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R.Rocca
04-27-2013, 03:48 PM
Several have already signed up for the full Y-chromosome sequencing by ordering the product first announced here:

http://www.anthrogenica.com/showthread.php?742-Full-Y-Chromosome-Sequencing-Phase-III-Pilot

I wanted to start this thread to keep track of any known participants. Here are the ones I know of so far:



Kit No.MDKAU152 Grouping


125963Jonas Eaton, b. 1637, Staple, Canterbury, EnglandL2+ Z49- Z367-


E11688Portonarius De Portonariis, Monteveglio, Bologna, ItalyL2+ Z49- Z367-


37207Johannes Crauss b. 4 Nov 1751, Ronshausen, Hesse, GermanyL2+ (Z49 and Z367 not tested)


N90341Pietro Rocca, b. 1559, Agira, Sicily, ItalyL2+ Z49- Z367-



As you can see it is very L2 heavy. I hope some Z36, Z56, L20, etc. kits test as well. If you know of anyone else, please include it on this thread so we can all track their progress.

Scarlet Ibis
04-27-2013, 07:00 PM
It looks attractive, but wow, is that price hefty. Thank goodness for those on this list who have taken the plunge. I'm looking forward to reading about any future developments.

haleaton
04-28-2013, 07:31 PM
Any thoughts on how to manage the large amounts of 50x Y-DNA data which soon should be available identifying the majority of mutations, but also to provide a reference database similar to 1K Genomes as testing becomes cheaper?

Cofgene
04-28-2013, 08:43 PM
Any thoughts on how to manage the large amounts of 50x Y-DNA data which soon should be available identifying the majority of mutations, but also to provide a reference database similar to 1K Genomes as testing becomes cheaper?

Initially it will not be that hard to manage. We will be looking at the listing of unique SNPs identified in the data. Comparison of the unique SNPs between individuals will help in positioning them. Some of the new SNPs will be upstream of U152. Those should be picked off by comparison to the results we have coming in from the U106 region. Similarly SNPs apparently upstream of U106 will be compared to the haplogroup G results to drop any new ones into specific regions up or downstream of G.

A diff comparison within Excel similar to Adriano's 23andMe spreadsheet will be the easiest way to track results. Using Excel to manage the full annotated list of y-SNPs from the data is not an unreasonable expectation.

Longer term the raw data will need to be mined in order to evaluate the lower quality, and lower coverage, SNP calls present in the data. We know what was reliably mined from the 1K genomes data. it will just take a lot longer to parse through more sequence present in the 50x data results.

With the 50x coverage the ole "number of generations/snp" discussion will rise again but we will have some very solid data available to guide that discussion.

Wayne
R-Z319+, CTS2509+ , L188+ phase II 50x beta sample.

haleaton
04-28-2013, 10:21 PM
What I meant was public storage of the raw data and summarized SNPs/STRs/UEPs. I was wondering if there was something that would be better than just a file and Excel spreadsheet. I am participating in Phase III pilot, but I am curious if Phase II got their and what they are doing with in terms of tools and storage?

Cofgene
04-29-2013, 10:24 AM
What I meant was public storage of the raw data and summarized SNPs/STRs/UEPs. I was wondering if there was something that would be better than just a file and Excel spreadsheet. I am participating in Phase III pilot, but I am curious if Phase II got their and what they are doing with in terms of tools and storage?
Phase II is due in about 2 weeks. Public storage of the raw data is an issue due to its size. I will probably spin up a Bioconductor system and see how it works on the data. http://www.bioconductor.org/

haleaton
05-03-2013, 03:23 PM
It will be interesting if FullGenomes (www.fullgenomes.com) will be able to report "All your Y chromosome SNP's" and "your Private SNP's" along with "over 300 Y STRs" due to 50x coverage instead of the few known SNPs we look at now. The full Y-SNP list should for U152 and down stream using the current reference sequence I think should be manageable size, though it may be some time for it to be sorted out. I think once complete genome testing becomes really cheap in the next couple or so years, having developed phylogenetic trees will encourage people to either get tested or to release their medical DNA Y data particularly if it can be linked to specific time periods and locations.

This could be the last Y-DNA test anyone needs. Particularly if Y amplification can be done with spit samples instead of whole blood or tissue samples. May bring some hope for more Ancient Y DNA tests.

R.Rocca
05-14-2013, 12:13 PM
I added the first non-L2 to the list...



Kit No.MDKAU152 Grouping


125963Jonas Eaton, b. 1637, Staple, Canterbury, EnglandL2+ Z49- Z367-


E11688Portonarius De Portonariis, Monteveglio, Bologna, ItalyL2+ Z49- Z367-


37207Johannes Crauss b. 4 Nov 1751, Ronshausen, Hesse, GermanyL2+ (Z49 and Z367 not tested)


N90341Pietro Rocca, b. 1559, Agira, Sicily, ItalyL2+ Z49- Z367-


10814Brantly Duncan b. 1821, SC, d. 1864, GAU152* (L2- Z36- Z56- DYS492=12)

haleaton
05-14-2013, 02:39 PM
Minor genealogy thing, but Jonas Eaton left Staple, England for Massachusetts in 1637 according to extant passenger record, but was born probably in Kent circa 1618, likely the son of Peter Eaton & Elizabeth Patterson Two male Eaton relatives also came to New World and several male descendants are close YSTR matches consistent with their New England paper trails, so it indicates which they are of family of the Dover, Kent, England Eatons at least back to 1540. There are other, dubious paper trails that go much farther so I just used 1637 as there was a specific paper record for it. One thing which is relevant to individual humans migrations even in those somewhat earlier days is that 1600s probate records for some these Eatons indicate that male children were sent to France from Kent to learn the language, so the English channel was not that much of a mobility barrier.

Webb
05-14-2013, 04:24 PM
Minor genealogy thing, but Jonas Eaton left Staple, England for Massachusetts in 1637 according to extant passenger record, but was born probably in Kent circa 1618, likely the son of Peter Eaton & Elizabeth Patterson Two male Eaton relatives also came to New World and several male descendants are close YSTR matches consistent with their New England paper trails, so it indicates which they are of family of the Dover, Kent, England Eatons at least back to 1540. There are other, dubious paper trails that go much farther so I just used 1637 as there was a specific paper record for it. One thing which is relevant to individual humans migrations even in those somewhat earlier days is that 1600s probate records for some these Eatons indicate that male children were sent to France from Kent to learn the language, so the English channel was not that much of a mobility barrier.

Are these "Eatons" possibly related to the Eaton family of Corryell County, Texas? They moved from Illinois to Texas with the Parker family and formed the first Protestant Church in Texas while it was still part of Mexico. They helped form Fort Parker.

haleaton
05-14-2013, 04:55 PM
Are these "Eatons" possibly related to the Eaton family of Corryell County, Texas? They moved from Illinois to Texas with the Parker family and formed the first Protestant Church in Texas while it was still part of Mexico. They helped form Fort Parker. Probably not, though I could not find a Haplogroup test looking quickly. "Eaton" is a common name probably with several separate origins in the British Isles. Getting back to Full Genomes data since it should find most of the family SNPs as well as Y STRs it has the potential to really aid more recent genealogy in addition to population studies.

warwick
05-16-2013, 04:49 PM
Initially it will not be that hard to manage. We will be looking at the listing of unique SNPs identified in the data. Comparison of the unique SNPs between individuals will help in positioning them. Some of the new SNPs will be upstream of U152. Those should be picked off by comparison to the results we have coming in from the U106 region. Similarly SNPs apparently upstream of U106 will be compared to the haplogroup G results to drop any new ones into specific regions up or downstream of G.

A diff comparison within Excel similar to Adriano's 23andMe spreadsheet will be the easiest way to track results. Using Excel to manage the full annotated list of y-SNPs from the data is not an unreasonable expectation.

Longer term the raw data will need to be mined in order to evaluate the lower quality, and lower coverage, SNP calls present in the data. We know what was reliably mined from the 1K genomes data. it will just take a lot longer to parse through more sequence present in the 50x data results.

With the 50x coverage the ole "number of generations/snp" discussion will rise again but we will have some very solid data available to guide that discussion.

Wayne
R-Z319+, CTS2509+ , L188+ phase II 50x beta sample.

We'll have a database to handle this though people will of course set-up their own analyses of their raw data as well, I'm sure.

emmental
05-19-2013, 08:30 PM
I just posted on the Z36 thread that I ordered the Full Y-Genome Test and thought I should post here also. Kit 204013 U152>Z36 (Z54- Z143- CTS188- L671-)

R.Rocca
05-19-2013, 09:13 PM
The updated list...



Kit No.MDKAU152 GroupingPhase


125963Jonas Eaton, b. 1637, Staple, Canterbury, EnglandL2+ Z49- Z367-Phase III


E11688Portonarius De Portonariis, Monteveglio, Bologna, ItalyL2+ Z49- Z367-Phase III


37207Johannes Crauss b. 4 Nov 1751, Ronshausen, Hesse, GermanyL2+ (Z49 and Z367 not tested)Phase III


N90341Pietro Rocca, b. 1559, Agira, Sicily, ItalyL2+ Z49- Z367-Phase III


10814Brantly Duncan b. 1821, SC, d. 1864, GAU152* (L2- Z36- Z56- DYS492=12)Phase III


204013Jacob Musselman b c1698, to Bucks Co, PA c1724 (Switzerland)Z36+ Z54- Z143- CTS188- L671-???

