Systems, methods and computer program products for guiding selection of a therapeutic treatment regimen based on the methylation status of the DNA

A method for treatment of a patient with a disease or medical condition, said method comprising:

• (A) isolating a DNA-containing sample from said patient;
• (B) analyzing cytosine methylation patterns at selected sites of the DNA contained in said sample;
• (C) providing data about the methylation status at selected sites of the DNA of the patient thereby creating a first knowledge base comprising said data, a second knowledge base comprising information about a plurality of different methylation statuses at selected sites of the DNA in cells with a known disease or medical condition and/or healthy cells, a third knowledge base comprising a plurality of expert rules for evaluating and selecting a type of disease or medical condition based on the methylation status at selected sites of the DNA of a patient, and
• (D) generating a ranked listing of diseases or medical conditions based on the data of the first knowledge base, the second knowledge base and the third knowledge base.

A system for guiding the selection of a therapeutic treatment regimen for a patient with a disease or medical condition, said system comprising:

• (A) a computing device comprising:
• a first knowledge base comprising information about a plurality of different methylation statuses at selected sites of the DNA in cells with a known disease or medical condition and/or healthy cells,
• a second knowledge base comprising a plurality of expert rules for evaluating and selecting a type of disease or medical condition based on the methylation status at selected sites of the DNA of a patient,
• (B) means for providing information about the methylation status at selected sites of the DNA of the patient to computing device;
• (C) means for generating in said computing device a ranked listing of diseases or medical conditions based on the information about the methylation status at selected sites of the DNA of the patient, the first knowledge base and the second knowledge base.

A computer program product for guiding the selection of a therapeutic treatment regimen for a patient with a disease or medical condition, said computer program product comprising

• a computer usable storage medium having computer readable program code means embodied in the medium, the computer readable program code means comprising:
• (A) computer readable program code means for generating:
• a first knowledge base comprising information about a plurality of different methylation statuses at selected sites of the DNA in cells with a known disease or medical condition and/or healthy cells,
• a second knowledge base comprising a plurality of expert rules for evaluating and selecting a type of disease or medical condition based on the methylation status at selected sites of the DNA of a patient,
• a third knowledge base comprising a plurality of different therapeutic regimens and/or preventive therapeutic regimens for diseased cells or medical conditions,
• a fourth knowledge base comprising a plurality of expert rules for evaluating and selecting therapeutic treatment regimens for diseased cells or medical conditions
• a fifth knowledge base comprising advisory information useful for the treatment of a patient with different constituents of said different therapeutic treatment regimens;
• and
• (B) computer readable program code means for providing information about the methylation status at selected sites of the DNA of the patient;
• (C) computer readable program code means for generating a ranked listing of diseases or medical conditions based on the information about the methylation status at selected sites of the DNA of the patient;
• and
• (D) computer readable program code means for generating in said computing device a ranked listing of available therapeutic treatment regimens for said patient.