Interpreting Cancer Copy-Number Alterations

Copy-number alterations are among the most common alterations in cancer, and affect more of the genome than any other alteration. We have been studying copy-number alterations genome-wide among thousands of cancers across dozens of cancer types. We find hundreds of regions that are recurrently amplified and deleted, and most of these do not encompass known oncogenes or tumor suppressor genes. Determining the driver genes that are “targeted” by recurrent copy-number changes will benefit from an improved accounting for the mechanisms by which those copy-number changes arise as well as an accounting for the effects of both positive and negative selection.