US 11,810,672 B2
Cancer score for assessment and response prediction from biological fluids
Shahrooz Rabizadeh, Agoura Hills, CA (US); and Patrick Soon-Shiong, Culver City, CA (US)
Assigned to NantOmics, LLC, Culver City, CA (US)
Appl. No. 16/754,088
Filed by Nantomics, Culver City, CA (US)
PCT Filed Oct. 11, 2018, PCT No. PCT/US2018/055481
§ 371(c)(1), (2) Date Apr. 6, 2020,
PCT Pub. No. WO2019/075251, PCT Pub. Date Apr. 18, 2019.
Claims priority of provisional application 62/571,414, filed on Oct. 12, 2017.
Prior Publication US 2020/0335215 A1, Oct. 22, 2020
Int. Cl. G16H 50/20 (2018.01); G16H 50/30 (2018.01); G16H 50/70 (2018.01); G16H 20/40 (2018.01); G16H 70/60 (2018.01); G16H 10/40 (2018.01); G16H 10/60 (2018.01); G16H 20/10 (2018.01); G16B 20/20 (2019.01); G16B 20/10 (2019.01); G16B 25/10 (2019.01)
CPC G16H 50/20 (2018.01) [G16B 20/10 (2019.02); G16B 20/20 (2019.02); G16H 10/40 (2018.01); G16H 10/60 (2018.01); G16H 20/10 (2018.01); G16H 20/40 (2018.01); G16H 50/30 (2018.01); G16H 50/70 (2018.01); G16H 70/60 (2018.01); G16B 25/10 (2019.02)] 18 Claims
 
1. A method of analyzing omics data and treating a patient having a cancer, the method comprising:
obtaining blood from the patient having or suspected to have the cancer;
obtaining, from the blood, omics data for a plurality of cancer-related genes, wherein the omics data comprise at least one of DNA sequence data, RNA sequence data, and RNA expression level data; providing an omics record computer system that includes at least one processor and at least one computer readable memory coupled to the processor and configured to digitally store the omics data for the plurality of cancer-related genes in the at least one memory;
calculating, in silico, a digital score from the digital omics data, wherein the digital score is calculated in silico by the sum of (i) counting the number of mutations of cancer-related genes, inflammation-related genes, and DNA-repair genes, (ii) counting changes in methylation or modifications in DNA of cancer-related genes and DNA-repair genes, (iii) counting upregulation or downregulation in expression levels of RNA of cancer-related genes, inflammation-related genes, and DNA-repair genes, (iv) counting the number of tumor- and patient-specific neoepitopes, (v) counting splice variants of cancer-related genes and DNA-repair genes, and (vi) counting changes in length of poly A tail of any cancer-related genes, inflammation-related genes, and DNA-repair genes;
associating the digital score with at least one of a health status, an omics error status, a cancer prognosis, a therapeutic recommendation, an effectiveness of a treatment; and
upon the digital score reaching a threshold value and a majority portion of the digital score is highly weighted as an overexpression of a specific neoepitope;
generating a personalized treatment option for the patient, wherein the personalized treatment option comprises a recombinant nucleic acid encoding one or more tumor- and patient-specific neoepitopes; and
treating the cancer by administering the personalized treatment option to the patient.