We have several cancer cell lines that have been reported as harboring multiple translocations, and I'd like to know the best ways to test them and verify these results. Recent papers have shown that tissue culture cells are less clonal than the field has assumed, so before investing a lot of time in studies we want to confirm that ~10 cell lines are harboring the translocations that have been reported previously (especially since there are publications with contradictory translocations reported).
We'd like to do this analysis informatically. Ideally we'd like a targeted panel for sequencing or even microarray/qPCR (performing FISH is outside of our realm of expertise). I'm imagining something analogous to whole exome-seq, where we're enriching for specific regions of the genome then sequencing.
Alternatively, if whole genome sequencing is considered the best option, what sequencing depth and analysis pipelines would you recommend to identify high confidence translocations in cell lines that may be polyploidy?
Thank you very much for the help!