Fig. 4.

Molecular taxonomy classification of individual prostate cancer (CaP) foci. (A) The discovery cohort. Each CaP focus was classified into seven groups that were the basis for a recently proposed molecular taxonomy for localized CaP. Classification was performed according to the presence of gene fusions involving ERG, ETV1, ETV4, or FLI1, or somatic mutations affecting SPOP, FOXA1, or IDH. ERG, ETV1, ETV4, and FLI1 gene fusions were predicted by both DeFuse and Cicero algorithms. Yes = CaP focus was classified into a molecular taxonomy group; No = CaP focus could not be classified; black cells = sample was not assayed; yellow highlights = predicted by DeFuse only; blue highlights = predicted by Cicero only. (B) Validation using publicly available data sets. Independent CaP foci from multifocal CaP radical prostatectomy specimens procured from 60 patients in four independent studies [14,15,27,28] were evaluated for the presence of seven The Cancer Genome Atlas (TCGA) classifiers as above. WGS = whole-genome sequencing; WES = whole-exome sequencing; FISH = fluorescent in situ hybridization. Evaluable = the TCGA classifiers can be evaluated in the data set used to profile the CaP focus; N/A = classifier not present; concordant foci = CaP foci classified according to the same TCGA classifier; discordant foci = CaP foci classified according to different TCGA classifier; classified 2× = same CaP focus classified according to two TCGA classifiers; not classified = CaP foci that could not be not classified according to any of the seven TCGA classifiers.