Somatic mutations and copy number alterations are the basis for cancer development and progression, and their identification is crucial for the development of novel diagnostics and therapies. Identification of somatic alterations has been greatly sped up by recent technological progresses, such as CGH and SNP arrays, and high-throughput DNA sequencing. An immense set of genomic data will be available in the near future. It will be mandatory to overlay and integrate multiple levels of genomic and functional information, aiming for the bigger picture of cancer biology. The ultimate goal will be a detailed understanding of pathways and mechanisms altered in cancer, leading the way to improved therapeutic strategies.