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Jean M
11-21-2013, 11:26 AM
CeCe Moore reports:


Dr. James Wilson from BritainsDNA has sent me a list of the alternate names for the Chromo2 Y-SNPs and has given me permission to post it for public access with his comments, as follows :

Please find attached a list of alternate names for chromo2 Y SNPs...This is based on comparisons some months ago now, although a few SNPs have been updated in the meantime...Where there is no alternative name for an S SNP it means it was not listed/named in any compendium, browser or database I had available when this file was put together and is not available in any other product as far as I am aware (of course apart from a complete Y chromosome sequence).

Note that all the SNPs on this list manufactured on the chip, but a small proportion do not give good genotyping clusters; I haven't had time to clean them out. There are also a small number of SNPs not on this list eg S28, S250, which we Taqman in the appropriate samples as Illumina appear to have removed them from the design and they have no proxies on the chip or none known.

http://www.yourgeneticgenealogist.com/2013/11/a-list-of-alternate-snp-names-for.html

The list is here: https://drive.google.com/folderview?id=0B7W0hlyChUPibkZFLXpCNy1GZW8&usp=sharing

Wing Genealogist
11-21-2013, 12:16 PM
I find the released SNP list rather disingenuous. It is comprised solely of the CTS SNPs on the Chromo2 test (I believe the full details of these SNPs should already be available through the Wellcome Sanger Institute), and does not contain a single proprietary S SNP. In addition, the only alternate names presented are the PF SNPs from Sardinia. It is impossible for me to believe none of the other researchers SNPs (such as Hammer, Underwood, or even the 1000 Genome SNPs) are included in any of these CTS SNPs.

Also, the timing of this release (after the very popular release of FTDNA's Big Y test) is very suspect. It appears to (admittedly somewhat jaded) me BritainsDNA sees a real potential in sales, and is hanging out the proverbial carrot in front of potential customers.

While I am seriously thinking about ordering this test sometime down the road, I will not be ordering it until their is full disclosure, allowing us to compare results from this test to other next-generation sequencing tests.

OOPS!! ME BAD.

Apparently I am only able to access PART of the spreadsheet released by BritainsDNA. I'm not sure WHY I cannot see the whole thing, but I've been told by several others that it does contain more than the CTS SNPs I mentioned.

GTC
11-21-2013, 12:44 PM
I find the released SNP list rather disingenuous. It is comprised solely of the CTS SNPs on the Chromo2 test (I believe the full details of these SNPs should already be available through the Wellcome Sanger Institute), and does not contain a single proprietary S SNP.

Here is the text of the correspondence as published by CeCe Moore:


"Please find attached a list of alternate names for chromo2 Y SNPs...This is based on comparisons some months ago now, although a few SNPs have been updated in the meantime...Where there is no alternative name for an S SNP it means it was not listed/named in any compendium, browser or database I had available when this file was put together and is not available in any other product as far as I am aware (of course apart from a complete Y chromosome sequence).

Note that all the SNPs on this list manufactured on the chip, but a small proportion do not give good genotyping clusters; I haven't had time to clean them out. There are also a small number of SNPs not on this list eg S28, S250, which we Taqman in the appropriate samples as Illumina appear to have removed them from the design and they have no proxies on the chip or none known.

In due course I also intend to share the genome co-ordinates to allow comparisons with whole Y chromosome sequences, despite this being a case of handing larger competitors the fruits of our investment. At present I have started to do that for individual SNPs that are queried on a case-by-case basis, as I don't as yet have the permissions of all of the sequenced individuals to hand out their SNPs in this way.

You can find the list here.

Thanks, Jim!

I'm unable to download this list, but from the bit that I have bolded in the quote I would have expected there to be plenty of "S" SNPs in it, so if there aren't any at all then that's just weird.

Wing Genealogist
11-21-2013, 01:54 PM
Post deleted by Wing Genealogist as I have discovered I was in error.

Sorry!

GTC
11-21-2013, 01:59 PM
I was able to download the list, and it included 32 pages of CTS SNPs and not a single S SNP.

Hmmm. Not sure what's going on then as member "rathna" has listed a bunch of "S" series ones in this thread:

http://www.anthrogenica.com/showthread.php?927-Rathna-s-assessment-of-genetic-materials&p=20290&viewfull=1#post20290

R.Rocca
11-21-2013, 02:06 PM
Their claim is that they test for thousands of SNPs that Geno 2.0 does not. The only way to see that for sure is if they provide a list with all of the "S" names and positions. The folks that ordered Chromo 2 should insist on this.

Clinton P
11-21-2013, 03:11 PM
I downloaded the chromo2_YSNP_alt_names[1].xlsx file from Google Drive.

