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Have you submitted your MtFullSequences to Genbank?

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  • AngeliaR
    replied
    submissions to GenBank ??

    Is it even possible for individuals to submit their result files directly to GenBank any more?

    One of my FGS/FMS matches received a message to the effect that they could no longer include FTDNA or BG on the GenBank "flat file" (proof copy of the submission page). This creates a privacy issue for people wishing to contribute... and brings the individual results submission process to a screeching halt until it gets resolved.

    The last I heard, no decision had yet been reached on how to deal with this situation. I have sent an inquiry to FTDNA to find out if this information is correct and if so, what the reasoning is. With luck they will already have worked something out and have a solution or work around available.

    I would be interested in knowing if anyone else has received similar correspondence.

    Leave a comment:


  • Bill Hurst
    replied
    Originally posted by similligan View Post
    I ordered the FMS for my father and myself back in late 2008. We received emails from FTDNA asking permission to use our results in studies and we gave our permission. There was no survey and we didn't receive any other reply after our consent.

    Is there a way to check if we are included in GenBank? Or would this have been referring to different studies?

    Susan
    Hi Susan,

    Last time I checked, the 4,265 new sequences, mostly from FTDNA, have not been added to GenBank. There is a new website, mtdnacommunity.org , that has tools to look for answers to various questions. Not all of it is working yet.

    I think this is the first time the consented sequences from FTDNA have been sent to GenBank. The 1,237 from FTDNA already on GenBank were directly submitted by the customers.

    Watch this space!

    Bill Hurst

    Leave a comment:


  • similligan
    replied
    I ordered the FMS for my father and myself back in late 2008. We received emails from FTDNA asking permission to use our results in studies and we gave our permission. There was no survey and we didn't receive any other reply after our consent.

    Is there a way to check if we are included in GenBank? Or would this have been referring to different studies?

    Susan

    Leave a comment:


  • Bill Hurst
    replied
    FTDNA does assign consent numbers, but I don't know if they used those in the new GenBank sequences. We'll probably have to wait until those 4,265 sequences (not all from FTDNA, by the way) from the new Behar paper are published before all these questions can be answered.

    Bill Hurst

    Leave a comment:


  • Ann Turner
    replied
    Originally posted by ashimmin View Post
    Is there any way of retrieving/refinding your accession number? I took the survey&consented on the ftdna home page after my mtfullsequence results came in and I believe it gave me a number- but I forgot to write it down, if it did. I would hate to create a duplicate entry by submitting my sequence myself.
    I see Bill already answered your question while I was off writing some instructions on how to see if your sequence (or one just like it) is in GenBank. But if you were given a number at all, it would not have been a GenBank accession number. Those were just assigned at the time of publication, and will be in the range JQ701803–JQ706067. They aren't online just yet.

    Leave a comment:


  • Bill Hurst
    replied
    Originally posted by ashimmin View Post
    Is there any way of retrieving/refinding your accession number? I took the survey&consented on the ftdna home page after my mtfullsequence results came in and I believe it gave me a number- but I forgot to write it down, if it did. I would hate to create a duplicate entry by submitting my sequence myself.
    Hi ashimmin and all,

    This is covered in the FTDNA FAQ here: http://www.familytreedna.com/faq/answers.aspx?id=10#583

    "Once a study is published, we attempt to inform research study participants that their results were used. We will also provide the access ID for the NCBI GenBank record associated with your mtDNA sequence.

    However, if the results are published with the study as part of the supporting data, then those results are accessible to other researchers for use in their studies as well. We cannot track published study data and its use in other publications; therefore, we are unable to track or notify you whenever additional studies are published using your results."

    The new Behar paper points out that FTDNA may not know who direct submissions belong to. Your mtDNA haplogroup project administrator may track direct submissions; I certainly do with the K and U8 ones.

    Please don't submit duplicate records.

    Bill Hurst

    Leave a comment:


  • ashimmin
    replied
    A way to retrieve forgotten accession #?

    Is there any way of retrieving/refinding your accession number? I took the survey&consented on the ftdna home page after my mtfullsequence results came in and I believe it gave me a number- but I forgot to write it down, if it did. I would hate to create a duplicate entry by submitting my sequence myself.

    Leave a comment:


  • JohnLloydScharf
    Guest replied
    Originally posted by AngeliaR View Post
    Since this last November, there have been 4 added to the H31 group.
    All 4 new entries originated from FTDNA.

    http://www.ianlogan.co.uk/sequences_..._sequences.htm

    I believe the credit should go to the information on these forums.
    Of the 9 total sequences listed, 7 are from FTDNA.
    So, better than half of my FMS (FGS) matches have submitted to GenBank.

