Most clinically distinguishable malignant tumors are characterized by specific mutations, specific patterns of chromosomal rearrangements and a predominant mechanism of genetic
instability. It has been suggested that the internal dynamics of genomic modifications as opposed to the external evolutionary forces have a significant and complex
impact on Darwinian species evolution. A similar situation can be expected for somatic
cancer evolution as the key mechanisms encountered in species evolution such as duplications, rearrangements or deletions of genes also constitute prevalent
mutation mechanisms in cancers with chromosomal
instability. The invention is an
algorithm which is based on a systems concept describing the putative constraints of the
cancer genome architecture on somatic
cancer evolution. The
algorithm allows the identification of therapeutic target genes in individual cancer patients which do not represent oncogenes or tumor
suppressor genes but have become putative therapeutic targets due to constraints of the
cancer genome architecture on individual somatic cancer evolution. Target genes or regulatory elements may be identified by their designation as essential genes or regulatory elements in cancer cells of the patient but not in
normal tissue cells or they may be identified by their
impact on the process of somatic cancer evolution in individual patients based on phylogenetic trees of somatic cancer evolution and on the constructed multilayered
cancer genome maps. The
algorithm can be used for delivering personalized
cancer therapy as well as for the industrial identification of novel anti-
cancer drugs. The algorithm is essential for designing
software programs which allow the prediction of the natural history of cancer
disease in individual patients.