There are 8,894 'S' series Y-SNPs. Of these 865 (~10%) have alternative names.

Meaning that, currently, 8,029 Y-SNPs are testable only at BritainsDNA etc. (excluding a complete Y chromosome sequence, of course).

It's not suprising that Dr. Jim Wilson makes the following comment....


In due course I also intend to share the genome co-ordinates to allow comparisons with whole Y chromosome sequences, despite this being a case of handing larger competitors the fruits of our investment. At present I have started to do that for individual SNPs that are queried on a case-by-case basis, as I don't as yet have the permissions of all of the sequenced individuals to hand out their SNPs in this way.

Clinton P

Wing Genealogist
11-21-2013, 05:39 PM
I have discovered I have erred when I stated the spreadsheet released by BritainsDNA only contains the CTS SNPs. Apparently, I am only able to access a portion of the entire spreadsheet, and others have stated the full spreadsheet does list other SNPs (such as their proprietary S-series SNPs) and compares them to other companies known SNPs as well.

I apologize for this mis-informed opinion, and have edited my original post.

haleaton
11-21-2013, 05:44 PM
I downloaded the chromo2_YSNP_alt_names[1].xlsx file from Google Drive.

There are 8,894 'S' series Y-SNPs. Of these 865 (~10%) have alternative names.

Meaning that, currently, 8,029 Y-SNPs are testable only at BritainsDNA etc. (excluding a complete Y chromosome sequence, of course).

It's not suprising that Dr. Jim Wilson makes the following comment....

Clinton P

Thanks! Dowloading from Google Docs was key. I did not check for duplicates but the total list is 14498 SNPs.

I was wonder the best locations for current SNP lists whether they include the location or not? Other than ISOGG of course.
I used to use SNPInfo on Finch2 and there was Z SNP spreadsheet, I think by GregM. And David Reynolds list of course.
I have old versions, but perhaps not the latest.

One thing to note is that without Krahns Ymap and SNPInfo FTDNA does not currently have mechanism to make SNP definitions public, though Admins can look at ones they sell.

About Big Y the comment to me from a query to FTDNA was "I do not have a time frame as to when any SNPs identified will be made public."

Joe B
11-21-2013, 07:53 PM
Just a word of caution with the list of alternate names for chromo2 Y SNPs https://drive.google.com/folderview?...W8&usp=sharing
Double check everything.
CTS1083 Z2103 is incorrect and was changed by Alice at ISOGG last July 15. This is a common mistake that should give a clue to the age of this SNP list.
SNP ID c2 alt ID
CTS1083 Z2103

This is correct CTS1078 Z2103
ISOGG Y-DNA SNP Index - 2013 (http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html), 3 October 2013
Z2103 R1b1a2a2 CTS1078 7246135 7186135 G->C

Rathna
11-22-2013, 07:04 AM
Their claim is that they test for thousands of SNPs that Geno 2.0 does not. The only way to see that for sure is if they provide a list with all of the "S" names and positions. The folks that ordered Chromo 2 should insist on this.

My Chromo 2 results are going to come. I have explained on other threads which are the answers it may give me: I expect to be positive for Z2103 and Z2105, negative for L277 (as I have said I didn't find L584, but I am negative from 23andMe). Of course I shall be negative for L943 and L946, the Silver's SNPs. I expect my results for Z2102 (we'll see its collocation as to Z2103/Z2105), for Z2109, that nobody has tested so far, and above all Z2110/CTS7822. Of course I am very curious about PF7580, found in Carnevali, Aghinitei and Goldschlager, and possibly the European ancestor of L584. It isn't a little. From this I'll be able to understand if some S SNPs are close to these ones.
I don't think that I should ask Jim Wilson the collocation of the S SNPs. As he said, they invested in this and there is a problem of competition.
We shouldn't forget that EthnoAncestry has been the unique company to resist to FTDNA, and I have denounced many times the cartel of that firm and the use they did about their data, not last the Hammer's conference and the sponsorship of the Middle Eastern origin of hg. R, you know it isn't my position.
Read the irony of Generalissinmo on another thread I thanked.

R.Rocca
11-22-2013, 12:44 PM
My Chromo 2 results are going to come. I have explained on other threads which are the answers it may give me: I expect to be positive for Z2103 and Z2105, negative for L277 (as I have said I didn't find L584, but I am negative from 23andMe). Of course I shall be negative for L943 and L946, the Silver's SNPs. I expect my results for Z2102 (we'll see its collocation as to Z2103/Z2105), for Z2109, that nobody has tested so far, and above all Z2110/CTS7822. Of course I am very curious about PF7580, found in Carnevali, Aghinitei and Goldschlager, and possibly the European ancestor of L584. It isn't a little. From this I'll be able to understand if some S SNPs are close to these ones.
I don't think that I should ask Jim Wilson the collocation of the S SNPs. As he said, they invested in this and there is a problem of competition.
We shouldn't forget that EthnoAncestry has been the unique company to resist to FTDNA, and I have denounced many times the cartel of that firm and the use they did about their data, not last the Hammer's conference and the sponsorship of the Middle Eastern origin of hg. R, you know it isn't my position.
Read the irony of Generalissinmo on another thread I thanked.

