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Thread: List of Alternate Names for the Y-SNPs from BritainsDNA's Chromo2 Test

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    List of Alternate Names for the Y-SNPs from BritainsDNA's Chromo2 Test

    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.co...names-for.html

    The list is here: https://drive.google.com/folderview?...W8&usp=sharing

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    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.
    Last edited by Wing Genealogist; 11-21-2013 at 05:36 PM.

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    Quote Originally Posted by Wing Genealogist View Post
    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.

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    Post deleted by Wing Genealogist as I have discovered I was in error.

    Sorry!
    Last edited by Wing Genealogist; 11-21-2013 at 05:37 PM. Reason: inaccurate information

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    Quote Originally Posted by Wing Genealogist View Post
    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/showthre...ll=1#post20290

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    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.
    Paternal: R1b-U152 >> L2 >> FGC10543, Pietro della Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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    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
    FullGenomes ID:FG1048A
    YFull ID:YF01371


    y-DNA.................................................. ..........................mt-DNA
    Hg: R1b1a1a1a1b3 [R-U106 > FGC3861 > L217]........Hg: H2a2b [RSRS]
    Shorthand: R-L217 or R-S1849......................................Extra Mutations: 309.1'C', 315.1'C', A16235'G', T16357'C', C16519'T'.

    ySearch & mtSearch ID: Hidden Content

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    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.

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    Quote Originally Posted by Clinton P View Post
    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."
    Last edited by haleaton; 11-21-2013 at 05:54 PM.

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    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, 3 October 2013
    Z2103 R1b1a2a2 CTS1078 7246135 7186135 G->C
    Last edited by Joe B; 11-22-2013 at 03:55 AM.

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