Methods for classification of tissue samples as positive or negative for cancer

A method for processing or analyzing a tissue sample of a subject, comprising:

• (a) obtaining said tissue sample from said subject;
• (b) subjecting at least a portion of said tissue sample to a diagnostic screening process which indicates said tissue sample as ambiguous or indeterminate;
• (c) assaying one or more nucleic acid molecules derived from a nucleic acid sample from said tissue sample of said subject to generate a data set;
• (d) using a programmed computer to process said data set to identify (i) a level of expression of one or more gene expression products in said nucleic acid sample, and (ii) one or more genetic mutations in said nucleic acid sample;
• (e) using a trained algorithm, computer processing said level of expression and said one or more genetic mutations identified in (d) to generate a classification of said tissue sample as positive or negative for a cancer;
• and
• (f) electronically outputting a report that identifies said classification of said tissue sample as positive or negative for said cancer.