Translating genome and proteome information into immune recognition

Recent advances in immunology prompt us to suggest an immediate, highly significant application of genomics information. The immune system considers peptides as key targets and has devoted an entire arm - one that essentially controls specific immune responsiveness - to peptide recognitions. Thus if one could predict how the immune system handles proteins, and how it generates, selects and recognises peptides, then one should be able to translate genomes/proteomes to immunogens, and thereby forecast immune recognition. Although many of the mechanisms involved in antigen presentation have been described in general terms, only few have been described in sufficient details to allow for accurate prediction of their outcome. We propose to integrate cell biology with bioinformatics to create a European databank of immune epitope and the accompanying data mining tools, which should allow scientists and clinicians to screen whole genomes and proteomes for the presence of immunogenic epitopes. The ability to identify immune targets will be of considerable practical utility. With computational prediction tool, whole genomes can be searched and the amount of time and resources spent in vaccine-relevant discovery can be significantly reduced. Capacity is an important issue when searching several pathogen genomes for conserved vaccine candidates. Time is also an issue when searching for patient-specific immunotherapy targets (e.g. cancer).