Question: Cancer database with both germline and genome-wide sequencing data
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gravatar for YanO
6 months ago by
YanO100
United Kingdom
YanO100 wrote:

I am looking for a database where I can find germline, genome-wide/noncoding sequencing data in cancer patients.

There are plenty of exome-sequencing studies and somatic variant calls available but I'm having real trouble finding something with my exact specifictions of germline & genome-wide/noncoding (& preferably breast cancer).

The TCGA database seems to me to have germline data from breast cancer patients, but I think it is only whole-exome-sequencing. So far I have found one study through the ICGC, it's controlled data from WGS in French patients. link here

Has anyone spotted a similar study/database?

At this stage I'd be willing to have a look at somatic variants without the germline filtered out, if that's possible, and failing that I'd be willing to branch out to ovarian cancer... Thanks!

ADD COMMENTlink modified 6 months ago by Samuel Brady230 • written 6 months ago by YanO100
1
gravatar for Samuel Brady
6 months ago by
Samuel Brady230
Samuel Brady230 wrote:

In this study 560 breast cancer whole-genomes were sequenced: http://www.nature.com/nature/journal/v534/n7605/full/nature17676.html. The data are deposited on EGA here: https://www.ebi.ac.uk/ega/studies/EGAS00001001178. At EGA you have to request data access but sometimes the process is relatively smooth. Good luck.

ADD COMMENTlink written 6 months ago by Samuel Brady230
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