, 10:20 PM
The status of my DNA sample has been updated at Full Genomes. The status bar now shows about 80% complete. See the following:

"Donald Byars - 93T65 - Status: We sequenced your kit and are analyzing the results
Your kit is currently being processed. Batch #3."

Same here.

haleaton
10-03-2013, 10:41 PM
I also belong to the III° batch. unfortunately my state is not yet changed:
"Status: We've sent your kit to the lab and will notify you when your results are available"

The status bar is still at about 50%.



Same Batch#3 and status here. So it is is either not updated or we are one of the 7 not sequenced yet from Batch 3.

I wonder if any of the Batch 3 U152+ or L2+ have returned yet?

GailT
10-04-2013, 12:23 AM
My L2+ results in Batch 3 were returned and are being processed - Johannes Crauss born 1741, Ronshausen, Hesse. I've set up sharing with Richard and can also share with you when the results are ready.

Gail

KerryODair
10-04-2013, 12:36 AM
My E-M35/V12 Results in batch 3 were returned and are being processed. Looking good for getting results soon.

David
10-04-2013, 12:40 AM
My DF21+ results are also in analysis. Any other DF21+ testers out there besides Alex, Erik, and Rory?

--david

MJost
10-04-2013, 12:54 AM
Batch 4 and nothing showing in my profile yet.

MJost

LarryWalker
10-04-2013, 04:49 PM
DF41+ and one of the batch 4's still in the lab.
Larry Walker

Sealgair
10-04-2013, 07:20 PM
My DF21+ results are also in analysis. Any other DF21+ testers out there besides Alex, Erik, and Rory?

--david

DF21 (P314.2-, Z246-) Charles Fueston (N36510), Batch 5 (not sent to lab yet.)

warwick
10-04-2013, 10:34 PM
As a summary:

22 of 29 Batch #3 samples' data have arrived to FGC
18 of 56 Batch #4 samples' data have arrived to FGC

40 arrived total in the latest round

45 pending at BGI
13 pending at UCLA

Erik_Maher
10-05-2013, 07:12 AM
Here are the known public Full Genomes testers that I could find here on Anthrogenica from all of your posts, put in comma-delimited format. You can easily import into Excel, LibreOffice, or another spreadsheet program; just make sure to choose "Import - separated by comma" or "comma-delimited", or else it will import as a tangled mess. Please check for errors. To give credit where credit is due, this format is loosely based on the Google Docs spreadsheet in the U152 Full Genomes forum - I just added a "major branch" first column, for easier sorting by haplogroup.

Major branch, FTDNA kit, FG kit, full name or surname, MDKA, haplogroup or cluster, batch, complete

D, 233764, 4RKX5, Martin Doroy, Alejandro Doroy b circa 1900 Babag Lapu Lapu Cebu Philippines, D*, phase 5, N

E, ?, ?, ?, ?, E-M35 V12, phase 3, ?

G, ?, ?, ?, ?, G, phase 1, ?
G, ?, ?, ?, ?, G, phase 1, ?
G, ?, ?, ?, ?, G, phase 1, ?

I1-M253, 37525, ?, Torgeir Gjermundson, ?, I1-L813 (CTS9346), ?, ?

J, ?, ?, ?, ?, J1, ?, ?
J, ?, ?, ?, ?, J2a3* L26+ L27+, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?
J, ?, ?, ?, ?, ?, ?, ?

N, ?, ?, ?, ?, N1c1, ?, ?

Q, ?, ?, ?, ?, Q1a-L527, ?, ?
Q, ?, ?, ?, ?, Q1b-L245, ?, ?
Q, ?, ?, ?, ?, Q1b-L245, ?, ?
Q, ?, ?, ?, ?, Q1b-L245, ?, ?
Q, ?, ?, ?, ?, Q1b-M378, ?, ?

R1a1, ?, ?, ?, ?, R1a1, ?, ?