Belgae
05-30-2013, 05:01 PM
I selected Full Genomes to sequence my Y chromosome :)
Will keep you informed.

https://www.facebook.com/FullGenomes?fref=ts

R.Rocca
05-30-2013, 05:38 PM
I selected Full Genomes to sequence my Y chromosome :)
Will keep you informed.

https://www.facebook.com/FullGenomes?fref=ts

Excellent. I know they are almost identical in STR values, but which FTDNA member is being tested, 195362 or 261198?

Belgae
05-30-2013, 05:53 PM
195362, kit will be sent soon to the Netherlands

R.Rocca
05-30-2013, 06:42 PM
The updated list...



Kit No.MDKAU152 GroupingPhase


125963Jonas Eaton, b. 1637, Staple, Canterbury, EnglandL2+ Z49- Z367-Phase III


E11688Portonarius De Portonariis, Monteveglio, Bologna, ItalyL2+ Z49- Z367-Phase III


37207Johannes Crauss b. 4 Nov 1751, Ronshausen, Hesse, GermanyL2+ (Z49 and Z367 not tested)Phase III


N90341Pietro Rocca, b. 1559, Agira, Sicily, ItalyL2+ Z49- Z367-Phase III


10814Brantly Duncan b. 1821, SC, d. 1864, GAU152* (L2- Z36- Z56- DYS492=12)Phase III


204013Jacob Musselman b c1698, to Bucks Co, PA c1724 (Switzerland)Z36+ Z54- Z143- CTS188- L671-???


195362Theodricus de Rocourt ±1550-1583, Liège-HasseltZ36+ Z54- Z143- CTS188- L671-???

emmental
05-30-2013, 08:55 PM
That's great news!! Another Z36!!

emmental
06-22-2013, 02:52 AM
Does anyone know if any Phase III results for U152 have come back yet? Or when they are expected?

I returned my (Early bird) kit 4 weeks ago and it still seems to be in limbo and hasn't been sent to the lab yet.

Acque agitate
06-22-2013, 08:25 AM
Does anyone know if any Phase III results for U152 have come back yet? Or when they are expected?

I returned my (Early bird) kit 4 weeks ago and it still seems to be in limbo and hasn't been sent to the lab yet.

Ciao Emmental,
I am Portonarius from Monteveglio (E11688 in FTDNA), L2 + Z49-Z367-,
I ordered the test April 3, 2013 and I am part of Phase III.
My sample arrived in Full Genomes April 13, 2013 and it was shipped to the laboratory in Hong Kong with other samples May 3, 2013.
Last week I asked about the status of the order at Full Genomes.
They responded very quickly: they have informed me that the Hong Kong laboratory is delayed and the results will come probably by the end of July 2013 (delay of 2 weeks).

Solothurn
06-22-2013, 09:51 AM
Are all the phase III results due in together?

haleaton
06-29-2013, 06:32 AM
Are all the phase III results due in together?

Jonas Eaton descendant here, R-U152-L2*. My sample also arrived at FullGenomes on April 13 as Portonarius and I think myself & Rocca L2* are in same batch. I don't know about the others on Rich's list. This project is a Beta so I am sure they are working things out in terms of analyses. Initially I thought we would just get the bam files, but they seem to be providing all the SNPs that differ from the reference sequence as well as a set of STRs. I do not know if they are doing a comparison against the 1K Genomes U152's but hopefully that will happen with Rich and others help.

It will be an interesting advance as SNPs will be defined and a large series of STRs defined but probably not be transferable to FTDNA which we do rely on currently for a lot of things like YSEARCH for example or all the DNA groups they sponsor. So it will be interesting if FTDNA gets out of the single SNP testing business which they repeat the Sanger sequencing until they get a result as in Deep Clade or if they develop there own product of Y-sequencing at similar prices.

R.Rocca
06-29-2013, 12:02 PM
Jonas Eaton descendant here, R-U152-L2*. My sample also arrived at FullGenomes on April 13 as Portonarius and I think myself & Rocca L2* are in same batch. I don't know about the others on Rich's list. This project is a Beta so I am sure they are working things out in terms of analyses. Initially I thought we would just get the bam files, but they seem to be providing all the SNPs that differ from the reference sequence as well as a set of STRs. I do not know if they are doing a comparison against the 1K Genomes U152's but hopefully that will happen with Rich and others help.

It will be an interesting advance as SNPs will be defined and a large series of STRs defined but probably not be transferable to FTDNA which we do rely on currently for a lot of things like YSEARCH for example or all the DNA groups they sponsor. So it will be interesting if FTDNA gets out of the single SNP testing business which they repeat the Sanger sequencing until they get a result as in Deep Clade or if they develop there own product of Y-sequencing at similar prices.

Hal, the initial timeline of 8 weeks will be the first week of July, but I was told that it is delayed for a few weeks. For those that can get me the BAM data, I can certainly run it against the datasets I have access to. It should be very interesting.

Belgae
07-01-2013, 10:44 PM
Hal, the initial timeline of 8 weeks will be the first week of July, but I was told that it is delayed for a few weeks. For those that can get me the BAM data, I can certainly run it against the datasets I have access to. It should be very interesting.

Of course Richard, I will give you access to my BAM data as soon as available, enabling you to discover novel downstream Z36 SNPs. We are entering an exciting novel DNA genealogy period, earlier than I anticipated about a year ago :)

emmental
07-02-2013, 01:38 AM
Of course Richard, I will give you access to my BAM data as soon as available, enabling you to discover novel downstream Z36 SNPs. We are entering an exciting novel DNA genealogy period, earlier than I anticipated about a year ago :)

Richard, I will also send you my BAM data.

Hallo Kees!

GailT
07-02-2013, 02:45 AM
My kit for R1b-L2, Kit no. 37207 Johannes Crauss was sent to Justin April 23, so with luck it might be included in the same batch as some of the others. I'll also share the BAM data.

Gail

haleaton
07-02-2013, 03:06 AM
Oh I plan to share my L2* data with Richard, just don't know if it is best to just e-mail a USB or find and pay for service to be able to upload it. Also I don't know if FullGenomes will release data only after they do their analysis.

Belgae
07-02-2013, 04:47 PM
Hallo Kees!

Hi Jim, we keep on hopping between all these social media :)

R.Rocca
07-02-2013, 11:50 PM
All BAM files will be welcomed. I put the list of participants here: https://docs.google.com/spreadsheet/ccc?key=0AgHBsIq9ZUahdFJ4MUdicTVKUmJvSmFsVTFOa2RPX 3c&usp=sharing

Mikewww
07-04-2013, 02:28 AM
Hi Jim, we keep on hopping between all these social media :)

Please stay on here. It's a nice format for showing different types of data (i.e. charts, graphics, etc.) and things are nicely subdivided so people can find their own niche of threads to work with.

I think Facebook and some of the others are good for catching people, as in fishing, but this is better for in-depth discussions and we have some great administrators (not me, I'm just a moderator) that have set this up and are actively engaged.

Belgae
07-09-2013, 11:45 PM
Please stay on here. It's a nice format for showing different types of data (i.e. charts, graphics, etc.) and things are nicely subdivided so people can find their own niche of threads to work with.

I think Facebook and some of the others are good for catching people, as in fishing, but this is better for in-depth discussions and we have some great administrators (not me, I'm just a moderator) that have set this up and are actively engaged.

I fully agree on your social media analyses. During the 2,5 yrs I am active in DNA genealogy, I moved twice to a novel forum.. I hope to stay here for a longer period to discuss in depth topics such as our full Y genome analysis.

Bolgeris
07-29-2013, 07:59 AM
Ciao,
some news about U152 Full Y Genomes?

R.Rocca
09-14-2013, 02:44 PM
Another person has ordered the Full Genomes product. The U152+ kits are now as follows:



Kit No.MDKAU152 GroupingBatch


125963Jonas Eaton, b. 1637, Staple, Canterbury, EnglandL2+ Z49- Z367-Batch 3


E11688Portonarius De Portonariis, Monteveglio, Bologna, ItalyL2+ Z49- Z367-Batch 3


37207Johannes Crauss b. 4 Nov 1751, Ronshausen, Hesse, GermanyL2+ (Z49 and Z367 not tested)Batch 3


N90341Pietro Rocca, b. 1559, Agira, Sicily, ItalyL2+ Z49- Z367-Batch 3


N114738Charles William Fowler b. 1731 d. 1810, Wandborough, Swindon, EnglandL2+ Z49- Z367-???


10814Brantly Duncan b. 1821, SC, d. 1864, GAU152* (L2- Z36- Z56- DYS492=12)Batch 3


204013Jacob Musselman b c1698, to Bucks Co, PA c1724 (Switzerland)Z36+ Z54- Z143- CTS188- L671-???


