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Thread: Submitting SNP placment requests to ISOGG?

  1. #1
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    Submitting SNP placment requests to ISOGG?

    This is a self-critical notion as much as anything but I find myself often thinking "this is no way to run a railroad".

    One sub-topic of that notion is in ISOGG submissions for SNP placement. It may be all very formal and clear and I just need catching up. If not I suggest we should start using some kind of specific format for submitting SNP placement requests and we should cc all such requests to some kind of publicly accessible message board so that anyone can go back and figure out why an SNP was placed as it was.

    Another thought would be to try to plan the submissions per haplogroup to work at on a top-down (older to younger) sequence. Occasionally we run into a haplogroup with very wide horizontal branching. DF13 comes to mind. Just ask Mark J about this but it is a killer to get all of the probable peers tested. In the case where the peers are old (and probably large) this can't be helped but in some cases there may be a number of younger "sub" peers that were coincidentally discovered first. If a number of these make the ISOGG chart first, it makes the efficiency of cross checking all of the sub peers quite poor. Ideally, you want to have the oldest SNPs tested first so that larger sections of the tree can avoid the cross checking when new SNP branch candidates present themselves.

    Perhaps this can't be helped but it is something to think about. A novel SNP like FGC5496 (under DF13) with very high diversity deserves priority at the least, when compared to a low diversity SNP (under DF13.)
    Last edited by TigerMW; 02-18-2014 at 09:07 PM.

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  3. #2
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    I received a response from ISOGG on this at the conversation linked to below.
    Alice Fairhurst wrote,
    "The idea of giving examples and/or having a form attached to the Listing Criteria is something we might want to examine.

    Phil Goff and Ray Banks are working on revising the Listing Criteria. Don't know if Gareth Henson has joined them."
    https://groups.yahoo.com/neo/groups/...s/topics/35355
    Last edited by TigerMW; 02-20-2014 at 05:53 PM.

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    I haven't gotten anything specific from ISOGG on this so I'm pushing ahead to the L21, DF27 and U106 groups.

    Here is the the L21 thread.
    https://groups.yahoo.com/neo/groups/...messages/19521

    Here is the U106 thread.
    https://groups.yahoo.com/neo/groups/...messages/20912

    Here is the DF27 thread.
    https://groups.yahoo.com/neo/groups/...s/messages/698

    Charles Moore who handles U106 for ISOGG says he does have a process but it is mostly in his head. I think he'll work on it a bit so I'm hoping he will give us a format for consistency's sake. I've sent him my initial proposal. My INITIAL PROPOSED FORMAT is below.

    Mark J appears to be the P312 ISOGG coordinator.

    Robert C has an alternative that he is using or will propose. That's fine with me too as long as it works for ISOGG. It's at this post:
    http://www.anthrogenica.com/showthre...ll=1#post32024


    ---- INITIAL PROPOSED FORMAT FOR SUBMITTING AN SNP FOR INSERTION (AND HG CREATION) ON THE CURRENT TREE.

    ----------- Subject line of email --------------------------
    SNP xyz (candidate SNP) Submission for ISOGG tree


    ----------- Outline format of body of email -------------------------


    Candidate SNP and synonym labels
    ----------------------------------------------
    SNP labels, Physical address info, URL to reference SNP details

    Candidate SNP diversity status
    ------------------------------------------
    Kit/ID #, Surname, Project/ URL, candidate SNP derived result, Genetic Distance from comparison
    Kit/ID #, Surname, Project URL, candidate SNP derived result (for comparison target)

    Immediate Ancestor (father) SNP currently on ISOGG chart
    ------------------------------------------------------------------
    SNP

    Ancestral and derived haplotypes proving descendant status
    ------------------------------------------------------------------------------
    Kit #, Surname, Project/details URL, ancestor SNP derived result, candidate SNP derived result
    Kit #, Surname, Project/details URL, ancestor SNP derived result, candidate SNP ancestral result

    Peer (brother) SNP currently on ISOGG chart (1 through n) (if applicable)
    -----------------------------------------------------------------
    Kit #, Surname, Project/details URL, peer SNP derived result, candidate SNP ancestral result

    Descendant (child) SNP currently on ISOGG chart (1 through n) (if applicable)
    -----------------------------------------------------------------
    Kit #, Surname, Project/details URL, descendant SNP derived result, candidate SNP derived result
    Kit #, Surname, Project/details URL, descendant SNP ancestral result, candidate SNP derived result

    ---------------------------------------------------------------------------------------------------------------------------------


    The net of my position is not that ISOGG has to change, although I think the more clearly and thoroughly they document their requirements, the better.

