Patent Document ID: 9569586
Application ID: 14374924
Patent Flag: 1

Claim One:
1. A computer-implemented method for identifying wild type or mutated target genes or regulatory elements for cancer therapy, comprising: identifying constraints mediated by a cancer genome architecture on somatic cancer evolution in a human cancer patient; identifying target genes which are involved in mediating the constraints, and which are not from classes of genes including, oncogenes, tumor suppressor genes, or caretaker genes, the identifying the target genes comprising: constructing a phylogenetic tree of somatic cancer evolution of a malignant human tumor within the human cancer patient based on multiple clinical samples of tissue from the human cancer patient, which are representative of clinical cancer progression within the human cancer patient, wherein the constructing the phylogenetic tree of somatic cancer evolution comprises the steps of: a) constructing at least one map of clinical cancer progression in individual patients based on the anatomical and temporal occurrence of a primary tumor and its metastases, b) obtaining DNA, RNA and proteins of unaffected tissue and of samples of the primary tumor, and of regional and distant metastases from the human cancer patient representing clinical cancer progression, c) extraction of genome wide genetic data out of the obtained tissues in order to determine the cancer genome architecture of analyzed tissue samples by determination of RNA and protein expression, of karyotypes, of gene losses and gains as well as of gene allele losses in tumor tissues; genetic data may be obtained by various molecular methods such as cDNA expression arrays, comparative genomic hybridization arrays, single nucleotide polymorphism arrays, as well as high throughput DNA sequencing, d) constructing a preliminary phylogenetic tree of the somatic cancer evolution, including clustering of the genetic data obtained by step (c) to obtain information, and, e) constructing of a definitive phylogenetic tree of somatic cancer evolution further including identifying cancer subclone populations and resolving contradictory results due to mixing of subclones by clustering the genetic data obtained by step (c) and applying the information obtained in step (d); wherein the cancer genome architecture comprises: the base composition of genes, of regulatory elements and, if present in cancer cells, of foreign (viral) DNA/RNA sequences, the presence and copy number of wild type or mutated genes, of regulatory elements, and if present in cancer cells, of foreign (viral) DNA/RNA sequences, the physical arrangement of genes, of regulatory elements, and, if present in cancer cells, of foreign (viral) DNA/RNA sequences within chromosomes as well as within mitochondrial DNA, including rearrangements of chromosomes or chromosome fragments, the chromatin organization including epigenetic modifications, interaction of DNA with RNAs and nuclear proteins and nuclear topology of chromosomes, and the status of gene transcription; and, treating the human cancer patient by targeting the identified target genes in order to kill cancer cells, or to slow, or stop clinical cancer progression in the human cancer patient.