195362Theodricus de Rocourt ±1550-1583, Liège-HasseltZ36+ Z54- Z143- CTS188- L671-???

haleaton
09-16-2013, 04:36 AM
About how many equivalent coverage U152 or downstream samples are publicly available from 1K Genomes, Personal Genomics, and other source? Is the public Y Genome database growing outside of Full Genomes? Keeping fingers crossed for Batch 3 to be ready in a few weeks and the BGI data will be good.

R.Rocca
09-16-2013, 12:22 PM
About how many equivalent coverage U152 or downstream samples are publicly available from 1K Genomes, Personal Genomics, and other source? Is the public Y Genome database growing outside of Full Genomes? Keeping fingers crossed for Batch 3 to be ready in a few weeks and the BGI data will be good.

128 - Sardinian Genome Project (that Francalacci used)
48 - 1000 Genomes Project
36 - Genome of the Netherlands (paper not yet released)
7 - Personal Genome Project

...and a couple of others that are not yet public.

Solothurn
11-08-2013, 03:55 PM
Are any U152 results in yet?

R.Rocca
11-08-2013, 08:11 PM
Are any U152 results in yet?

Unfortunately, not yet. Here is an update sent out today by Full Genomes:


We have sent the team to BGI to Hong Kong to investigate the continued slowdown in the processing of samples. BGI has been responsible for the delays, for the delays in processing the samples and for the choice in which samples are sequenced. We will have meetings with BGI in the next week in person by members of the team to press them to complete their work.

Also, we've gone further to recruit new suppliers at UCLA and elsewhere to speed the process. The UCLA beta-test is in-process to confirm UCLA as an alternative supplier and the team will be meeting with BGI in-person shortly to address the delays.

Solothurn
11-09-2013, 01:38 PM
Thanks Rich

Itai Perez has got his, so hopefully shouldn't be too long.

http://www.yourgeneticgenealogist.com/2013/11/first-look-at-full-genomes-y-sequencing.html


Unfortunately, not yet. Here is an update sent out today by Full Genomes:

R.Rocca
11-10-2013, 06:15 PM
A few updates:

Obviously the big news is the release of the Big-Y test by FTDNA. Since I don't want to maintain two spreadsheets, I renamed the "Full Genomes" tracking spreadsheet to "Full Y-Chromosome U152+ Samples". I already added two Big-Y kits: 83685 (Z56+) and N1950 (L2+Z49+Z192+).

I'm also going to add the singleton SNPs from academic full sequencing.

haleaton
11-16-2013, 10:17 PM
Are any U152 results in yet?

My FullGenomes Profile just changed to "Status: We sequenced your kit and are analyzing the results" consistent with statement about receiving remaining 46 BGI kits late last night. My impression was the analysis turn-around was greatly sped up. I look forward to monitoring this U152 thread.

Kwheaton
11-17-2013, 03:42 AM
Haleaton
Hooray, hooray hooray! The Wheaton group has ordered.....hopefully you and the rest will get the full results soon!

R.Rocca
11-17-2013, 12:52 PM
Congratulations to all! Please send me your data as soon as you get it as I was able to go a few steps further on the analysis on the DF103 sample. I fully expect that we will find some more DF103 samples in this run as it is likely the 3rd largest clade of L2.

Now onto a little bit of a "bummer" for me...my kit has once again failed the quality control test. Justin will send me multiple kits so we ensure enough DNA material this time and he will send it to the UCLA lab.

Kwheaton
11-17-2013, 01:07 PM
Congratulations to all! Please send me your data as soon as you get it as I was able to go a few steps further on the analysis on the DF103 sample. I fully expect that we will find some more DF103 samples in this run as it is likely the 3rd largest clade of L2.

Now onto a little bit of a "bummer" for me...my kit has once again failed the quality control test. Justin will send me multiple kits so we ensure enough DNA material this time and he will send it to the UCLA lab.

Rich,

So sorry to hear this. I guess that insures that all the other samples get your attention first. Nice for them but a REAL bummer for you who deserves to be at the top of the list. I have heard io others who failed multiple times but mostly with the spit kits. Seems the swab kits have a lower fail rate. Just thinking out loud: it will be interesting to compare the results that didn't pass QC to what hopefully you get from UCLA. Fingers crossed this happens quickly and passes QC. Good luck!

R.Rocca
11-17-2013, 01:49 PM
Rich,

So sorry to hear this. I guess that insures that all the other samples get your attention first. Nice for them but a REAL bummer for you who deserves to be at the top of the list. I have heard io others who failed multiple times but mostly with the spit kits. Seems the swab kits have a lower fail rate. Just thinking out loud: it will be interesting to compare the results that didn't pass QC to what hopefully you get from UCLA. Fingers crossed this happens quickly and passes QC. Good luck!

Yes, Justin is sending me both spit kits and swab kits. At this point, I'm willing to send him one of my kidneys :P

Kwheaton
11-17-2013, 01:54 PM
Rich,

My husband, who has a habit of brushing his teeth so hard he's wearing off the enamel---drew blood with his swab kit....which might be easier than sending a kidney! It didn't seem to adversely effect the results either :-)

Kwheaton
11-17-2013, 06:20 PM
Debbie Kennett has a new blog post that should be of interest to Full Genome testers. It looks like perhaps a nice place to compare cross platform. For example Full Y vs Big y vs Chromo2.0 etc.

So some of you may want to start a group there???? or maybe Full Y will have similar functionality down the road.....
http://cruwys.blogspot.co.uk/2013/11/the-y-chromosome-sequence.html

haleaton
11-17-2013, 07:14 PM
Congratulations to all! Please send me your data as soon as you get it as I was able to go a few steps further on the analysis on the DF103 sample. I fully expect that we will find some more DF103 samples in this run as it is likely the 3rd largest clade of L2.

Now onto a little bit of a "bummer" for me...my kit has once again failed the quality control test. Justin will send me multiple kits so we ensure enough DNA material this time and he will send it to the UCLA lab.

Sorry to hear that Rich, hope they put you at the front of the batch. I scrapped my teeth and tongue against my mouth before spitting when I heard about it the first time.

Has DF103 been tested before anywhere aside from the FullGenomes and other "academic project sequencing"? TBD on BIG Y, CHROMO2.

Are some of the other rarer or more recent L2 SNPs on the U152 and Subclades Phylogenetic Tree possibly below DF103, but I guess did now show up on Crauss sample?

Belgae
11-22-2013, 02:00 AM
Also from me Richard, sorry to read your sample did not pass, all will be fine in the end I am sure. Just an hour ago, my Full Y results have arrived! Its too late out here to dive into analizing them right now, and I hope you can offer some assistance in comparing with other incoming analyses :)

emmental
11-22-2013, 06:09 AM
My FGC results are in!!!!!!

23 private quality SNPs (FGC6436 thru FGC6458)

I also share FGC6411 thru FGC6435 with NA121144 who I assume is someone in 1k genomes - Rich, can you tell me more about NA12144?

Also, Rich and Kees, I forwarded my results.

Acque agitate
11-22-2013, 10:39 AM
My results came last night.

Kwheaton
11-22-2013, 05:27 PM
My results came last night.
I can hardly wait to hear the L2(* no longer) results.

I imagine you have all made them available to Rich and he is number crunching as I write this. I wonder what SNPs he can verify now?

haleaton
11-22-2013, 06:24 PM
Oh I got my FGC Y data yesterday and forwarded them to Rich, though getting the bam files to him make take a little longer to wait for space on FGC's google docs transfer page. I would guess this is not Rich's day job.

It may take some time and additional samples before these Private SNPs deserve their own asterisk. I may be R-L2* for awhile.

Had a couple of single SNP public matches with 1K Genomes non-U152 guys from Ho Chi Minh City and Sierra Leone but will assume independent point mutations.

Also got e-mail this morning on my BritainsDNA though when I logged on for Y-DNA, which is all I ordered, it had "Results need further sequencing - we will contact you when ready." I don't know if they are really doing actual further sequencing from the chip test, though Dr. Wilson may, or just repeating something. I don't know if you can call single snp chip tests "sequencing." From the recent list of BDNA chip snps neither U152 or L2 is tested specifically, though maybe it is inferred as some known downstream snps are tested.

If I remember L2 was accidentally dropped from 23andMe V3, though V2 did. Hope they include it on their new chip.

It will be interesting for me to look at bam data, though I may finally have to learn to use samtools. FTDNA claims Arpeggi provided some improved data analysis capability, so we will see in February.

Sorry I wandered of topic as this thread is for U152 Full Genomes Corp data. And I should say I am very pleased with what I have received and I have only scratched the surface.

MitchellSince1893
11-22-2013, 09:03 PM
FYI
I tested with 23&me v3 and was identified as L2.

haleaton
11-22-2013, 09:49 PM
FYI
I tested with 23&me v3 and was identified as L2. My error. Tested also tested with V2+V3 positive for L2 or rs2566671. It may have been going from V1 to V2 or just a brain freeze on my part. There was a great spreadsheet with the differences between V1, V2, V3 differences but I cannot find it at the moment. I could also be wrong about not being BritainsDNA though I checked the multiple names for U152 and L2.

