Pharmacogenomics of Intergenic Single-Nucleotide Polymorphisms and in Silico Modeling for Precision Therapy

A method for simulating the effects of a therapeutic drug treatment on a patient or a group of patients, the method comprising:

• a) screening a tissue sample extracted from a patient selected to receive a drug for single-nucleotide polymorphisms (SNPs),
• b) identifying gene products associated with the SNPs from the patient tissue sample having altered expression;
• c) retrieving from one or more databases information on altered gene product expression associated with adverse or beneficial effects of the drug;
• d) simulating the adverse or beneficial drug effect occurring when the drug is administered to the patient based on the gene products that are associated with both the SNPs from the patient tissue sample and the adverse or beneficial effects of the drug.

A non-transitory computer-readable storage medium having a software program containing computer-executable instructions for performing a method for identifying drug candidates to treat a selected disease, said method comprising:

• a) searching a first database for single-nucleotide polymorphisms (SNPs) associated with presence of the selected disease, and generating a set of disease SNPs;
• b) searching a second database for gene products having altered expression associated with each of the disease SNPs;
• c) selecting two or more disease SNPs which share at least one gene product having altered expression from the second database, and generating a set of one or more SNP pairs;
• d) analyzing the one or more SNP pairs and generating a similarity value for each SNP pair based on similarity of biological mechanisms between each SNP within the SNP pair;
• e) generating a set of prioritized SNP pairs where higher prioritized pairs have a higher similarity value;
• and
• f) identifying a drug able to interact with the shared gene product having altered expression from a prioritized SNP pair.

A pharmacogenomic system for identifying drug candidates to treat a disease comprising:

• a) a disease SNP module comprising information which identifies a plurality of SNPs associated with presence of the disease;
• b) an altered gene product module comprising information on gene products having altered expression and the plurality of SNPs;
• c) a pairing module connected to the disease SNP module and the altered gene product module able to generate a set of one or more SNP pairs where both SNPs in each pair are associated with a same gene product having altered expression;
• d) an analyzing module connected to the pairing module able to predict similarity of biological mechanisms between each SNP within a generated SNP pair, and able to generate a set of prioritized SNP pairs having increased similarity of biological mechanisms;
• e) a drug and molecular target module comprising information on a plurality of drugs and molecular targets affected by each of the plurality of drugs;
• and
• f) an identification module able to identify one or more drugs from the plurality of drugs which affects a molecular target which is the same as the gene product having altered expression from a prioritized SNP pair.