Optimizing therapeutic options in personalized medicine

Abstract

In an aspect, a method includes obtaining patient data for a patient, the patient data including one or more molecular biomarkers specific to the patient, standardizing and curating the patient data, classifying the standardized and curated patient data including classifying the one or more molecular biomarkers by one or more of its functional effects, using the one or more functional effects for the one or more molecular biomarkers to identify a combination of available therapeutic options by targeting biomarkers with relevant functional effects based on the patient data, applying a learning method to optimize results for presentation to a user, and presenting optimized results to the user.

1 - 110 . (canceled) 
     
     
         111 . A method for providing therapeutic recommendations to a user, the method comprising:
 (a) obtaining patient data for a patient, the patient data comprising a list of molecular biomarkers specific to the patient;   (b) classifying molecular biomarkers from the list of molecular biomarkers by their functional effects;   (c) generating therapeutic recommendations for the patient using the following steps:   (i) generating therapeutic options comprising therapies acting on molecular biomarkers from the list of molecular biomarkers by using combinations of available drugs that target one or more molecular biomarkers comprising alterations considered functionally impacting a disease course for the patient, wherein the available drugs are chosen from approved drugs and/or experimental drugs;   (ii) optionally, filtering out potentially unwanted therapeutic options by querying a database containing known or predictable negative interactions, or containing drug toxicity or contraindication data, or containing pharmacogenomics data;   (iii) scoring the generated therapeutic options or therapeutic options remaining after filtering out potentially unwanted therapeutic options from the generated therapeutic options, wherein the scoring is based on at least an efficiency-toxicity balance for each therapeutic option, thereby producing a numerical or qualitative score for each therapeutic option;   (iv) optionally, setting a threshold score for the generated therapeutic options and filtering out therapeutic options having scores that do not meet or exceed the threshold score;   (v) sorting therapeutic options remaining after steps (ii)-(iv) by one or more relevant criteria selected by a user, wherein the one or more relevant criteria comprise at least one of the following: the numerical or qualitative score of a given therapeutic option generated in step (iii), a number of drugs in a given therapeutic option, a number of biomarkers covered by a given therapeutic option, a number of biomarkers not covered by a given therapeutic option, a presence of acceptable targeting redundancies, a presence of pharmacological class redundancies,   thereby generating a list of therapeutic options;   d) presenting the list of therapeutic options to the user.   
     
     
         112 . The method of  claim 111 , wherein in step (v), the therapeutic options remaining after steps (ii)-(iv) are sorted based on a number of biomarkers covered by a given therapeutic option and having alterations considered functionally impacting the disease course for the patient. 
     
     
         113 . The method of  claim 111 , wherein the patient data are obtained by methods of genomic profiling, epigenomics profiling, transcriptomic profiling, proteomic profiling, metabolomics profiling, or biochemistry profiling. 
     
     
         114 . The method of  claim 111 , wherein the patient data comprises a medical history and demographics data, wherein the medical history and demographics data comprises one or more of age, gender, a histological diagnosis, a previous treatment, a current treatment, a comorbidity, a familial history, and an inherited syndrome. 
     
     
         115 . The method of  claim 111 , wherein the available drugs comprise immunotherapy. 
     
     
         116 . The method of  claim 111 , wherein the list of molecular biomarkers is obtained via at least one of: a biopsy;
 an external resource;   transcriptomic profiling, wherein the transcriptomic profiling comprises one or more of a microarray, RNA sequencing, real-time polymerase amplification;   genomic profiling, wherein the genomic profiling comprises one or more of histone modification assay, chromatin immunoprecipitation, restriction landmark analysis, bisulfate sequencing;   proteomic profiling, wherein proteomic profiling comprises one or more of an immunoassay and mass spectrometry; and   one or more of metabolomics profiling and biochemistry profiling.   
     
     
         117 . The method of  claim 111 , wherein presenting the list of therapeutic options to the user comprises:
 displaying the list of therapeutic options in a user interface hosted by a web server; or   presenting the list of therapeutic options in a report.   
     