Bolgeris
11-22-2013, 10:21 PM
My error. Tested also tested with V2+V3 positive for L2 or rs2566671. It may have been going from V1 to V2 or just a brain freeze on my part. There was a great spreadsheet with the differences between V1, V2, V3 differences but I cannot find it at the moment. I could also be wrong about not being BritainsDNA though I checked the multiple names for U152 and L2.

Years ago with 23andme ... identified L2 and L20..
i remember L20 was identified when me and Dr Faux compared . 23andme results..
L2 id. was similar..
i remember in the year 2008.. may be,,
ciao.

Acque agitate
11-22-2013, 11:33 PM
My results:

Private SNPs (99%) 26
Private SNPs * (95%) 24
Private Indels (99%) 2
Private Indels (95%) 1

Total high quality 53

These are listed as FGC5330 to FGC5681, + PF7600

I do not own the 4 new SNPs of Crauss: 13685121 (C / T), 9020396 (TAGA / -) 21885515 (C / T), 2872259 (A / G).

I sent my data to Rich who is currently also comparing them with its database and those of Haleaton.
I look forward to his work.

haleaton
11-23-2013, 01:54 AM
My U152-R-L2* result numbers representing Jonas Eaton of Kent, England.

Private SNPs (99%) 21
Private SNPs * (95%) 17
Private Indels (99%) 4
Private Indels * (95%) 1

Total high quality Private 44 (+2 Single Reference Sample Matches)
Total lower quality Private 255

These high quality snp/indels are listed as FGC288+ to FG329+, M6559+ (aka rs112201686)
The low quality Private were not given FGC numbers, just b37 positions

I had many public matches with large groups of reference samples as expected, but also had two single SNP matches with 1K Genomes reference samples which led to the defining of two FGC snps, though they are far from U152.

FGC5286+ HG03432 E1b1a1a1f* according to YFULL, sample from Sierra Leone
FGC5287+ HG01840 O2a1a according to YFULL, sample from Vietnam

Though independent mutations, they would also be high quality Private SNPs for me too which brings my total to 46.

Myself, I did not note seeing the 4 new Crauss SNPs in my data, though I will defer to Rich's detailed study of our samples. Perhaps there is more in the lower quality matches or a detaled look at the bam files which have not been provided yet, but soon.

One thing I did/do not understand was about the quality issues of NGS sequencing limiting SNP discovery at this current state-of-the art, though I am very happy and excited about my FGC
results. I am sure there is a lot more to find out.

Belgae
11-23-2013, 12:54 PM
And here is a Full Y summary from the Dutch Z36 delegation, with roots in the Walloon region, Liege. (FTDNA: 195362).

Private SNPs (99%) = 28
Private SNPs* (95%) = 27
Private Indels (99%) = 2
Private Indels* (95%) = 3

This sums to a total of high quality markers of 60

I do not see any matches other than at the Z36 level yet. There are however a number of Z36 matches (NA .., HG ... numbers), I am not familiar with. And indeed, I also hope Rich can enlighten us further with additional full genome U152 insights or analysis.

R.Rocca
11-23-2013, 01:11 PM
All, I have analyzed the previously U152* Full Genomes data (FTDNA kit no. 10814). Here is what I sent to the kit owner:



Congratulations, you have shed your U152* star. Your results are very interesting. You belong to the following group:

U152+ PF6658+ Z193+

The PF6658 group is the parent group of Z192 and Z194 which you were negative for. PF6658 is not tested for on the Geno 2.0 chip. It was first observed in 1000 Genomes Project samples primarily from Tuscany. However, the peak of this group seems to be In Sardinia where it makes up 58.6% of all U152+ males.

The Z193+ result might be surprising to you as you show up as negative for it as per Geno 2.0. That is because Z193 seems to be heterozygous. What this means is that it displays both ancestral and derived results in a single sample. In yours, there were 305 reads of the derived (positive) value of "T" and 70 reads of ancestral (negative) value of "G". A little problematic, but is not all that important right now as PF6658 shares the same branch with Z193.

Interestingly, the only other two PF6658+ samples in our FTDNA U152 project are from Ireland, but they are positive for downstream markers Z192 and Z194 which you are negative for.

In addition to the comparison that FG did with the 1KG samples, I compared them to several other databases (Francalacci, Genome of the Netherlands, a private UK dataset. I've started on the other samples that have sent me their data and will report back later today and tomorrow.

Kwheaton
11-23-2013, 02:25 PM
All, I have analyzed the previously U152* Full Genomes data (FTDNA kit no. 10814). Here is what I sent to the kit owner:



In addition to the comparison that FG did with the 1KG samples, I compared them to several other databases (Francalacci, Genome of the Netherlands, a private UK dataset. I've started on the other samples that have sent me their data and will report back later today and tomorrow.

I think we all want to publically acknowledge Richard Rocca for his incredible expertise and dogged persitence in getting us all sorted and this is while he has had the hardest time getting his samples to pass quality control.

Thank you Rich! :thumb::thumb::thumb:

R.Rocca
11-23-2013, 02:33 PM
I think we all want to publically acknowledge Richard Rocca for his incredible expertise and dogged persitence in getting us all sorted and this is while he has had the hardest time getting his samples to pass quality control.

Thank you Rich! :thumb::thumb::thumb:

Thanks, my personal testing is starting to resemble something out of the "Book of Job". Full Genomes has been great and they've sent me two vials this time in case the first does not have enough DNA material. I have no doubt third time will be a charm.

R.Rocca
11-23-2013, 03:26 PM
Here are the results for U152+Z36* kit no. 204013 (Musselman from Switzerland). He shares the following SNPs with 1000 Genomes sample NA12144 (American residing in Utah):

FGC6412+
FGC6413+
FGC6414+
FGC6415+
FGC6416+
FGC6417+
FGC6418+
FGC6419+
FGC6420+
FGC6421+
FGC6422+
FGC6423+
FGC6424+
FGC6425+
FGC6426+
FGC6427+
FGC6428+
FGC6429+
FGC6430+
FGC6431+
FGC6433+
FGC6434+
FGC6435+
FGC6460+ (Deletion)
5920868 A>C (SNP un-named)
18090795 G>A (SNP un-named)
3453526 A>G (SNP un-named)

Belgae
11-23-2013, 04:51 PM
Here are the results for U152+Z36* kit no. 204013 (Musselman from Switzerland). He shares the following SNPs with 1000 Genomes sample NA12144 (American residing in Utah)

These are a lot of SNPs in common... Should these independent SNPs are all downstream Z36 (?), I would presume a medieval relationship when using a SNP mutation rate of 10(-8) per base per generation (http://biochem218.stanford.edu/16SNPs.pdf). This equals about one novel SNP per 100 Mbp per generation. Since FGC sequenced about 25 Mbp of the Y, and presuming simple statistics, each novel SNP represents about four generations.

Thus these are 4* about 27 = 108 generations in common = 108 times 30 years is about 3250 years after SNP Z36 has occured. According to previous STR calculations, Z36 is about 4000 years old, so a common ancestor would be at about 4000 - 3250 = 750 years ago = 1250 AD +/- x years of deviation ...

haleaton
11-23-2013, 05:27 PM
FTDNA 111 Y-STRS versus FGC Reports Comparison for Jonas Eaton Sample - Quick Look

76 FGC STRs matched FTDNA, though two were low confidence
4 FGC STRs did not match FTDNA, but all were noted as low confidence
24 FTDNA STRS were not available in FGC reports to the best I could determine
7 FTDNA STRS were available, but were not reported or no reads in my sample
----
111

Currently the web site advertises 300 STRs, though my superficial look is that half that may be more reasonable though there may be currently undefined by name STRs.

I must say I am really impressed with the FGC reports once I delved into them to the extent I am able to comprehend them. I refreshing change from the "here is your data" with little else.

emmental
11-23-2013, 07:14 PM
These are a lot of SNPs in common... Should these independent SNPs are all downstream Z36 (?), I would presume a medieval relationship when using a SNP mutation rate of 10(-8) per base per generation (http://biochem218.stanford.edu/16SNPs.pdf). This equals about one novel SNP per 100 Mbp per generation. Since FGC sequenced about 25 Mbp of the Y, and presuming simple statistics, each novel SNP represents about four generations.

Thus these are 4* about 27 = 108 generations in common = 108 times 30 years is about 3250 years after SNP Z36 has occured. According to previous STR calculations, Z36 is about 4000 years old, so a common ancestor would be at about 4000 - 3250 = 750 years ago = 1250 AD +/- x years of deviation ...


NA12144 (American residing in Utah) and I share about half of the 52 new quality SNPs and Indels found in my results (FGC6410 through 6461). Therefore we should be related at about half the distance between the birth of Z36 and now.

