System and method for classification of patients

A system for classifying a biological sample from a cancer patient, comprising:

• at least one processor;
• and
• at least one storage medium containing program instructions for execution by said processor, said program instructions causing said processor to execute steps comprising:
• accepting input data in the form of expression levels of a set of nucleic acid marker molecules in the biological sample, wherein the nucleic acid marker molecules are any combination of 100 or more genes in Table 4;
• comparing the expression levels of the set of nucleic acid marker molecules in the biological sample to expression levels of the set of nucleic acid marker molecules in a set of reference samples, each member of the set of reference samples having a pre-assigned value for each of one or more clinically significant variables selected from the group consisting of disease state, disease prognosis, and treatment response,
• the comparing of expression levels in the biological sample to the expression levels in the reference samples comprising one or more analysis methods, the analysis methods comprising at least one statistical classification program trained to distinguish among said pre-assigned values on the basis of that part of the reference data corresponding to expression levels of the nucleic acid marker molecules;
• and
• assigning a pre-assigned value of the one or more clinically significant variables to the biological sample on the basis of the comparison of the expression levels of the set of nucleic acid marker molecules in the biological sample to expression levels of the set of nucleic acid marker molecules in the set of reference samples using the statistical classification program,
• wherein the one or more clinically significant variables is selected from the group consisting of disease state, disease prognosis, and treatment response.