Structural variation of cancer cell lines

Question

[fusion.slope]

Hello,

I am wondering if there is a database with annotated the structural variations as also the SNPs for cancer cell lines such as K562, HepG2 and MCF-7.

Any idea? Thanks in advance

Answer 1

[Kevin Blighe]

Try Cancer Cell Line Encyclopedia: https://portals.broadinstitute.org/ccle

I was looking there just yesterday evening and they now have structural variants, fusion genes, mutations, and expression data for hundreds of cell-lines.

You will have to register an account in order to gain access to the data.

Kevin

[fusion.slope]

awesome Kevin, Just in time for my revision then :) Thanks a lot

[Kevin Blighe]

Sure thing - best of luck with the revision and re-submission

[Kevin Blighe]

For my own curiosity, I went and looked and they do indeed have structural variants in the file 'CCLE structural variants (SvABA calls) for 329 cell lines', which you'll see once you gain access. They have duplications, inversions, deletions, and transversions, from what I can see.

MCF-7 and HepG2 are definitely listed, but I could not see K562 (although I note that cell-lines can go by different names).

So, you are indeed in luck.