I sure wish this guy wasn't anonymous.

haleaton
11-23-2013, 10:08 PM
NA12144 (American residing in Utah) and I share about half of the 52 new quality SNPs and Indels found in my results (FGC6410 through 6461). Therefore we should be related at about half the distance between the birth of Z36 and now.

I sure wish this guy wasn't anonymous.

It would be possible, but unethical, to track this Caucasian Utah Mormon family down who so generously gave to advance science. However another Utah Z36+ might be found.

NA10846 1334-01 male father
NA10847 1334-02 female mother
NA12144 1334-10 male pat grandfather
NA12145 1334-11 female pat grandmother
NA12146 1334-12 male mat grandfather
NA12239 1334-13 female mat grandmother

Belgae
11-24-2013, 12:36 AM
NA12144 (American residing in Utah) and I share about half of the 52 new quality SNPs and Indels found in my results (FGC6410 through 6461). Therefore we should be related at about half the distance between the birth of Z36 and now.

I sure wish this guy wasn't anonymous.


Hi Jim,

That's an interesting alternative way of calculating. So, then we would end up at about 0 AD, presuming Z36 to be orginating at about 2000 BC. Of course, a major flaw of my calculations might be that there are more SNPs in common, which are now at a lower sequencing quality.

Hope you will retrieve more information on your 'close' cousin, as also provided by haleaton.

emmental
11-24-2013, 01:08 AM
Hi Jim,

That's an interesting alternative way of calculating. So, then we would end up at about 0 AD, presuming Z36 to be orginating at about 2000 BC. Of course, a major flaw of my calculations might be that there are more SNPs in common which are now at a lower sequencing quality of below the detection limit.

Hope you will retrieve more information on your 'close' cousin, as also provided by haleaton.

Hi Kees,

Or, Z36 might be older than 4000 bp. I have 52 SNPs below Z36 and you have 60. I've seen posts on this forum and elsewhere suggesting that there is a new SNP, on average, every three generations, or 90 years. If you take our average of 56 SNPs X 90 years, the approximate age of Z36 would be 5040 bp. I'm certainly not suggesting this is true - just throwing it out for discussion.

It looks like we are descended from different sons or grandsons of Mr. Z36. We don't seem to have anything common under Z36.

My 'close' cousin may have tested closer, but you and I have a stronger connection. We have been friends since we were the first two Z36 positives at FTDNA (Aug, 2011), and here we are the first two Z36 tested at FGC!

I'm working on a comparative spreadsheet. I'll email you soon.

Jim

Belgae
11-24-2013, 01:55 AM
It looks like we are descended from different sons or grandsons of Mr. Z36. We don't seem to have anything common under Z36. We have been friends since we were the first two Z36 positives at FTDNA (Aug, 2011), and here we are the first two Z36 tested at FGC! I'm working on a comparative spreadsheet. I'll email you soon.
Jim

Hi Jim,
Thanks for your posting! Yep, we are leading the Z36 family again, probably we share some epigenetic factors also:). Interesting theory: indeed should we not share any SNPs below Z36, then we would have branched early after mr "Z36" (we should give him a name). Each son or grandson in a different valley or novel site at the river? I noticed at the FTDNA-U152 page that new BigY/FGC Z36 orders are placed, so the detailed-Y family will soon grown again. I am very interested in receiving your spreadsheet, Jim.
Kees

emmental
11-24-2013, 08:42 PM
It would be possible, but unethical, to track this Caucasian Utah Mormon family down who so generously gave to advance science. However another Utah Z36+ might be found.


Yeah, I'm not going to go snooping around where I'm not supposed to be. But, I did check out the peopling of Utah and there were a lot of Swiss (Mormon) immigrants and settlements in the mid 19th Century. My male line goes back to Switzerland, so that makes sense.

haleaton
11-25-2013, 04:04 AM
I am still R-L2* in the strict sense though now with 45 (I miscounted) Private high quality SNPs & InDels shown in table below.
Rich had no luck matching my sample up to other L2+ kits, including Stefano's and Crauss--but a few more are coming and then a flood of Big Y's next year.

My BritainsDNA was held up for "further sequencing" but I offered them my private SNPs if they would provide any S definitions for them--oops I gave them away below.

Hopefully a Eaton/Whitney STR Surname project kit that is 10-24 generations removed from me will also be testing to identify a few of the more recent ones.

I thought about taking up the offer of Thomas Krahn with his new company's "Wish a SNP" having primers defined and available for all 45 for $1 apiece, though I don't know who would actually pay the $35 to actually test until they match another L2.

Look forward to Wheaton and Rocca Full Genomes data in the by and by. The value I got so far from FGC was tremendous. The reports are fantastic filled with so much information mined from the bam files. I originally thought I was going to using samtools but Greg Magoon put an incredible amount of work into automated reports. The STR data was not the large number originally advertised but should be very useful once matches are found. The mtDNA matched my previous testing.

I would definitely recommend others consider testing with Full Genomes Corporation. They always said they were a beta, but they were far better than other products that really were in the early stages but did not openly say so.

FTDNA Kit #125963, Full Genomes Corp # FG1059-A, L2+ Z49- Z367-, Jonas Eaton, b. c. 1618, Kent England, arrived MA 1637
Private SNPs Found in FGC Sequencing Batch 3 (2013)


SNP/InDel rsID Rel b37 position Reference Sample Match
FGC5286+ 6827507 G A HG03432
FGC5287+ 14660607 T C HG01840
FGC5288+ * 3088816 T G
FGC5289+ * 3463656 C T
FGC5290+ * 3915368 C T
FGC5291+ * 4200262 A G
FGC5292+ * 4608804 G A
FGC5293+ * 5112364 C T
FGC5294+ * 5547084 G T
FGC5295+ * 6403864 T A
FGC5296+ 6985619 G A
FGC5297+ 7015529 C T
FGC5298+ 7022935 A G
FGC5299+ 7115859 T C
FGC5300+ * 7832161 T C
FGC5301+ * 7899592 C T
FGC5302+ * 7969590 T C
FGC5303+ * 8320779 A C
FGC5304+ * 9156208 T C
FGC5305+ * 13329890 A G
FGC5306+ 14420067 T C
FGC5307+ 14675249 G T
FGC5308+ 14865182 A C
FGC5309+ 15909364 T C
FGC5310+ 15931829 T C
FGC5311+ 16267644 C G
FGC5312+ 16338151 C T
FGC5313+ 17008323 A C
FGC5314+ 17557325 T G
FGC5315+ 17794885 G A
FGC5316+ 18825164 G A
FGC5317+ 18964422 T C
FGC5318+ 21260230 T C
FGC5319+ 21382958 T G
FGC5320+ 21409985 G A
FGC5321+ 21654553 A G
FGC5322+ * 22294291 C T
FGC5323+ * 22489310 G T
FGC5324+ 23051944 A G
FGC5325+ 7390278 CG C
FGC5326+ * 9971546 CT C
FGC5327+ 17052814 TC T
FGC5328+ 18919932 A ACT
FGC5329+ 22539817 T TTA
M6559+ rs112201686 * 7681861 A G

Rel = no flag: over 99% likely genuine; *: over 95% likely genuine

Kwheaton
11-25-2013, 05:25 AM
Hal,
I hope our Wheaton sample will provide a match or two on your SNP list. Sure would be nice to have a few more L2* testing, but as you say maybe you'll get some Big Y or even Chromo 2.0 matches. At least you have the lay of the land. Interesting that no other matches were found among other datasets. It may be like I warned our group that we are rare enough no one else is going to find this stuff for us. The painstaking process of finding likely test subjects and getting them tested.

Solothurn
11-25-2013, 02:50 PM
Rich

In your opinion will PF6658+ Z193+ be on the BIGY search and then maybe offered as SNPs at FTDNA?

adv(thanks)ance :)


All, I have analyzed the previously U152* Full Genomes data (FTDNA kit no. 10814). Congratulations, you have shed your U152* star. Your results are very interesting. You belong to the following group:

U152+ PF6658+ Z193+

The PF6658 group is the parent group of Z192 and Z194 which you were negative for. PF6658 is not tested for on the Geno 2.0 chip. It was first observed in 1000 Genomes Project samples primarily from Tuscany. However, the peak of this group seems to be In Sardinia where it makes up 58.6% of all U152+ males.

R.Rocca
11-26-2013, 07:48 PM
While taking a second look at some of this past week's data, I noticed that L2+ Z49- Z367- kit no. E11688 from Bologna, Italy is positive for PF7600. Dr. Francalacci has confirmed its presence in two L2+ Z49- Z367- samples from Sardinia.

haleaton
11-26-2013, 08:56 PM
While taking a second look at some of this past week's data, I noticed that L2+ Z49- Z367- kit no. E11688 from Bologna, Italy is positive for PF7600. Dr. Francalacci has confirmed its presence in two L2+ Z49- Z367- samples from Sardinia.