R1b-U106, ?, ?, Vince Tilroe, ?, U106>L199.1, phase 2, ?
R1b-U106, ?, ?, Clinton Platt, ?, U106>L217.1, ?, ?
R1b-U106, ?, ?, Robert McMillan, ?, U106>z156, ?, ?
R1b-U106, ?, ?, Mikhail Rogov, ?, U106>Z159, phase 2, ?
R1b-U106, ?, ?, Dave Pacek, ?, U106>L44, phase 2, ?
R1b-U106, ?, ?, Charles Moore, ?, U106>Z7>CTS10893, phase 2, ?
R1b-U106, ?, ?, Benjamin Ellis, ?, U106>Z7>CTS10893, ?, ?
R1b-U106, ?, ?, Philippe Creuly, ?, U106>Z9>Z8, phase 2, ?
R1b-U106, ?, ?, Dan Woodruff, ?, U106>Z9>Z8, ?, ?
R1b-U106, ?, ?, Wayne Kaufman, ?, U106>Z319>L188, phase 2, ?
R1b-U106, ?, ?, Justin Loe, ?, U106>Z319>Z81, phase 1, ?
R1b-U106, ?, ?, Don Byars, ?, U106>Z1>CTS7080, ?, ?
R1b-U106, ?, ?, Dave Wooten, ?, ?, phase 2, ?

R1b-P312, ?, ?, Goldenhind, ?, R-P312>DF99, ?, Y

R1b-P312>DF27, 134765, ?, Bob Dickinson, ?, DF27* (Z196- L617- Z225- Z229- L194- L1231- DF84- DF83- DF81- DF79-) 'Rox2', ?, ?
R1b-P312>DF27, N3036, ?, ?, ?, DF27* Rox2, ?, ?

R1b-P312>U152, 125963, ?, ?, Jonas Eaton b. 1637 Staple Canterbury England, L2+ Z49- Z367-, phase 3, ?
R1b-P312>U152, E11688, ?, ?, Portonarius De Portonariis Monteveglio Bologna Italy, L2+ Z49- Z367-, phase 3, ?
R1b-P312>U152, 37207, ?, ?, Johannes Crauss b. 4 Nov 1751 Ronshausen Hesse Germany, L2+ (Z49 and Z367 not tested), phase 3, ?
R1b-P312>U152, N90341, ?, ?, Pietro Rocca b. 1559 Agira Sicily Italy, L2+ Z49- Z367-, phase 3, ?
R1b-P312>U152, N114738, ?, ?, Charles William Fowler b. 1731 d. 1810 Wandborough Swindon England, L2+ Z49- Z367-, ?, ?
R1b-P312>U152, 10814, ?, ?, Brantly Duncan b. 1821 SC d. 1864 GA, U152* (L2- Z36- Z56- DYS492=12), phase 3, ?
R1b-P312>U152, 204013, ?, ?, Jacob Musselman b c1698 to Bucks Co PA c1724 (Switzerland), Z36+ Z54- Z143- CTS188- L671-, ?, ?
R1b-P312>U152, 195362, ?, ?, Theodricus de Rocourt ±1550-1583 Liège-Hasselt, Z36+ Z54- Z143- CTS188- L671-, ?, ?

R1b-P312>L21, 148326, ?, MJost, ?, DF13**, ?, ?
R1b-P312>L21, 186947, ?, Edgecombe, ?, DF13*, ?, ?
R1b-P312>L21, N55408, ?, Smith, ?, DF13*, ?, ?
R1b-P312>L21, 11143, ?, Chandler, ?, DF13* (9919 cluster), ?, ?

R1b-P312>L21, 129036, ?, Bill Harrison, ?, DF49 (DF23-), ?, ?
R1b-P312>L21, 117117, ?, Holladay, ?, DF49 (DF23-), ?, ?
R1b-P312>L21, 159039, ?, Trainor, ?, DF49>DF23>Z2961* (M222-), ?, ?
R1b-P312>L21, 8999, ?, David Wilson, ?, DF49>M222, ?, ?
R1b-P312>L21, N7406, ?, Donaldson, ?, DF49>M222, ?, ?
R1b-P312>L21, ?, ?, ?, ?, DF49>M222, ?, ?

R1b-P312>L21, 228772, ?, Reid, ?, L513**, ?, ?

R1b-P312>L21, 77349, ?, Robert Casey, ?, Z253>L226, ?, ?
R1b-P312>L21, 233265, ?, Mathieu Le Gall, Brittany Bretagne, Z253>Z2534*, ?, ?
R1b-P312>L21, 205635, ?, Murta, ?, Z253 (Z2534-), ?, ?

R1b-P312>L21, 107327, ?, Iles, ?, L1335>L1065, ?, ?
R1b-P312>L21, 258447, ?, Taylor, ?, L1335>L1065*, ?, ?

