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Thread: DF27 Phylogeny from FGC

  1. #1
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    DF27 Phylogeny from FGC

    Is FGC at all concerned about the way YFull is sticking their new names on FGC named SNPs? They are using these names in their tree without any indication that the SNPs were previously identified and named by FGC. See YFull's tree for R-Z2571 where the SNPs under Y-8397 are all SNPs previously named by FGC, but there is no way to identify them as such in the YFull tree.

    Is YFull just trying to fill a vacuum or are they trying to subvert normal naming protocols and take that over?

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    Quote Originally Posted by rgd View Post
    Is FGC at all concerned about the way YFull is sticking their new names on FGC named SNPs?
    Does FGC check YFull's database before assigning names?

    Actually, though, there is indeed a fundamental philosophical difference in naming practice. FGC follows the old publish-or-perish academic rule of naming every single arguable private SNP, in order to claim discovery. The disadvantage is that in our new era of full-Y scanning, this will quickly lead to millions of SNP names and a bloated spreadsheet. (The Z series has already needed a second, "supplemental" spreadsheet just for itself.)

    YFull assigns an internal YFS name to every SNP, but only publishes reliable SNPs confirmed in two or more examples. This has the advantage of keeping the spreadsheet manageable.
    Last edited by lgmayka; 01-13-2015 at 10:02 PM.

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    We name all SNPs because those are generally asked for by our customers. The second point is that ISOGG has the standard tree which has multiple confirmations for each SNP.

    As for third parties everyone has their own approach.

    We don't make money off of naming SNPs so it serves as info for the community to use as appropriate demands require.
    Last edited by FGC Corp; 01-13-2015 at 10:40 PM.

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    Secondly we don't limit our data releases so that all data becomes public as it becomes available. Put differently we make $0 from naming SNPs.

    I think I would essentially note that SNP naming/phylogenetic discovery, while some measure of progress just isn't fundamental to a genetics business. For that, new sequencing products or biotech technology drive any business in this area; SNP discovery is part of the hobby but it doesn't contribute to the business, so I would regard YFull as somewhat helpful since it serves as an additional 3rd party assessment of products, particularly with respect to Y chr coverage of the different products.
    Last edited by FGC Corp; 01-13-2015 at 10:30 PM.

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    Quote Originally Posted by lgmayka View Post
    Does FGC check YFull's database before assigning names?


    YFull assigns an internal YFS name to every SNP, but only publishes reliable SNPs confirmed in two or more examples. This has the advantage of keeping the spreadsheet manageable.
    I don't understand how YFull sticking new names on previously identified and named SNPs keeps the spreadsheet manageable--perhaps it makes their spreadsheet more managable, but not mine. Perhaps your question should have been does YFull check whether a SNP has been named and then use that rather that sticking a new name on it. If they don't why not?

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    Quote Originally Posted by rgd View Post
    I don't understand how YFull sticking new names on previously identified and named SNPs keeps the spreadsheet manageable--perhaps it makes their spreadsheet more managable, but not mine. Perhaps your question should have been does YFull check whether a SNP has been named and then use that rather that sticking a new name on it. If they don't why not?
    As I discussed with a community member a while back a SNP database is needed, since it is better for this type of task, but that is a mission for third parties. It's inevitable given the current set-up for some SNPs to have multiple names, in the absence of a dynamically updated central public database.
    Last edited by FGC Corp; 01-13-2015 at 10:40 PM.

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    How much does it really matter if YFull or FGC puts their names on an SNP first? If anything it's proof of independent verification from two separate groups, and both designations will show up eventually in YBrowse and the ISOGG tree anyway.

    Also, is there any place where I can find a full list of FGC SNPs and their phylogenetic importance? I'm not really familiar with their findings so far.

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    How much does it really matter if YFull or FGC puts their names on an SNP first?
    I don't see that it matters.

    If anything it's proof of independent verification from two separate groups, and both designations will show up eventually in YBrowse and the ISOGG tree anyway.
    I agree.

    Also, is there any place where I can find a full list of FGC SNPs and their phylogenetic importance?
    Email us.

    As I see it, this is the future:
    https://www.fullgenomes.com/news/
    Last edited by FGC Corp; 01-14-2015 at 12:41 AM.

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    Quote Originally Posted by rgd View Post
    I don't understand how YFull sticking new names on previously identified and named SNPs
    You didn't get my point at all, which is that both companies have more important things to do than to check for duplication of SNP names. I suspect that YFull made a copy of the Ybrowse database about a year ago, and does not duplicate names found there at that time.

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    Just echoing:

    It does take a significant amount of time to download, audit, curate, and re-import into their respective internal databases. This *is* done (i.e. FGC had stated elsewhere that they do this every 4 to 6 weeks typically), but is not as frequently as some would like.

    Unfortunately, ISOGG simply does not posses the financial or human resources to host and curate the centralized open-access Y-SNP repository database that we all long to to have.

    I really wish that organizations and institutions such as NCBI, the Wellcome Trust, Erasmus University, KU Leuven, and so forth, would join forces on a cooperative level with citizen science to set something like this up. Oh, silly dreams.

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