Question: How to download DNA sample files in dbGap?
2
gravatar for mangfu100
4.1 years ago by
mangfu100610
Korea, Republic Of
mangfu100610 wrote:

Hello.

I read the paper "Whole-exome sequencing identifies a recurrent NAB2-STAT6 fusion in solitary fibrous tumors" briefly.

After reading it, I tried to find the gene fusion in my exome sequence data with cancer patients from hospital.

But I think that it is a better strategy to identify the gene fusion case through the use of the public data that is specified in the above paper before trying to test on my own set.

So I tried to find an explanation about how to access public data in the paper to identify the gene fusion.

Finally I found the bold sentence (below).

Accession code. Sequence data used for this analysis are available at the database of Genotypes and Phenotpyes(dbGap) under accesssion. phs000568.v1.p1. 

Just reading it, I think I can download data if i have permission. So I go to dbGap stite and search phs000568.v1.p1 and many results occur to me. But I don't know how to access above databases and also don't know how to download.

So Is there anyone who have experienced this before?

If so, I need your help!

Thank you.

 

sequence next-gen gene • 3.0k views
ADD COMMENTlink modified 4.1 years ago by Obi Griffith17k • written 4.1 years ago by mangfu100610
4
gravatar for Jeremy Leipzig
4.1 years ago by
Philadelphia, PA
Jeremy Leipzig17k wrote:

http://www.ncbi.nlm.nih.gov/sra?linkname=gap_sra_all&from_uid=874173

ADD COMMENTlink written 4.1 years ago by Jeremy Leipzig17k

Thank you for your reply.

I clicked the site and looked into what the pages contained.

It has many whole-exome sequencing data.

Is that right exome data that i am looking for ?

If it's right, how to i confirm and download?

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by mangfu100610

Did you apply for request through the authorized access system?

https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?adddataset=phs000568&page=login

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Jeremy Leipzig17k

Not yet .

I think that it is out of my ability.

I have read the whole context about the authorized access system, I am figuring out that it's a task which a professor or dean of my school may have to do..not me. Is that right? (I'm an ordinary student studying in the biology field)

ADD REPLYlink modified 4.1 years ago by Obi Griffith17k • written 4.1 years ago by mangfu100610

Yes. It is perhaps a bit too restrictive. Good luck.

ADD REPLYlink written 4.1 years ago by Jeremy Leipzig17k
1

This is the problem in a nutshell with the dbgap firewall. It prevents researchers from easily accessing the data they need to explore, reproduce or develop new analyses. All under the (mostly false) premise of protecting patient privacy.

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Obi Griffith17k
3
gravatar for Obi Griffith
4.1 years ago by
Obi Griffith17k
Washington University, St Louis, USA
Obi Griffith17k wrote:

You can find the relevant dbgap study record by searching dbgap for accession "phs000568.v1.p1". This will get you to the appropriate dbgap study page:
http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000568.v1.p1

From there we can learn that the study is available for "General Research Use" and does not require IRB. This makes the process much easier than it would be otherwise. But, you still need to have a PI apply for permission to access the data and they will have to agree to follow/supervise the proper protocols in terms of how the data is used and stored.

If your PI is USA-based and has applied for funding then they will most likely have an ERA commons account and be able to login and initiate request for access. You will then probably have to wait some time for your institution signing official and then dbgap to approve your request.  I have no idea how this works for non-USA based researchers though.

 

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Obi Griffith17k
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