PF7600 was also in GENO 2.0 of course. For awhile the FTDNA Group group project was collecting and summarizing GENO 2.0 Results if they were uploaded to FTDNA, but then deferred to http://itai.perez.free.fr/GenoCompare/ when that became available though not many have submitted data, including me. I did not see any PF7600+ in the summary of the samples they have. Perhaps there is a GENO 2.0 out there that is PF7600+ that is only in the vaults of Genographic Project.

R.Rocca
11-26-2013, 10:07 PM
PF7600 was also in GENO 2.0 of course. For awhile the FTDNA Group group project was collecting and summarizing GENO 2.0 Results if they were uploaded to FTDNA, but then deferred to http://itai.perez.free.fr/GenoCompare/ when that became available though not many have submitted data, including me. I did not see any PF7600+ in the summary of the samples they have. Perhaps there is a GENO 2.0 out there that is PF7600+ that is only in the vaults of Genographic Project.

There is one sample in the R1a project, so while it is a little problematic that this SNP appears in multiple haplogroups, I don't think it is that much of an issue given how many Geno 2 results are available. It could also be that PF7600 is a few sublcades down from L2 and one or several of E11688's private SNPs are intermediate.

Acque agitate
11-26-2013, 10:22 PM
First, Richard, thank you very much.
To the readers of the forum I specify these things:
1) Richard has confirmed to me that Francalacci not fully mapped the area covered by Full Genomes. The analysis that I have done leads me to conclude that at least 10/15 of my private snp has not been mapped by Francalacci and then some of these snp may be shared by two samples of Sardinia PF7600+.
2) PF7600 was also found in a sample: N114137 (Jakob Venzke: R1a1a1g; http://www.familytreedna.com/public/vikingydna/default.aspx?section=ysnp link). I conclude that PF7600 is tested by FTDNA (Geno 2.0);

Solothurn
11-27-2013, 12:16 PM
I have emailed Genographic and FTDNA:

"I tested negative to an SNP: Z193. Another 'tester' surname Duncan (FTDNA kit 10814) also tested negative to Z193. He now has a Full Genomes data result ($1,250) and is positive for Z193.
Does this mean my Z193- result could also be wrong?"

If the Colangelo L159.2+/- fiasco is anything to go by I don't expect a 'positive' reply >:(

R.Rocca
11-27-2013, 01:47 PM
I have emailed Genographic and FTDNA:

"I tested negative to an SNP: Z193. Another 'tester' surname Duncan (FTDNA kit 10814) also tested negative to Z193. He now has a Full Genomes data result ($1,250) and is positive for Z193.
Does this mean my Z193- result could also be wrong?"

If the Colangelo L159.2+/- fiasco is anything to go by I don't expect a 'positive' reply >:(

Just remember what I wrote in my earlier post regarding Z193:


The Z193+ result might be surprising to you as you show up as negative for it as per Geno 2.0. That is because Z193 seems to be heterozygous. What this means is that it displays both ancestral and derived results in a single sample. In yours, there were 305 reads of the derived (positive) value of "T" and 70 reads of ancestral (negative) value of "G". A little problematic, but is not all that important right now as PF6658 shares the same branch with Z193.

It could be that with Sanger testing this SNP shows up as negative since with NGS it shows up as heterozygous.

Solothurn
11-27-2013, 02:42 PM
Thanks Rich

So in NGS it shows as heterozygous, so could be c190+ and c190- (derived, ancestral)?

In Full Y-Genomes is it still shown as heterozygous? Or are they taking the 305+ vs 70- and therefore gives a positive result? :P




Just remember what I wrote in my earlier post regarding Z193:



It could be that with Sanger testing this SNP shows up as negative since with NGS it shows up as heterozygous.

R.Rocca
11-27-2013, 03:25 PM
Thanks Rich

So in NGS it shows as heterozygous, so could be c190+ and c190- (derived, ancestral)?

In Full Y-Genomes is it still shown as heterozygous? Or are they taking the 305+ vs 70- and therefore gives a positive result? :P

It looks like FG has a threshold based on the value of "Heterozygous fraction". I'm not sure what their value needs to be to reach a consensus derived call, but clearly Z193 met that criteria with 80%+ derived calls.

haleaton
11-27-2013, 05:37 PM
In my FGC data was a Private SNP that already had a definition and two labels one from a later M'series which used to mean the University of Arizona lab and the other from NCBI dbSNP database



FTDNA Kit #125963, Full Genomes Corp # FG1059-A, L2+ Z49- Z367-, Jonas Eaton, b. c. 1618, Kent England, arrived MA 1637
Private SNPs Found in FGC Sequencing Batch 3 (2013)

SNP/InDel rsID Rel b37 position Reference Sample Match
M6559+ rs112201686 * 7681861 A G

Rel = no flag: over 99% likely genuine; *: over 95% likely genuine

It is interesting which SNP labels FGC chose and which were chosen to omit. If they are omitted then they do not always appear on the any of the summary listings so we would have to go to bam files.

My understanding is that for a SNP to have a definition means that it has been found in another sample, usually human or primate. Some studies also required at least two relevant genealogically distant samples have the SNP before it was reported at all, though others reported as in WTY were often Private singletons.

I could not find where my new Private SNP M6559 was defined, but its equivalent rs112201686 was able to lookup in the NCBI database http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=112201686 which gave the source which was included in a paper with even a photo of Mr. KB1 http://genetics.med.harvard.edu/reich/Reich_Lab/Publications_files/2010_Nature_Priya_Nick_Bushman_Paper.pdf.

Bolgeris
11-29-2013, 09:12 PM
My Britains DNA results arrived.
i was L20+ for geno 2.0..
now i am only S255 (S255/Z367) ... L2/S139 .. why not also..L20/S144??????
Mah.......! B)

Your subtype is R1b-S255 (S255/Z367)
You do not carry the downstream S372 (????) or S368 (S368/Z34) markers. You may carry markers that further define your subtype, but do not yet appear on our tree. You will find these in your genetic signature.

R1b-S28 Your Genetic Signature

This is your Y chromosome genetic signature: a list of all the markers from the chromo2 chip for which you are positive, that is where you differ from Y chromosome Adam. A plus sign indicates that you carry the marker, or as geneticists say you are derived for that marker, e.g. S190+. Markers are named with a letter followed by the number of the marker. The letter is usually one of M, S or P: M is for markers, S is for SNP (the scientific name of the kind of marker being tested) and P is for polymorphism, another word for marker. Other prefixes include the initials of the discoverer (e.g. CTS or PF). If you do not carry the marker it is not listed in your signature, but can be found in the raw data file. In a few cases a marker might arise, for example, by the DNA letter A changing to C, then much later in time in someone with the C it changes back to an A again; this is called back-mutation. One such example is the marker S163: if you carry the ancestral A it is not shown in your signature. If you carry the C, it would be shown as S163(+) and if you carry the back-mutated A, it is shown as S163!. We can tell the back-mutations from the ancestral variants using the other markers you carry.
CTS10008+, CTS10149+, CTS11150+, CTS11226+, CTS11468+, CTS11575+, CTS11948+, CTS11991+, CTS12057+, CTS12633+, CTS12773+, CTS1738+, CTS2134+, CTS2254+, CTS2480+, CTS2569+, CTS2664+, CTS3229+, CTS3315+, CTS3316+, CTS3358+, CTS3654+, CTS3818+, CTS3844+, CTS4293+, CTS4437+, CTS4740+, CTS4944+, CTS5139(+), CTS5248+, CTS524+, CTS543+, CTS6058+, CTS6327+, CTS6376+, CTS6383+, CTS6445+, CTS7206+, CTS7301+, CTS7604+, CTS7659+, CTS7922+, CTS7941+, CTS8627+, CTS8728+, CTS9200+, CTS927+, CTS9556+, CTS9760+, F1794+, L1002+, L1013+, L1053+, L1084+, L1098+, L1105+, L1118+, L1123+, L1129+, L1130+, L1137+, L1143+, L1145+, L1150+, L1179+, L1220+, L132+, L1345+, L1350+, L1352+, L265+, L278+, L320+, L352+, L438+, L440+, L468+, L470+, L479+, L498+, L508+, L543+, L58+, L604+, L741+, L752+, L757+, L768+, L773+, L822+, L82+, L875+, L882+, L969+, M213+, M228+, M235+, M294+, M299+, M415+, M42+, M523+, M526+, M74+, P128+, P131+, P135+, P139+, P140+, P141+, P142+, P143+, P151+, P158+, P159+, P160+, P163+, P224+, P225+, P226+, P229+, P230+, P232+, P233+, P234+, P236+, P239+, P242+, P244+, P245+, P280+, P282+, P284+, P285+, P294+, P295+, P297+, P305+, P310+, PAGE081+, PAGE083+, PF1030+, PF1067+, PF1081+, PF1252+, PF1253+, PF1416+, PF1695+, PF1911+, PF256+, PF2590+, PF2592+, PF2615+, PF2617+, PF2619+, PF2621+, PF2622+, PF2624+, PF2626+, PF2629+, PF2651+, PF2653+, PF2655+, PF2658+, PF2660+, PF2677+, PF2679+, PF2683+, PF2684+, PF2685+, PF2688+, PF2690+, PF2700+, PF2702+, PF2704+, PF2709+, PF2716+, PF2718+, PF2722+, PF2734+, PF2736+, PF2737+, PF2739+, PF2742+, PF2747+, PF2748+, PF2760+, PF2762+, PF2775+, PF3495+, PF3500+, PF5459+, PF5461+, PF5480+, PF5495+, PF5857+, PF5861+, PF5865+, PF5869+, PF5870+, PF5872+, PF5873+, PF5885+, PF5887+, PF5893+, PF5898+, PF5908+, PF5912+, PF5914+, PF5917+, PF5918+, PF5923+, PF5927+, PF5936+, PF5940+, PF5941+, PF5945+, PF5949+, PF5953+, PF5957+, PF5958+, PF5964+, PF5966+, PF5977+, PF5980+, PF5981+, PF5982+, PF6016+, PF6040+, PF6047+, PF6055+, PF6056+, PF6063+, PF6065+, PF6079+, PF6082+, PF6114+, PF6115+, PF6116+, PF6129+, PF6136+, PF6143+, PF6145+, PF6242+, PF6246+, PF6249+, PF6258+, PF6263+, PF6265+, PF6267+, PF6269+, PF626+, PF6271+, PF6272+, PF6399+, PF6409+, PF6410+, PF6419+, PF6429+, PF6430+, PF6432+, PF6434+, PF6435+, PF643+, PF6443+, PF6451+, PF6463+, PF6467+, PF6469+, PF6471+, PF6475+, PF6481+, PF6484+, PF6487+, PF6495+, PF6497+, PF6506+, PF6507+, PF6524+, PF6528+, PF653+, PF6541+, PF679+, PF733+, PF744+, PF825+, PF834+, PF869+, PF948+, S10266+, S10738+, S11330+, S1159+, S11638+, S116+, S12547(+), S128+, S138+, S1572+, S16059+, S163(+), S19777+, S1984(+), S19862(+), S1+, S2003+, S2017+, S20246+, S20315+, S255+, S26361+, S26903+, S26911+, S27544+, S27668+, S2906+, S3023+, S349+, S3509+, S351+, S3826+, S3848+, S3856+, S3+, S4276+, S4888+, S492+, S4+, S5681+, S583+, S6378+, S6814+, S8235+, S8587+, S8620+, S8645+, S8649+, S8701+, S8705+, S8709+, S8714+, S8742+, S8751+, S8889+, S9041+, S9158+, S959+, SRY10831(+), V102+, V104+, V126+, V168+, V186+, V187+, V221+, V226+, V231+, V241+, V244+, V29+, V41+, V52+, V9+, YSC0167+, YSC0186+, YSC0203+, YSC0227+, YSC1297+, Z1244+