    I was sort of hoping for a new subclade, but doesn't look like we are quite there yet. Think I'll drop an "update" note to my distant kin and see if we can't encourage a few more contributions.

    This seems somehow more manageable that just being "H" as designated officially at both FTDNA and 23andMe.
    23andMe is very limited in their mtDNA testing. On Facebook in the H3 haplogroup we encourage all members with FGS to submit to Genebank. A few dozen have done so. The more unique full genome mitochondrion sequences that are published, the quicker subclades can be established. These are the ones from FTDNA that have not yet been assigned to subclades of H3:
    JN003634.1
    JN006760.1
    JN020360.1
    JN112339.1
    JN202491.1
    JN212576.1
    JN409387.1
    JN674560.1
    JN942526.1

    Leave a comment:


  • AngeliaR
    replied
    H31 at GenBank

    Since this last November, there have been 4 added to the H31 group.
    All 4 new entries originated from FTDNA.

    http://www.ianlogan.co.uk/sequences_..._sequences.htm

    I believe the credit should go to the information on these forums.
    Of the 9 total sequences listed, 7 are from FTDNA.
    So, better than half of my FMS (FGS) matches have submitted to GenBank.

    I was sort of hoping for a new subclade, but doesn't look like we are quite there yet. Think I'll drop an "update" note to my distant kin and see if we can't encourage a few more contributions.

    This seems somehow more manageable that just being "H" as designated officially at both FTDNA and 23andMe.

    Leave a comment:


  • JohnLloydScharf
    Guest replied
    Published 21-NOV-2011

    Originally posted by AngeliaR View Post
    I agree and understand the reasoning behind testing companies assigning more conservative designations. However, I misunderstood and believed for a while there was nothing left to be gained from a closer examination of the mtdna results. In reality, there is still a lot to be learned and the tree continues to develop just as it does with ydna. It is a moving target just as it is with Ydna and many branches of the tree have yet been to be defined.

    H is a pretty bland label and doesn't say much. But a subgroup of H... that has potential to mean something more... especially if it hasn't been explored and documented to the fullest extent. Possibly not for everyone, but for me, H was discouraging more than informative. With H31 it seems more hopeful... possibly because it narrows things if only by a little.

    By the way, my GenBank accession number is JQ028728.
    It has yet to be published, but is in the works.
    http://www.ncbi.nlm.nih.gov/nuccore/JQ028728

    Leave a comment:


  • Ann Turner
    replied
    Originally posted by tomcat View Post
    Thank you for that clarification. By "unique" I assume you mean a mutation not shared with the other two.
    Right.

    Leave a comment:


  • tomcat
    replied
    Originally posted by Ann Turner View Post
    AFAIK, that is still correct. The method to determine "not evidently-related" is a requirement for each of the three to have at least one unique mutation in addition to the new motif.
    Thank you for that clarification. By "unique" I assume you mean a mutation not shared with the other two.

    Leave a comment:


  • Ann Turner
    replied
    Originally posted by tomcat View Post
    The rules used to be: three, not evidently-related persons, having the same haplo and the same mutation, not seen in others of their haplo, was the predicate for making a case for a new clade.

    If the rules have changed someone will correct me.

    All you genealogically-interested folk are interested in history, no? Could be this is a chance to make a little history. Could be your unpublished results would supply the third instance needed for the establishment of a new clade for your haplo.
    AFAIK, that is still correct. The method to determine "not evidently-related" is a requirement for each of the three to have at least one unique mutation in addition to the new motif.

    Leave a comment:


  • tomcat
    replied
    The rules used to be: three, not evidently-related persons, having the same haplo and the same mutation, not seen in others of their haplo, was the predicate for making a case for a new clade.

    If the rules have changed someone will correct me.

    All you genealogically-interested folk are interested in history, no? Could be this is a chance to make a little history. Could be your unpublished results would supply the third instance needed for the establishment of a new clade for your haplo.

    Leave a comment:


  • tomcat
    replied
    Yes, yes, yes! FTDNA has always been conservative is assigning clades, both in Mt and Y. And that is odd as FGS has always been on the bleeding edge (still is) as is Y-111 and WTY.

    (They could do something that might redound to their benefit ... publicize their policy ... emphasize customer participation in exploration ... publish links to other sites more forward-leaning in classification ... etc.)

    Leave a comment:

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