Pathway Analysis of Genomic Pathology Tests for Prognostic Cancer Subtyping.

•Genomic pathology reports are mined for patient subtyping informative for research and patient prognosis.•A novel method retrospectively analyzes pathology reports of tumor samples and identifies pan-cancer subtypes of prognostic value.•Proposed patient similarity algorithm based on biological pathways affected by gene mutations circumvents cancer heterogeneity and is replicated in a validation dataset.•Biological pathways associated with poorer survival prognosis are identified, validated in a separate dataset, and can be utilized for patient subtyping, prognosis and treatment selection.