    My position that we should control and provide organization to what we can. Down at the project administrator level, the better we can encourage an accurate and standard process the better.

    The railroad needs to use the same size tracks.

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    Does anyone know what happened with Dave R., who has been the coordinator for P312 SNPs? Has he been replaced?

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    Quote Originally Posted by GoldenHind View Post
    Does anyone know what happened with Dave R., who has been the coordinator for P312 SNPs? Has he been replaced?
    He has been replaced; Mark Jost is now ISOGG's R1b-P312+ coordinator.

    Stephen

  9. #6
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    Mike, I'll forward to you some correspondence about this subject that I had this time last year with Henry Zenker, who copied me on emails he had, from Vince Tilroe to Alice Fairhurst. That is a bit too private to be posted on a forum, but may include suggestions or formatting you could incorporate into what you are doing here.

    At the time, I was just hoping to get the occurrences of L484 straightened out. My cousin's Geno2 test showed that CTS4065 really belongs above the L484 group we're in; and I thought it would be folly to try to hang something on the ISOGG tree when we know perfectly well there are some twigs missing, above it. A lot has happened since, including the creation of our DF27 haplogroup project -- but that phylogeny is still somewhat below the ISOGG radar. Actually, Chromo2 results have just refined it again. And who knows what Big Y and FGC tests might bring -- in a few more days?

    All in all, I think waiting was OK. But probably not much longer.
    Last edited by razyn; 02-26-2014 at 03:55 AM.

  10. #7
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    ISOGG Y-DNA Haplogroup Tree - Listing Criteria for SNP Inclusion

    Initially, "The first phylogenetic chart to unify nomenclature was published in 2002 by the Y Chromosome Consortium (YCC). The 2003 Y-DNA phylogenetic chart appeared in Mark A. Jobling and Chris Tyler-Smith, The Human Y Chromosome: An Evolutionary Marker Comes of Age Nature Reviews|Genetics, Figure 5. In 2005 Family Tree DNA created the 2005 Y-Chromosome Phylogenetic Tree. An ISOGG group was formed in November 2005 to create a web-based document using Richard Kenyon's style of an indented list which could be updated to keep pace with the rapid developments in the field. ...

    The Y Haplogroup classification of the male Y-chromosome is currently used to estimate the population group of the paternal line. The haplogroups are identified by the letters, A through T. Haplogroups are subdivided into one or more levels, called subclades, and thus forming a tree. The Y-chromosome haplogroup is determined by performing a sequence of SNP tests"

    SNPs development indicated by beginning letters chosen by a number of researchers from "A" to "Z".

    ISOGG has taken responsibility of maintaining and updating the phylogenetic Tree Chart for Professional and Amateur Scientific usage. In April 2014, ISOGG (International Society of Genetic Genealogy) provided an updated "Acceptance Process for Placing a SNP on the ISOGG Y-DNA Haplotree". These recommendations are to assure that there is a uniform set of criteria for accepting new mutations for inclusion on the ISOGG Y-DNA haplogroup tree. The criteria is found here: http://www.isogg.org/tree/

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

  11. #8
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    For the R-P312 and below subclades I have created a standardized submission work sheet for ISOGG Y-DNA Haplogroup Tree - Listing Criteria for SNP Inclusion. This has been designed to be in a standardized format to assist in submitting new SNPs with specific requirement examples associated with the various type of test results and placement. This format may need revised as needed going forward but is the basis for general submissions.

    P312 and below Submission Spreadsheet Version 1 date: May 15, 2014 Mark Jost (Subject to future revision as required) is found here.

    http://tinyurl.com/SNPSubP312

    I will accept constructive comments and will make possible submission form changes as needed going forward as needed to maintain the a standardized format that follows the uniform set of criteria for accepting new mutations for inclusion on the ISOGG Y-DNA haplogroup tree.

    MJost
    148326, FGC-0FW1R, YSID6 & YF3272 R-DF13>FGC5494>*7448>*5496>*5521>*5511>*5539>*5538>* 5508>*5524
     
    Watterson USA GD1/67 & GD3/111, *5508+. GD1ís fatherís sister-23andme pred. 3rd Cous w/ 0.91% DNA shared-3 seg. Largest on Chr1 w/non-Euro admix affirms my NPE paternal Watterson line via aDNA & YDNA. A 2nd pred. 4th cous has same DKA b. 1840's Georgia and MDKA d 1703 IOM. 3rd Cousin FtDNA FF is from the Watterson Ala. *5538+ b. IOM w/ GD6/67 & GD8/111 -SGD3. FGC5539+ a Scot-Ross GD13/111 -SGD8

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