Honestly, that is absurd. If you turn up positive for 5 new "S" snps, how will you even know which ones they are compared to people that are testing Big-Y or FG???

You knowing you are positive for one single SNP is not a good value at all.

GTC
11-22-2013, 01:00 PM
Honestly, that is absurd. If you turn up positive for 5 new "S" snps, how will you even know which ones they are compared to people that are testing Big-Y or FG???

You knowing you are positive for one single SNP is not a good value at all.

I agree. What's the use of this without an accepted published tree?

I've always considered this secrecy from Wilson as pure BS. Like the rest of us he's had the advantage of access to public haplotrees published by YCC, ISOGG and Thomas Krahn for years.

Rathna
11-22-2013, 02:58 PM
This is what Jim Wilson wrote to Ce ce Moore:
"Please find attached a list of alternate names for chromo2 Y SNPs...This is based on comparisons some months ago now, although a few SNPs have been updated in the meantime...Where there is no alternative name for an S SNP it means it was not listed/named in any compendium, browser or database I had available when this file was put together and is not available in any other product as far as I am aware (of course apart from a complete Y chromosome sequence).
Note that all the SNPs on this list manufactured on the chip, but a small proportion do not give good genotyping clusters; I haven't had time to clean them out. There are also a small number of SNPs not on this list eg S28, S250, which we Taqman in the appropriate samples as Illumina appear to have removed them from the design and they have no proxies on the chip or none known.
In due course I also intend to share the genome co-ordinates to allow comparisons with whole Y chromosome sequences, despite this being a case of handing larger competitors the fruits of our investment. At present I have started to do that for individual SNPs that are queried on a case-by-case basis, as I don't as yet have the permissions of all of the sequenced individuals to hand out their SNPs in this way".

Of course I'd agree with you that without knowing the S SNPs every tree will be incomplete, but...
1) I have said that even with these known SNPs I'll be able to solve the most part of my questions about the origin of R-Z2105* and perhaps of R1b1* which is my purpose.
2) That I think that the S SNPs are ordered like subclades of a known SNP, then it shouldn't be difficult to understand their collocation.
3) Jim Wilson's fight (by a commercial point of view) is heroic and merits comprehension.
4) Everyone fights his (commercial) wars with the means at his disposal, and I'd want you didn't forget Thomas Krahn, Ray Banks (read a letter of his on eng.molgen), the sponsors of National Geographic, many results from FTDNA that don't fit (I have written a lot about many M269 which probably aren't so), that it isn't guaranteed that the BIG Y SNPs will be released, etc etc
5) Richard Rocca knows that I contributed to test Diana Panara for her FMS. I exchanged some letters with her and William Hurst on eng.molgen and I did many hypotheses. After I had no reply.

Rathna
11-23-2013, 03:18 AM
Perhaps what David Faux has written on Rootsweb is useful to understand the context:

"Indeed I agree with the use of the "S" series (I will down in history for
coming up with that designation - my rationale - there was no haplo S that
could be confused with the marker numbers). My business partner Dr.
Wilson developed a number of key SNPS which were later published by someone
else under the "U" tag. Alas we were in business to at least stay afoat if
not make money. If you give away all of your findings, the "big boys" will
market them and you are left holding all the bills. Been there, done
that. I won't begin to discuss what I lost in my foray into the DNA
testing business as co-owner of EthnoAncestry - but I got burnt. The word
profit is not a dirty word - it is what fuels further discovery. I will
always respect FTDNA's BG for giving us two years to market the SNPs -
unfortunately we had insufficient resources to do a full enough job. We
were always torn between publish, or market. Tricky line to walk.

Also, in the most recent published survey of for example the R1b subclades,
Jim and team used the S tag nomenclature and so it would make sense to
continue down this route. So for example, S21 and S28 may be seen in
other work as U106 and U152 respectfully, but hopefully the scientific
community will follow Dr. Wilson's lead here".

Rathna
11-23-2013, 04:40 AM
From this message posted by bjlb at tx.rr.com I think it is clear all what I have supposed and said:
Chrome 2 results received from BritainsDNA. I am still R1b-S145/S461 = R1b-L21+**, called by them "Pretani". Their message is that "you not belong to any of the currently defined subtypes of S145" which they identify as S474,215,163,175,219,218,192,300,388,393,530 and 1136, twelve in all. They offer the consolation that "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".

