# US 11,299,782 B2 · Methods for predicting anti-cancer response > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 11,299,782 B2 - Document ID: US11299782B2 - Status: Granted - Kind: B2 - Application number: 16/235,247 - Filed: 2018-12-28 - Published: 2019-05-09 - Granted: 2022-04-12 - Earliest claimed: 2012-02-23 - Assignees: Children's Medical Center Corporation; Technical University of Denmark; Dana-Farber Cancer Institute, Inc.; The Brigham and Women's Hospital, Inc. - Applicants: Children's Medical Center Corporation; The Technical University of Denmark; Dana-Farber Cancer Institute, Inc.; The Brigham and Women's Hospital, Inc. - Inventors: Zoltan Szallasi; Nicolai Juul Birkbak; Aron Eklund; Daniel Silver; Zhigang Wang; Andrea Richardson - Web page: https://patentgrep.com/patent/US11299782B2 ## CPC - C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation - C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575) - C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism - C12Q 2600/154: Methylation markers - C12Q 2600/156: Polymorphic or mutational markers - C12Q 2600/158: Expression markers - G01N 2800/52: Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) ## Abstract The present invention is based, in part, on the identification of novel methods for defining predictive biomarkers of response to anti-cancer drugs. ## Claims ### Claim 1 A method of administering an anti-cancer treatment to a human patient, the method comprising: (1) directing a clinical laboratory to (a) detect a plurality of chromosomal aberrations in chromosomal segments comprising a plurality of loci in a sample from a human patient, wherein chromosomal aberrations are detected in at least one pair of human chromosomes of a cancer cell of the patient, wherein each of the chromosomal segments is at least 12 Mb in length, extends to and involves the telomere but does not cross the centromere, (b) calculate a telomeric imbalance score (NtAI) by summing the number of chromosomal aberrations detected in step (a), and (c) communicate an NtAI to the clinician, and (2) administering an anti-cancer therapy selected from the group consisting of platinum-comprising therapy, DNA damaging agent comprising therapy, anthracycline-comprising therapy, topoisomerase I inhibitor-comprising therapy and PARP inhibitor comprising therapy to the patient in whose sample an NtAI of at least 8 is calculated. ### Claim 2 (depends on 1) The method of claim 1, wherein said detecting a plurality of chromosomal aberrations is in at least two, five, ten or 21 pairs of human chromosomes. ### Claim 3 (depends on 1) The method of claim 1, wherein the DNA damaging agent is cisplatin, carboplatin, oxalaplatin, or picoplatin, said anthracycline is epirubincin or doxorubicin, said topoisomerase I inhibitor is campothecin, topotecan, or irinotecan, and/or said PARP inhibitor is iniparib, olaparib or velapirib. ### Claim 4 (depends on 1) The method of claim 1, wherein the cancer is selected from the group consisting of breast cancer, ovarian cancer, melanoma, transitional cell bladder cancer, bronchogenic lung cancer, thyroid cancer, pancreatic cancer, prostate cancer, uterine cancer, testicular cancer, gastric cancer, soft tissue and osteogenic sarcomas, neuroblastoma, Wilms' tumor, malignant lymphoma (Hodgkin's and non-Hodgkin's), acute myeloblastic leukemia, acute lymphoblastic leukemia, Kaposi's sarcoma, Ewing's tumor, refractory multiple myeloma, and squamous cell carcinomas of the head, neck, cervix, colon cancer, or vagina. ### Claim 5 A method of administering an anti-cancer treatment to a human patient, the method comprising: (1) receiving a telomeric imbalance score (NtAI) of at least 8 from a clinical laboratory, wherein the NtAI is determined by the steps of: (a) detecting a plurality of chromosomal aberrations in chromosomal segments comprising a plurality of loci in a sample from a human patient, wherein chromosomal aberrations are detected in at least one pair of human chromosomes of a cancer cell of the patient, wherein each of the chromosomal segments is at least 12 Mb in length, extends to and involves the telomere but does not cross the centromere, and (b) calculating the NtAI score by summing the number of chromosomal aberrations detected in step (a), and (2) administering to said patient an anti-cancer therapy selected from the group consisting of platinum-comprising therapy, DNA damaging agent comprising therapy, anthracycline-comprising therapy, topoisomerase I inhibitor-comprising therapy and PARP inhibitor comprising therapy. ### Claim 6 (depends on 5) The method of claim 5, wherein said detecting a plurality of chromosomal aberrations is in at least two, five, ten or 21 pairs of human chromosomes. ### Claim 7 (depends on 5) The method of claim 5, wherein the DNA damaging agent is cisplatin, carboplatin, oxalaplatin, or picoplatin, said anthracycline is epirubincin or doxorubicin, said topoisomerase I inhibitor is campothecin, topotecan, or irinotecan, and/or said PARP inhibitor is iniparib, olaparib or velapirib. ### Claim 8 (depends on 5) The method of claim 5, wherein the cancer is selected from the group consisting of breast cancer, ovarian cancer, melanoma, transitional cell bladder cancer, bronchogenic lung cancer, thyroid cancer, pancreatic cancer, prostate cancer, uterine cancer, testicular cancer, gastric cancer, soft tissue and osteogenic sarcomas, neuroblastoma, Wilms' tumor, malignant lymphoma (Hodgkin's and non-Hodgkin's), acute myeloblastic leukemia, acute lymphoblastic leukemia, Kaposi's sarcoma, Ewing's tumor, refractory multiple myeloma, and squamous cell carcinomas of the head, neck, cervix, colon cancer, or vagina.