Patent Document ID: 10095842
Application ID: 13118395
Patent Status: 1

Claim One:
1. A therapeutic method against a hematological cancer, the method comprising: a) providing a biological sample from blood or bone marrow of a patient suffering from a hematological cancer, the sample comprising cells; b) providing a plurality of control molecules as a set of control molecules, wherein each control molecule of the set is independently selected from the group consisting of a microRNA, a small molecule, a peptide, a protein, a cytokine, and a metabolite; c) isolating cancer cells using density gradient centrifugation; d) obtaining RNA sequence data from the cancer cells and selecting a subset of control molecules from a measure of enrichment in differentially expressed genes in groups including targets of the control molecules and their neighbors within a network model of intracellular interactions, wherein the enrichment in differentially expressed genes is measured by measuring and comparing RNA expression data of the cancer cells and the control cells; e) assaying the subset of control molecules with the cells using an endpoint assay to obtain a set of assay results for a biological effect, wherein the endpoint assay is selected from the group consisting of an assay that determines growth, survival, or death of a living cell or an assay that determines differentiation from one cell type to another cell type under in vitro testing conditions providing a significant correlation between the effects of the same drugs in vitro and in vivo; f) executing a software platform that manages design of combinations with an algorithm, exchanges files between liquid handling and plate readout equipment, maps combinations to measured data, and compiles results; g) searching with a liquid handler, multi-well plates and a plate reader, an experimental space over iterations of measurements; h) retrieving and storing files from a database to identify reagents, track reagent combinations dispensed in wells of a series of multi-well plates, maintain assay data measured for each combination, and generate plate maps and files for interfacing liquid handlers and plate readers while searching the experimental space; i) searching the set of assay results to identify a subset of control molecules, wherein i) the subset of control molecules is composed of at least three of the plurality of control molecules, ii) each of the control molecules of the subset binds at least three targets, iii) each of the at least three targets binds at least three of the control molecules in the subset, and iv) at least three of the control molecules of the subset bind to one or more shared targets, wherein a shared target is a target that binds at least two of the control molecules; further wherein each target is a molecule independently selected from the group consisting of a cellular protein, an RNA, and a metabolite; j) providing the identified subset of control molecules as contributing to a combinatorial therapy for a patient having a same hematological cancer; and k) administering the subset of control molecules to the patient.