Question: Looking for cancer sequencing data.
1
gravatar for reza.haffari
3.2 years ago by
reza.haffari10
Australia
reza.haffari10 wrote:

Hi All,

I am looking for some next-gen sequencing data for cancer patients in either of the following scenarios:

- matched tumor/normall of some cancer patients/cell-lines 

- sequencing of cancer patients/cell-lines at multiple times and/or multiple regions

It would be fine if it is WGS, WES, or targeted. Any comments would be appreciated about publicly available data or those in DbGap/EGA etc that you have worked with.

Thanks,

sequencing next-gen data genome • 1.2k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by reza.haffari10
1
gravatar for Sean Davis
3.2 years ago by
Sean Davis24k
National Institutes of Health, Bethesda, MD
Sean Davis24k wrote:

TCGA has several thousand such samples.  Any human data (except cell lines) will likely require dbGAP access and TCGA is no exception.

ADD COMMENTlink written 3.2 years ago by Sean Davis24k
0
gravatar for reza.haffari
3.2 years ago by
reza.haffari10
Australia
reza.haffari10 wrote:

Thanks for your reply. I have worked with TCGA data in the past but they didn't provide the actual reads. It seems from their website that they are providing the bam files now too (not sure for all projects or some of them though). Can you point to some cancer sequencing projects that have actual reads?

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by reza.haffari10
1

Please use the comment mechanism when replying to answers.  

As to your comment above, the reads are available after going through the dbGaP data access request process.  TCGA is no exception.  You will not find any projects that make patient reads available "publicly" because it is unethical to do so without some very unusual circumstances.

 

ADD REPLYlink written 3.2 years ago by Sean Davis24k

I know that there are ethical issues for "truly public" data, but by public I meant the arrangement that you apply to get accession. now instead of going through these obvious stuff, I'd appreciate if you answer the question by "concretely" mentioning some of the datasets for the scenarios i mentioned above, in case you know of any (particularly, the multi-time multi-region case).

ADD REPLYlink written 3.2 years ago by reza.haffari10
1

I'm sorry that you find my answers less than helpful.  If you find the answers provided here by VOLUNTEERS unsatisfactory, you are welcome to pursue other options.  

It appears that perhaps my answer was not detailed enough for you, so I'll try to clarify.  I was addressing the first point in your original question by suggesting TCGA as a source of read data for matched tumor/normal data.  You mentioned that TCGA does not provide reads, which is incorrect.  The reads are available after going through the process described here.

https://cghub.ucsc.edu/access/get_access.html

And to be concrete about available data, please see this page:

https://cghub.ucsc.edu/summary_stats.html

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Sean Davis24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1409 users visited in the last hour