Why we need to get our DNA results to Genebank

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Permalink Reply by Peiternella Suzzanna Hymen on March 6, 2010 at 6:20pm

I, like many others, need to get our FGS or HVR1 and HVR2 to Genabank. Why! one may ask should we...here is the main reason. Genealogist are manly hobbyists who do not have access to many academic papers to source the data so they can make up comprehensive data bases and studies for any particular haplogroups, new clades etc or data for study and writing their own papers. I have a H3 data base ( currently building an H database) and it has revealed quite a bit of data concerning numerous, as yet, undefined sub glades within the H3 branches. Example is that I am classed as an H3 only but I have a particular mutation T12811C which I share with 2 other people which we sourced from Genbank. I am with FTDNA and have no close matches.
Only HVR1 and 2 results are published on the public site at FTDNA due to privacy issues.I and many others who are interested cannot see the coding region mutations and this is what we need. Therefore, if as many DNA participants get there results on Genbank the better for our group.
Heres how we can go about it: Ian Logan can do all the work for you, use the link below http://www.ianlogan.co.uk/checker/genbank.htm
No names have to be mentioned just your Kit number and place you had your sequence done. All very private..no worries of your medical company finding your data LOL
Good luck guys.

Permalink Reply by Mardon Erbland on April 4, 2010 at 8:29am

Just thought I'd let you know that my mtDNA FGS was published at GenBank yesterday. The GenBank accession number for my sequence is HM034770.1.

As Peiternella has said, your GenBank sequence submission does not have to identify you by name in their database. Things can be kept private. That said, I chose to associate my name with my sequence.

GenBank is reluctant to publish the submitter's name as a co-author because of the potential for unforeseen, future negative consequences of making your coding region public. Once the submitter associates his or her name with their sequence by listing themselves as a co-author, the information is in the public domain and privacy can never be restored. This is true even if the sequence is removed from GenBank, because once it goes into GenBank, other databases and researchers download it and there is no trail of who has it or where it has gone. Having said that, I still chose to list my name as a co-author for my sequence. I guess I'm just 'a risk taker' and figured that there might be unforeseen future benefits of doing so as well as unforeseen future dangers.

My sequence can be seen here:
http://www.ncbi.nlm.nih.gov/nuccore/292597332?report=genbank

There are no 100% matches to me in the GenBank database. Using BLAST (http://preview.tinyurl.com/ykv7frm) I found that the closest to me is EU151553.1 which matches me 16562 out of 16569 positions.

BTW Peiternella, I assume that when you wrote 'GenaBank' in the first line it was just a typo because you used 'GenBank' after that.

Permalink Reply by Peiternella Suzzanna Hymen on April 14, 2010 at 3:19am

Hi Mardon, Yes I did make a spelling mistake and my proof reading sucks big time. LOL. Yours and my submission went in at the same time to Genbank. But so far they are not showing up, however it was last week I looked. So how easy did you find doing the Blast>

Permalink Reply by Mardon Erbland on April 14, 2010 at 4:00am

Hi Peiternella,

My sequence was published by GenBank on April 4th (HM034770.1). It has been public ever since. My GI number is: 292597332. You can see my sequence here: http://www.ncbi.nlm.nih.gov/nuccore/292597332?report=genbank
You will see my name listed as a co-author: " Erbland, M.J."

I find BLAST very easy to use. I start with the BLAST search page at:
http://preview.tinyurl.com/ykv7frm

If you enter a BLAST Acsession number in the first box, and click "BLAST", you will get a list of the GenBank sequences that most closely match the one you've entered. The rCRS (NC_012920.1) sequence is shown in the first box by default. If you click the "Align two or more sequences" check box, then another box will appear where you can enter GenBank Accession numbers. If you enter "NC_012920.1" (rCRS) in the first box and your own GenBank Accession number in the second box, and click "BLAST" you will get a comparison of your sequence to rCRS.

At the top of the comparison page you will see a line that says "Query ID". Your Genbank Ascension number will be at the right end of that line. Click on it and you will see the details for your sequence as submitted, including your GI number.

Hope this helps, Mardon

Permalink Reply by Kay Fordham on May 10, 2010 at 4:59pm

Hi - I entered my FGS into Genebank on 2 March - succession # is GU945760. FTDNA has me as H11. PhyloTree as H11a (perhaps H11a1). No close matches thus far.

Regards, Kay Fordham