Sequence-based cancer genomics: progress, lessons and opportunities

The genomics revolution has catalysed the development of new technologies that can be applied to provide a comprehensive view of the molecular changes that occur during cancer development.Three independent projects — the Cancer Genome Anatomy Project (CGAP), the Human Cancer Genome Project (HCGP) and the Cancer Genome Project (CGP) — have applied sequence-based technologies to produce synergistic data sets that are amenable to integration.The data of these projects are derived from the human genome (through sequencing of gene exons to identify cancer mutations), as well as from the human transcriptome in the form of expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE) tags that are generated from tumours and normal tissues.The CGAP has facilitated the interface of the human genome sequence with the cytogenetic map through FISH-mapping of BAC clones that were substrates for generating the finished genome sequence. This linkage facilitates the characterization of chromosomal aberrations that are associated with cancer.A suite of informatics tools is accessible through the CGAP website that allow in silico analysis of CGAP and HCGP gene-expression data, polymorphisms and chromosomal aberrations of cancer. In the future, these data sets will be integrated with the mutation analysis of the CGP.The data sets that are generated by these projects are a platform for a variety of applications in cancer research, such as the design and generation of microarrays.