R1b-P312>L21, N36510, ?, Charles Fueston, ?, DF21 (P314.2- Z246-), phase 5, N
R1b-P312>L21, 20437, ?, David Reynolds, ?, DF21>L627, ?, ?
R1b-P312>L21, 28714, ?, Rory Cain, ?, DF21>L658, ?, ?
R1b-P312>L21, 196041, ?, Alex Williamson, ?, DF21>S190, ?, ?
R1b-P312>L21, N3362, 11R9D, Erik Maher, John Maher b circa 1831 Noughaval Co. Clare, DF21* (L1336 no-call), phase 5, N

R1b-P312>L21, 240201, ?, Walker, ?, DF41 (CTS2501), ?, ?
R1b-P312>L21, 176148, ?, Duffy, ?, DF41, ?, ?
R1b-P312>L21, ?, ?, ?, ?, DF41 (41-1426C-A), ?, ?

R1b-P312>L21, 139697, ?, Munn (Godwin?), ?, Z251, ?, ?
R1b-P312>L21, 193834, ?, Yurzditsky, ?, Z251>L583, ?, ?

snake86413
10-05-2013, 08:49 AM
Thanks Erik,

Another R1b-U106 placed a FG order a couple of days ago who is not on the list I posted: John Gordon, U106*

KerryODair
10-05-2013, 06:17 PM
List of E-M35 members to my understanding who have ordered FullGenomes test:

E-M35-V68-M78-Z1902-V12-F3599

E-M35-V68-M78-Z1919-L618-V13

E-M35-V68-M78-Z1919-V22

E-M35-Z827-L19

E-M35-Z827-L19-M81-M183-L351

E-M35-Z827-Z830-M123-M34-M84 (Two Tests)

Kwheaton
10-05-2013, 06:28 PM
My L2+ results in Batch 3 were returned and are being processed - Johannes Crauss born 1741, Ronshausen, Hesse. I've set up sharing with Richard and can also share with you when the results are ready.

Gail
Gail,

I can't wait to see what turns up below L2* I am sorry that Rich's results did not come in yet----but perhaps this gives you his undivided attention. ;) I am waiting on the L2* results to make a decision on ordering the Full Y for our modal WHEATON L2*

Kelly

R.Rocca
10-05-2013, 06:40 PM
Gail,

I can't wait to see what turns up below L2* I am sorry that Rich's results did not come in yet----but perhaps this gives you his undivided attention. ;) I am waiting on the L2* results to make a decision on ordering the Full Y for our modal WHEATON L2*

Kelly

My dumb luck - not enough saliva when I was part of batch 2 and now it looks like BGI bumped me for some batch 4 samples. Oh well.... :noidea:

Kwheaton
10-05-2013, 07:02 PM
My dumb luck - not enough saliva when I was part of batch 2 and now it looks like BGI bumped me for some batch 4 samples. Oh well.... :noidea:

Murphy's law. I am so sorry after all you do for us!!!! But hopefully you can scour Gail's and then you'll have a good head start sorting anything promising. It also buys me a little time to get all the funds collected---and maybe in the meantime we will hear from the Chromo2.

Wait, wait, wait. And I have a new grandson arriving this month....wait, wait wait.:biggrin1:

George Chandler
10-05-2013, 07:17 PM
It's been posted that the FGS is producing about one SNP for every 3 generations. How consistant is that from the test kit results so far?

George

GoldenHind
10-05-2013, 11:11 PM
It's been posted that the FGS is producing about one SNP for every 3 generations. How consistant is that from the test kit results so far?

George

I believe they found 47 SNPs in my sample that do not appear in any public database.

RCO
10-06-2013, 03:56 AM
J1 Full Genomes

Batch 3 - 11 kits sequenced under analysis

Arab
9 are L222.2+
1 is L858+

European
L858+ sequenced under analysis

Batch 4,
J1b M365+ (my kit, results not received)

gottex
10-06-2013, 12:52 PM
I ordered the kit and paid by bank transfer on 05-02-2013.
Kit returned the 05-27-2013. I still do not have any news. Is this normal?

I look forward to the results.
With WTY, Thomas Krahn had found seven new SNPs!
And now even more?

GailT
10-06-2013, 03:19 PM
I believe they found 47 SNPs in my sample that do not appear in any public database.

Assuming 1 SNP every 3 generations, and an average generation of 30 years, 47 SNPs would suggest an age of 4230 years for R1b-DF99. I don't know if there are any age estimates for DF99 based on STR data, but assuming it is somewhat younger than the major P312 subclades, this could be roughly consistent with 1 SNP in 3 generations.

In mtDNA testing we sometimes see very large variability in SNPs. For examples, in a subclade estimated to be 6000 years old, some people can have zero SNPs while others can have 7 or more SNPs. It will be interesting to see if there is similar variability in Y DNA. Hopefully, given the much larger size of the Y genome, the variability in SNP counts will be much smaller.