     
         118 . The method of  claim 111 , further comprising:
 recommending a specific dosage of each drug in the list of therapeutic options.   
     
     
         119 . The method of  claim 111 , wherein therapies acting on molecular biomarkers comprise a combinational therapy. 
     
     
         120 . The method of  claim 111 , wherein therapies acting on molecular biomarkers comprise a monotherapy. 
     
     
         121 . A computer program product comprising computer executable code embodied in a non-transitory computer readable medium that, when executing on one or more computing devices, performs the steps of:
 (a) obtaining patient data for a patient, the patient data comprising a list of molecular biomarkers specific to the patient;   (b) classifying molecular biomarkers from the list of molecular biomarkers by their functional effects;   (c) generating therapeutic recommendations for the patient using the following steps:   (i) generating therapeutic options comprising therapies acting on molecular biomarkers from the list of molecular biomarkers by using combinations of available drugs that target one or more molecular biomarkers comprising alterations considered functionally impacting a disease course for the patient, wherein the available drugs are chosen from approved drugs and/or experimental drugs;   (ii) optionally, filtering out potentially unwanted therapeutic options by querying a database containing known or predictable negative interactions, or containing drug toxicity or contraindication data, or containing pharmacogenomics data;   (iii) scoring the generated therapeutic options or therapeutic options remaining after filtering out potentially unwanted therapeutic options from the generated therapeutic options, wherein the scoring is based on at least an efficiency-toxicity balance for each therapeutic option, thereby producing a numerical or qualitative score for each therapeutic option;   (iv) optionally, setting a threshold score for the generated therapeutic options and filtering out therapeutic options having scores that do not meet or exceed the threshold score;   (v) sorting therapeutic options remaining after steps (ii)-(iv) by one or more relevant criteria selected by a user, wherein the one or more relevant criteria comprise at least one of the following: the numerical or qualitative score of a given therapeutic option generated in step (iii), a number of drugs in a given therapeutic option, a number of biomarkers covered by a given therapeutic option, a number of biomarkers not covered by a given therapeutic option, a presence of acceptable targeting redundancies, a presence of pharmacological class redundancies,   thereby generating a list of therapeutic options;   d) presenting the list of therapeutic options to the user.   
     
     
         122 . A system comprising:
 a server;   a computing device in communication with the server over a network, the computing device including a processor and a memory, the memory bearing computer executable code configured to perform the steps of:   (a) obtaining patient data for a patient, the patient data comprising a list of molecular biomarkers specific to the patient;   (b) classifying molecular biomarkers from the list of molecular biomarkers by their functional effects;   (c) generating therapeutic recommendations for the patient using the following steps:   (i) generating therapeutic options comprising therapies acting on molecular biomarkers from the list of molecular biomarkers by using combinations of available drugs that target one or more molecular biomarkers comprising alterations considered functionally impacting a disease course for the patient, wherein the available drugs are chosen from approved drugs and/or experimental drugs;   (ii) optionally, filtering out potentially unwanted therapeutic options by querying a database containing known or predictable negative interactions, or containing drug toxicity or contraindication data, or containing pharmacogenomics data;   (iii) scoring the generated therapeutic options or therapeutic options remaining after filtering out potentially unwanted therapeutic options from the generated therapeutic options, wherein the scoring is based on at least an efficiency-toxicity balance for each therapeutic option, thereby producing a numerical or qualitative score for each therapeutic option;   (iv) optionally, setting a threshold score for the generated therapeutic options and filtering out therapeutic options having scores that do not meet or exceed the threshold score;   (v) sorting therapeutic options remaining after steps (ii)-(iv) by one or more relevant criteria selected by a user, wherein the one or more relevant criteria comprise at least one of the following: the numerical or qualitative score of a given therapeutic option generated in step (iii), a number of drugs in a given therapeutic option, a number of biomarkers covered by a given therapeutic option, a number of biomarkers not covered by a given therapeutic option, a presence of acceptable targeting redundancies, a presence of pharmacological class redundancies,   thereby generating a list of therapeutic options;   d) presenting the list of therapeutic options to the user.