R.Rocca
11-29-2013, 10:07 PM
My Britains DNA results arrived.
i was L20+ for geno 2.0..
now i am only S255 (S255/Z367) ... L2/S139 .. why not also..L20/S144??????
Mah.......! B)

Your subtype is R1b-S255 (S255/Z367)
You do not carry the downstream S372 (????) or S368 (S368/Z34) markers. You may carry markers that further define your subtype, but do not yet appear on our tree. You will find these in your genetic signature.

R1b-S28 Your Genetic Signature

This is your Y chromosome genetic signature: a list of all the markers from the chromo2 chip for which you are positive, that is where you differ from Y chromosome Adam. A plus sign indicates that you carry the marker, or as geneticists say you are derived for that marker, e.g. S190+. Markers are named with a letter followed by the number of the marker. The letter is usually one of M, S or P: M is for markers, S is for SNP (the scientific name of the kind of marker being tested) and P is for polymorphism, another word for marker. Other prefixes include the initials of the discoverer (e.g. CTS or PF). If you do not carry the marker it is not listed in your signature, but can be found in the raw data file. In a few cases a marker might arise, for example, by the DNA letter A changing to C, then much later in time in someone with the C it changes back to an A again; this is called back-mutation. One such example is the marker S163: if you carry the ancestral A it is not shown in your signature. If you carry the C, it would be shown as S163(+) and if you carry the back-mutated A, it is shown as S163!. We can tell the back-mutations from the ancestral variants using the other markers you carry.
CTS10008+, CTS10149+, CTS11150+, CTS11226+, CTS11468+, CTS11575+, CTS11948+, CTS11991+, CTS12057+, CTS12633+, CTS12773+, CTS1738+, CTS2134+, CTS2254+, CTS2480+, CTS2569+, CTS2664+, CTS3229+, CTS3315+, CTS3316+, CTS3358+, CTS3654+, CTS3818+, CTS3844+, CTS4293+, CTS4437+, CTS4740+, CTS4944+, CTS5139(+), CTS5248+, CTS524+, CTS543+, CTS6058+, CTS6327+, CTS6376+, CTS6383+, CTS6445+, CTS7206+, CTS7301+, CTS7604+, CTS7659+, CTS7922+, CTS7941+, CTS8627+, CTS8728+, CTS9200+, CTS927+, CTS9556+, CTS9760+, F1794+, L1002+, L1013+, L1053+, L1084+, L1098+, L1105+, L1118+, L1123+, L1129+, L1130+, L1137+, L1143+, L1145+, L1150+, L1179+, L1220+, L132+, L1345+, L1350+, L1352+, L265+, L278+, L320+, L352+, L438+, L440+, L468+, L470+, L479+, L498+, L508+, L543+, L58+, L604+, L741+, L752+, L757+, L768+, L773+, L822+, L82+, L875+, L882+, L969+, M213+, M228+, M235+, M294+, M299+, M415+, M42+, M523+, M526+, M74+, P128+, P131+, P135+, P139+, P140+, P141+, P142+, P143+, P151+, P158+, P159+, P160+, P163+, P224+, P225+, P226+, P229+, P230+, P232+, P233+, P234+, P236+, P239+, P242+, P244+, P245+, P280+, P282+, P284+, P285+, P294+, P295+, P297+, P305+, P310+, PAGE081+, PAGE083+, PF1030+, PF1067+, PF1081+, PF1252+, PF1253+, PF1416+, PF1695+, PF1911+, PF256+, PF2590+, PF2592+, PF2615+, PF2617+, PF2619+, PF2621+, PF2622+, PF2624+, PF2626+, PF2629+, PF2651+, PF2653+, PF2655+, PF2658+, PF2660+, PF2677+, PF2679+, PF2683+, PF2684+, PF2685+, PF2688+, PF2690+, PF2700+, PF2702+, PF2704+, PF2709+, PF2716+, PF2718+, PF2722+, PF2734+, PF2736+, PF2737+, PF2739+, PF2742+, PF2747+, PF2748+, PF2760+, PF2762+, PF2775+, PF3495+, PF3500+, PF5459+, PF5461+, PF5480+, PF5495+, PF5857+, PF5861+, PF5865+, PF5869+, PF5870+, PF5872+, PF5873+, PF5885+, PF5887+, PF5893+, PF5898+, PF5908+, PF5912+, PF5914+, PF5917+, PF5918+, PF5923+, PF5927+, PF5936+, PF5940+, PF5941+, PF5945+, PF5949+, PF5953+, PF5957+, PF5958+, PF5964+, PF5966+, PF5977+, PF5980+, PF5981+, PF5982+, PF6016+, PF6040+, PF6047+, PF6055+, PF6056+, PF6063+, PF6065+, PF6079+, PF6082+, PF6114+, PF6115+, PF6116+, PF6129+, PF6136+, PF6143+, PF6145+, PF6242+, PF6246+, PF6249+, PF6258+, PF6263+, PF6265+, PF6267+, PF6269+, PF626+, PF6271+, PF6272+, PF6399+, PF6409+, PF6410+, PF6419+, PF6429+, PF6430+, PF6432+, PF6434+, PF6435+, PF643+, PF6443+, PF6451+, PF6463+, PF6467+, PF6469+, PF6471+, PF6475+, PF6481+, PF6484+, PF6487+, PF6495+, PF6497+, PF6506+, PF6507+, PF6524+, PF6528+, PF653+, PF6541+, PF679+, PF733+, PF744+, PF825+, PF834+, PF869+, PF948+, S10266+, S10738+, S11330+, S1159+, S11638+, S116+, S12547(+), S128+, S138+, S1572+, S16059+, S163(+), S19777+, S1984(+), S19862(+), S1+, S2003+, S2017+, S20246+, S20315+, S255+, S26361+, S26903+, S26911+, S27544+, S27668+, S2906+, S3023+, S349+, S3509+, S351+, S3826+, S3848+, S3856+, S3+, S4276+, S4888+, S492+, S4+, S5681+, S583+, S6378+, S6814+, S8235+, S8587+, S8620+, S8645+, S8649+, S8701+, S8705+, S8709+, S8714+, S8742+, S8751+, S8889+, S9041+, S9158+, S959+, SRY10831(+), V102+, V104+, V126+, V168+, V186+, V187+, V221+, V226+, V231+, V241+, V244+, V29+, V41+, V52+, V9+, YSC0167+, YSC0186+, YSC0203+, YSC0227+, YSC1297+, Z1244+

From what I've heard, there are many markers not working on their chip, including U152 and L20. Also, not telling people what position S372 or any "S' series SNP has is meaningless.

haleaton
11-29-2013, 11:06 PM
From what I've heard, there are many markers not working on their chip, including U152 and L20. Also, not telling people what position S372 or any "S" series SNP has is meaningless.
S372=Z258

http://www.yourgeneticgenealogist.com/2013/11/a-list-of-alternate-snp-names-for.html has link to google doc spreadsheet, which has to be downloaded not just viewed. Though it does not show locations which at this point it is silly not too. Based on the number of SNPs listed and what is advertised this is the list of working SNPs on the chip.