MacUalraig
10-06-2013, 03:21 PM
I ordered the kit and paid by bank transfer on 05-02-2013.
Kit returned the 05-27-2013. I still do not have any news. Is this normal?


I am in batch #4 and sent my kit back to them on May 29th, my status when I log in says "We're working on processing your order and will mail your kit soon"
even though they told me it had been sent out to BGI at the end of June. So I hope my status message is wrong!!

R.Rocca
10-06-2013, 03:40 PM
Assuming 1 SNP every 3 generations, and an average generation of 30 years, 47 SNPs would suggest an age of 4230 years for R1b-DF99. I don't know if there are any age estimates for DF99 based on STR data, but assuming it is somewhat younger than the major P312 subclades, this could be roughly consistent with 1 SNP in 3 generations.

In mtDNA testing we sometimes see very large variability in SNPs. For examples, in a subclade estimated to be 6000 years old, some people can have zero SNPs while others can have 7 or more SNPs. It will be interesting to see if there is similar variability in Y DNA. Hopefully, given the much larger size of the Y genome, the variability in SNP counts will be much smaller.

I don't follow the SNP counting calculations much, but I would assume that the SNPs that may be sub-branch forming but are also found in more than one haplogroup might need to be taken into account as well.

George Chandler
10-06-2013, 03:41 PM
Assuming 1 SNP every 3 generations, and an average generation of 30 years, 47 SNPs would suggest an age of 4230 years for R1b-DF99. I don't know if there are any age estimates for DF99 based on STR data, but assuming it is somewhat younger than the major P312 subclades, this could be roughly consistent with 1 SNP in 3 generations.

In mtDNA testing we sometimes see very large variability in SNPs. For examples, in a subclade estimated to be 6000 years old, some people can have zero SNPs while others can have 7 or more SNPs. It will be interesting to see if there is similar variability in Y DNA. Hopefully, given the much larger size of the Y genome, the variability in SNP counts will be much smaller.

Have they placed DF99 yet? I noticed under ISOGG it was "still under investigation".

gottex
10-06-2013, 04:43 PM
I ordered the kit and paid by bank transfer on 05-02-2013.
Kit returned the 05-27-2013. I still do not have any news. Is this normal?

I look forward to the results.
With WTY, Thomas Krahn had found seven new SNPs!
And now even more?

e-mail from Justin :N° Batch You’re in batch#4 and BGI should have results for you in the next 2-3 weeks.
Great !
Thanks Justin

GoldenHind
10-06-2013, 04:57 PM
Have they placed DF99 yet? I noticed under ISOGG it was "still under investigation".

Although seven P312>DF99+ have been found (four in Holland, one each in Peru, Tuscany and England), I am the only one with identified STRs. Normally ISOGG requires at least two to demonstrate the SNP isn't private. Dave R. was going to try to see if he could get that requirement waived for DF99, but I haven't heard whether he was successful. Since FTDNA doesn't offer DF99, it may be a while before we have a second sample with STRs.

George Chandler
10-06-2013, 05:47 PM
That's interesting. So it's found to be directly below P312 and above DF27?

Itai
10-06-2013, 06:34 PM
Well, it seems that this is the main place to discuss the FullGenomes test. My haplogroup is G-L91 and I am in batch 4. My results have just been sequenced and are under analysis from the FullGenomes team.

MacUalraig
10-06-2013, 07:26 PM
Well, it seems that this is the main place to discuss the FullGenomes test. My haplogroup is G-L91 and I am in batch 4. My results have just been sequenced and are under analysis from the FullGenomes team.

That's encouraging news, I think you are the first from batch 4 I've seen reporting his data is back. Lucky you!

razyn
10-06-2013, 07:32 PM
That's interesting. So it's found to be directly below P312 and above DF27?

No, just below P312. Not above DF27 (or L21, or U152).

Celtarion
10-06-2013, 10:49 PM
e-mail from Justin :N° Batch You’re in batch#4 and BGI should have results for you in the next 2-3 weeks.
Great !
Thanks Justin

Great ;-)

You are in the game... Very soon from mow :)

warwick
10-09-2013, 09:49 PM
Quote:

Customer feedback thus far (anonymized):

1.
My first impression about the results is quite impressive! Really great work!

Another:
2.
I will just say very simply at this point "more than what I expected", and I am a happy camper. So, thanks to the Full Genomes team for the great work!

