The present disclosure provides a diagnostic method based on pairwise comparison of cancers using transcriptome expression data. In one embodiment, the method comprises the steps of: obtaining a first gene expression profile of a first cancer sample having a first cancer type; obtaining a second gene expression profile of a second cancer sample having a second cancer type, wherein the second cancer type is different from the first cancer type; comparing said first gene expression profile with said second gene expression profile; and selecting N genes that are most differentially expressed in the first and the second gene expression profiles to generate pairwise differentially expressed genes (DEGs), wherein N is an integer between 10 and 100.