Conclusion We briefly reviewed the current challenges and perspectives of integrative cancer genomics, focusing particularly on the complexity of omics data and cancer biology. Integromic approaches with functional evaluation should be considered even for clinical as well as mechanistic applications of cancer genome data. Necessarily, the challenges of big data (particularly the NGS platforms) and integromics should be considered in the study design. A deep understanding of both cancer biology and omics data characteristics is necessarily required for successful cancer genome analysis. Moving forward, it is clear that progress will come through large-scale, wide-scope, and multi-disciplinary collaborations and sharing systems, which will accelerate the realization of translational and personalized medicine in the near future.