Itai
10-10-2013, 06:30 AM
Analyses are done. We're making them available over the next few days.

I am so excited ! :)

snake86413
10-10-2013, 07:32 AM
I am so excited ! :)


I'm confused, Itai. While your message contains a quote by warwick that states "Analyses are done. We're making them available over the next few days." I have yet to find the original post by warwick. I checked all of warwick's messages and, nope, not there.

Am I missing something?

I'm really happy that you are excited, Itai, and I would like to be excited along with you, but I'm not sure what's going on. Has old age finally caught up with me , and my mind is playing tricks on me?

Still scratching my head.........

Itai
10-10-2013, 09:18 AM
I'm confused, Itai. While your message contains a quote by warwick that states "Analyses are done. We're making them available over the next few days." I have yet to find the original post by warwick. I checked all of warwick's messages and, nope, not there.

Am I missing something?

I'm really happy that you are excited, Itai, and I would like to be excited along with you, but I'm not sure what's going on. Has old age finally caught up with me , and my mind is playing tricks on me?

Still scratching my head.........

This quote comes from an answer he made on the Full Genome Y sequencing Facebook group.

snake86413
10-10-2013, 09:58 AM
This quote comes from an answer he made on the Full Genome Y sequencing Facebook group.


Thanks, Itai. This does get confusing. I don't do Facebook!

Now I can be excited along with you and others who might have seen warwick's post on Facebook.

Boy, business is definitely done differently in this modern era. One has to be adept at forum-hopping to keep up with what's going on, wondering all the while if you might have missed a thread somewhere and something important along with it.

Itai
10-10-2013, 11:07 AM
Well it seems more logical to post information on what is an almost official Full Genomes discussion group than in a thread hidden in an external forum. It took me a while to find this place. Anyway, be reassured, there is much more information in here than in FB. But this was a direct answer to a question by warwick, and I thought it would be interesting to share it here.

snake86413
10-10-2013, 01:19 PM
Well it seems more logical to post information on what is an almost official Full Genomes discussion group than in a thread hidden in an external forum. It took me a while to find this place. Anyway, be reassured, there is much more information in here than in FB. But this was a direct answer to a question by warwick, and I thought it would be interesting to share it here.


Thanks again, Itai. I must have missed the official memo about the "almost official Full Genomes discussion group" on Facebook, especially since I'm not on Facebook, and you talking about this "thread hidden in an external forum" and "It took me a while to find this place" is something that I can relate to. That's kinda my point, isn't it. Well anyway, it's good to know that your quote from warwick, aka Justin, wasn't just wishful thinking or a misinterpretation on someone's part. And, as you say, I thought this thread was where all the important FG information was being posted--my point again--but it looks as if one has to keep tabs on multiple forums to get the complete story--dare I say it: my poin......... I've sad quite enough, I think. I'm sure I've made my point.

Anyway, this is great news. All this is about to become academic for some of us who've been trying to keep tabs on this for a while now. Now the really fun stuff begins.

GailT
10-10-2013, 03:01 PM
This quote comes from an answer he made on the Full Genome Y sequencing Facebook group.


I'm looking at the facebook site and can't find the the question or the answer. The facebook site does not have many updates and I have not found it to be a good source of information.

haleaton
10-10-2013, 03:20 PM
I'm looking at the facebook site and can't find the the question or the answer. The facebook site does not have many updates and I have not found it to be a good source of information.

There is a Full Genomes Y sequencing Facebook group, which is separate from the company's Facebook page. He cross posts announcements usually, but not always comments on Facebook. They are probably very busy at the moment, which is a good thing.

GailT
10-10-2013, 03:46 PM
There is a Full Genomes Y sequencing Facebook group, which is separate from the company's Facebook page. He cross posts announcements usually, but not always comments on Facebook. They are probably very busy at the moment, which is a good thing.

I guess I'm showing my age - Is there a link to the separate facebook group? I can't find it.

Itai
10-10-2013, 03:49 PM
Here's the link: https://www.facebook.com/groups/fullgenomesY/

GailT
10-12-2013, 08:44 PM
There is a summary of 10 J-L222 full Y test results at molgen (http://j1tree.com/images/fgc.png). They found 1 SNP in 3 generations, and an average of 40.5 SNPs in L222 with a standard deviation of 7.6 in the 10 kits.

That seems to indicate quite a bit of variability in the rate of accumulation of SNPs in individual lines, so we will need large numbers of samples to estimate average numbers of SNPs for age estimates. I was hoping the mutation rate would be more uniform.