| CPC G16B 30/10 (2019.02) [G16B 30/00 (2019.02)] | 8 Claims |
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1. A computer-implemented method of identifying a treatment for a virus associated tumor of a patient, comprising:
obtaining, by a computer and from a sequence database, a whole genome nucleic acid sequence from a reference non-diseased tissue of the patient, a whole genome sequence from a diseased tissue of the same patient, and a nucleic acid sequence of a virus;
merging the whole genome nucleic acid sequence from the reference non-diseased tissue and the nucleic acid sequence of the virus to obtain a chimeric reference nucleic acid sequence;
aligning the chimeric reference nucleic acid sequence and the nucleic acid sequence from the diseased tissue, using incremental synchronized alignment, by the computer, to identify an integration of the viral nucleic acid sequence in the chimeric reference nucleic acid sequence with the nucleic acid sequence from the virus-associated tumor;
identifying a co-amplification of an oncogene sequence of the diseased tissue of the patient and the viral nucleic acid sequence, wherein the oncogene sequence comprises the nucleic acid sequence from the virus-associated tumor of the patient, and wherein the oncogene is ERBB2 (Erythroblastic Leukemia Viral Oncogene Homolog 2);
treating, upon identifying integration and co-amplification, the virus associated tumor in the patient by using a drug targeting the oncogene;
wherein the virus is an HPV virus (Human Papillomavirus).
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