Looking for cancer sequencing data.

Question

[reza.haffari]

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,

Answer 1

[Sean Davis]

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

Answer 2

[reza.haffari]

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?

[Sean Davis]

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.

[reza.haffari]

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).

[Sean Davis]

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.

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