From tdesmon at lycos.com

See the link on this page which translates the "S" series SNPs to their ISOGG names:

http://www.yourgeneticgenealogist.com/2013/11/a-list-of-alternate-snp-names-for.html



S474 = DF49

S215 = DF1 L956 L513

S163 = L69 PF2681

S175 = L144

S219 = Z255

S218 = Z253

S192 = DF21

S300 = L371

S388 = L744

S393 = L555

S530 = L1335

S1136 = CTS4466

GTC
11-23-2013, 05:56 AM
[David Faux has written on Rootsweb]: "I will always respect FTDNA's BG for giving us two years to market the SNPs -
unfortunately we had insufficient resources to do a full enough job. We were always torn between publish, or market. Tricky line to walk.

So, they were given a sporting chance but they couldn't muster the necessary resources. I see no "cartel" type conspiracy here, simply the inability to raise sufficient capital in the time allowed and/or grow market share. A very common reason for businesses failure.

Rathna
11-23-2013, 09:04 AM
So, they were given a sporting chance but they couldn't muster the necessary resources. I see no "cartel" type conspiracy here, simply the inability to raise sufficient capital in the time allowed and/or grow market share. A very common reason for businesses failure.

I have said all what I had to say and I'd prefer to come back to genetics, otherwise we should dig up again old stereotypes and it wouldn't be useful for you and above all for me. But you should know that the cartel arises when someone gets so much capital to permit himself to sell below cost till the competitors fail. This play is succeeding very well to Chinese: their Full Y, which seems pretty good also for the FSM, at a little low price will rout all the opposing teams, and they are doing this not only on genetics.
Another sample is 23andMe: only 99$, and I had through it also pretty all my FSM, I paid 300$ to FTDNA.

Diana
01-11-2014, 06:09 PM
Hello,

Was there something I didn't respond to Gio? I always appreciate your help!


This is what Jim Wilson wrote to Ce ce Moore:
"Please find attached a list of alternate names for chromo2 Y SNPs...This is based on comparisons some months ago now, although a few SNPs have been updated in the meantime...Where there is no alternative name for an S SNP it means it was not listed/named in any compendium, browser or database I had available when this file was put together and is not available in any other product as far as I am aware (of course apart from a complete Y chromosome sequence).
Note that all the SNPs on this list manufactured on the chip, but a small proportion do not give good genotyping clusters; I haven't had time to clean them out. There are also a small number of SNPs not on this list eg S28, S250, which we Taqman in the appropriate samples as Illumina appear to have removed them from the design and they have no proxies on the chip or none known.
In due course I also intend to share the genome co-ordinates to allow comparisons with whole Y chromosome sequences, despite this being a case of handing larger competitors the fruits of our investment. At present I have started to do that for individual SNPs that are queried on a case-by-case basis, as I don't as yet have the permissions of all of the sequenced individuals to hand out their SNPs in this way".

Of course I'd agree with you that without knowing the S SNPs every tree will be incomplete, but...
1) I have said that even with these known SNPs I'll be able to solve the most part of my questions about the origin of R-Z2105* and perhaps of R1b1* which is my purpose.
2) That I think that the S SNPs are ordered like subclades of a known SNP, then it shouldn't be difficult to understand their collocation.
3) Jim Wilson's fight (by a commercial point of view) is heroic and merits comprehension.
4) Everyone fights his (commercial) wars with the means at his disposal, and I'd want you didn't forget Thomas Krahn, Ray Banks (read a letter of his on eng.molgen), the sponsors of National Geographic, many results from FTDNA that don't fit (I have written a lot about many M269 which probably aren't so), that it isn't guaranteed that the BIG Y SNPs will be released, etc etc
5) Richard Rocca knows that I contributed to test Diana Panara for her FMS. I exchanged some letters with her and William Hurst on eng.molgen and I did many hypotheses. After I had no reply.

SnowYorker
01-27-2014, 02:46 PM
I don't know if this might shed some light on why Dr Jim Wilson is protective of his newly found SNPs but an extract of the blurb on BritainsDNA website goes as follows;

"In order to discover new markers we may in the future send your DNA to a reputable genome sequencing centre, which could be abroad...... Newly discovered markers may be used in future ancestry tests and marker frequencies used to improve products. "

Or, as I read it, if your Chromo2 test points to you being of high interest we may give you a free Y-FGS to help advance the science. If BritainsDNA are forking out their own money to give people FGS tests why shouldn't they reap the benefits from that research for a while?

For the full context of the quote see the "How will the study be carried out?" section on http://www.britainsdna.com/about/research-study-participant-information