Hi,

I am currently curating a list of prognostic genes and gene variants responsible for prostate and/or breast cancer. I am currently concentrating only upon germline variants, but am also collecting the somatic variants as when I run into them. Is there a database which already has such a list of genes and also the papers relating to them? The information which I am looking for and curating are the genes, gene locations, mutation type and the link to the paper. Is there any publicly available database which lists all this information.

Thanks,
Venkat


You can look at some of the resources from [Open Targets][1], such as Open Targets Genetics and Open Targets Platform. With the latter, you can find genes associated with [prostate carcinoma][2] and [breast carcinoma][3] based on [somatic mutations][4], germline variants (giving rise to what we call [genetic associations][5]) and many other types of different [data sources][6]. The main entry points here is a gene or disease name.

With [Open Targets Genetics][7], you can find common (germline) variants linked to those traits of interest and the genes that are (potentially) functionally implicated by these common variants. Have a look at these two random examples of studies: 1) [Breast cancer][8] by Michailidou K (2017) in Nature and 2) [Prostate cancer][9] by Schumacher FR (2018) in Nat Genet. And the cool thing is that you can also compare different studies, such as the two above in the "[Compare overlapping studies][10]" page. The main entry points here is the variant (rs ID or GRCh38 coordinates), gene or study/trait names.

Both Open Targets Platform and Open Targets Genetics complement each other (with links from the latter to the former) and there is plenty of things you can do with them, some of them depicted in our short tutorial videos on [YouTube][11].


  [1]: https://www.biostars.org/p/196813/
  [2]: https://www.targetvalidation.org/disease/EFO_0001663/associations
  [3]: https://www.targetvalidation.org/disease/EFO_0000305/associations
  [4]: https://docs.targetvalidation.org/data-sources/somatic-mutations
  [5]: https://docs.targetvalidation.org/data-sources/genetic-associations
  [6]: https://docs.targetvalidation.org/data-sources/data-sources
  [7]: https://www.biostars.org/p/350961/
  [8]: https://genetics.opentargets.org/study/GCST004988
  [9]: https://genetics.opentargets.org/study/GCST006085
  [10]: http://%20https://genetics.opentargets.org/study-comparison/GCST004988?studyIds=GCST006085
  [11]: https://www.youtube.com/channel/UCLMrondxbT0DIGx5nGOSYOQ