S28/U152, S138/L2, S144/L20 do not appear on the list which indicates that they likely failed manufacturing by Illumina, who makes the current Chromo2 chip. I am told Illumina actually guarantees only 80% of the SNPs actually working but actually does better than 90%. Just not this time for U-152 et al which a pretty important, at least with my bias.

In my case (U152+ L2*) they are willing to release unofficial data which shows me as P312/S116* and negative for all subtypes of S28/U152 (that are working) and will do further sequencing, likely just Sanger sequencing S139/L2 which will find the known result of L2*. This is an additional expense for them.

So it is sort of sad, until they make a new chip, that some important SNPs are not working or did not have multiple proxies as they did work on previous Illumina chips.

R.Rocca
11-30-2013, 12:49 AM
S372=Z258

http://www.yourgeneticgenealogist.com/2013/11/a-list-of-alternate-snp-names-for.html has link to google doc spreadsheet, which has to be downloaded not just viewed. Though it does not show locations which at this point it is silly not too. Based on the number of SNPs listed and what is advertised this is the list of working SNPs on the chip.

S28/U152, S138/L2, S144/L20 do not appear on the list which indicates that they likely failed manufacturing by Illumina, who makes the current Chromo2 chip. I am told Illumina actually guarantees only 80% of the SNPs actually working but actually does better than 90%. Just not this time for U-152 et al which a pretty important, at least with my bias.

In my case (U152+ L2*) they are willing to release unofficial data which shows me as P312/S116* and negative for all subtypes of S28/U152 (that are working) and will do further sequencing, likely just Sanger sequencing S139/L2 which will find the known result of L2*. This is an additional expense for them.

So it is sort of sad, until they make a new chip, that some important SNPs are not working or did not have multiple proxies as they did work on previous Illumina chips.

From what I've seen of the spreadsheet, it does not include any "S" names, just CTS and PF.

haleaton
11-30-2013, 01:00 AM
From what I've seen of the spreadsheet, it does not include any "S" names, just CTS and PF.

It has 8895 "S" names in the main column and 6 other SNPs are equivalence to "S" names int the second. You have to actually download in Google Drive to see them and open in Excel or other viewr. The Google docs viewer hides most of the content.

haleaton
11-30-2013, 01:36 AM
Getting back to Full Genomes results for U152, one thing I did notice was that they chose particular SNP names to use probably in a consistent way based on the data sets they used at the time. But there are some SNPs that they do not report on though they are well defined but maybe don't fall within their criteria for brevity. If we were positive for them they would report of course, but it is nice to know when do have a high reliability negative for some SNPs without having to go to the bam files or wait for it to be on the ISOGG tree.

I was thinking of DF103 for which I am likely negative as it did not appear in my report based on b37 location.

So I was wondering if we should try to get them to add a few recent SNPs relevant to U152? Maybe the they do not want tentative SNPs as we can always go to the bam files, but it is nice to get their analysis even on negatives.

Also FGC uses a lot of what must be new "M" snps which I thought was the University of Arizona, but I cannot find definitions of them except of course in the reports where B37 location is always listed.

Solothurn
12-10-2013, 12:59 PM
Thanks Rich

Geno have said the only way for sure regarding Z193 is to test for it directly.

Maybe somebody who tested Geno (not doing BigY) could request Z193 at YSEQ :D

I just hope we have more success with the BigY with Z193 'type' SNPs! As testing FGC is out of our reach $$$$ :(


Just remember what I wrote in my earlier post regarding Z193:



It could be that with Sanger testing this SNP shows up as negative since with NGS it shows up as heterozygous.

R.Rocca
03-02-2014, 08:09 PM
Here is some great news for those of us that are U152+ and awaiting Full Genomes results. From the Full Genomes Y sequencing Facebook page:

Leon Kull: "Happy March 1st to everyone! Starting from this Monday the data will start to arrive to the FGC data analysis team and from there - after some time - to our customers. We are on schedule (+ two days)."

haleaton
03-03-2014, 12:39 AM
Also for those with completed FGS Full Y. it will be good to get, requested from GregM, the updated variantCompare and haplogroupCompare reports for batches 1 through 4, after these next batch results come in.

Acque agitate
03-03-2014, 10:44 AM
I hope this is the right time.

Tom Fowler
04-04-2014, 02:28 PM
I received my FG results this morning. I'm still trying to figure out the information (pretty much overwhelmed at this point), but here's what I've found so far:

Match #1: R-L2
*Extras: V161.1+, V190+, F1345*, Z1842+, M118+, M236+, P9.2+, P80+, Z346*, IMS-JST029149+, CTS616+, IMS-JST022457+, P266+, V203*
R1b1a2a1a2b1


Also, it appears I have 55 private SNPs...with no matches, but a lot of question marks. Six are 95% likely genuine, the rest are 99% genuine. (That's based on Mr. Eaton's earlier post: Rel = no flag: over 99% likely genuine; *: over 95% likely genuine; I hope I got that right.) I can't figure out how to post a chart here, but below is a list of the private SNPs


1682

haleaton
04-04-2014, 03:18 PM
I received my FG results this morning. I'm still trying to figure out the information (pretty much overwhelmed at this point), but here's what I've found so far:

Match #1: R-L2
*Extras: V161.1+, V190+, F1345*, Z1842+, M118+, M236+, P9.2+, P80+, Z346*, IMS-JST029149+, CTS616+, IMS-JST022457+, P266+, V203*
R1b1a2a1a2b1


Also, it appears I have 55 private SNPs...with no matches, but a lot of question marks. Six are 95% likely genuine, the rest are 99% genuine. (That's based on Mr. Eaton's earlier post: Rel = no flag: over 99% likely genuine; *: over 95% likely genuine; I hope I got that right.) I can't figure out how to post a chart here, but below is a list of the private SNPs


1682

Great you got your FGC data! The "ynot" file Match has the same terminal SNP R-L2 with the same extras as mine. The names of the private SNPs do not match mine, though you should also check the Private Indels and comparison with other kits which should include mine, I think. I think that FGC would have flagged if we matched downstream of L2, though Rich Rocca will check and check against other datasets if you provide him the data which also shows the B37 locations.

I use the table format manually editing the formatting in Excel, but there may be a better & more space efficient way to display column data in these posts and to get things to line up and also be cut and pastable.

Kwheaton
04-04-2014, 03:24 PM
Tom,
I am so excited to see your post!!!! I believe you may be the closest geographically to our WHEATON L2* group whose results are in upcoming batch 6. We are 20/37 so not close but we don't get very close to anyone. M.Hanni is I believe is our closest at 24/37 Although we have not a definitive locale for our most distant ancestor we believe it is SW England or Wales most likely Devon, Somerset Glamorgan or Monmouth. The yera of immigration to the colonies was by 1636.

Thanks you for sharing we look forward to comparing SNPS when our arrive.
Kelly

Tom Fowler
04-04-2014, 03:42 PM
Great you got your FGC data! The "ynot" file Match has the same terminal SNP R-L2 with the same extras as mine. The names of the private SNPs do not match mine, though you should also check the Private Indels and comparison with other kits which should include mine, I think. I think that FGC would have flagged if we matched downstream of L2, though Rich Rocca will check and check against other datasets if you provide him the data which also shows the B37 locations.

I use the table format manually editing the formatting in Excel, but there may be a better & more space efficient way to display column data in these posts and to get things to line up and also be cut and pastable.


I found your kit. We apparently share 125 SNPs and 42 Indels. We don't share any of the private Indels.

Tom Fowler
04-04-2014, 03:47 PM
Tom,
I am so excited to see your post!!!! I believe you may be the closest geographically to our WHEATON L2* group whose results are in upcoming batch 6. We are 20/37 so not close but we don't get very close to anyone. M.Hanni is I believe is our closest at 24/37 Although we have not a definitive locale for our most distant ancestor we believe it is SW England or Wales most likely Devon, Somerset Glamorgan or Monmouth. The yera of immigration to the colonies was by 1636.

Thanks you for sharing we look forward to comparing SNPS when our arrive.
Kelly

We aren't a very close match to anyone either. I look forward to seeing your results. Maybe your results will give us some answers.

Kwheaton
04-04-2014, 03:52 PM
Tom,

I have just been doing a little more searching on the Fowlers in this area. I will PM you so we can take this off line.
Kelly