Supplementary Information from Impact of Therapy on Genomics and Transcriptomics in High-Risk Prostate Cancer Treated with Neoadjuvant Docetaxel and Androgen Deprivation Therapy

Supplementary Methods, Figures, Table Legends Supplementary Figure 1: Representative Hematoxylin and Eosin stained photomicrographs of prostatectomy specimens demonstrating the effects of neoadjuvant chemohormonal therapy. Supplementary Figure 2: Quality metrics for targeted DNA sequencing of FFPE biopsy and RP specimens. Supplementary Figure 3: Somatic mutations detected pre- and post-treatment through targeted DNA sequencing. Supplementary Figure 4: Differences in the number and allelic frequency of somatic mutations between treated and untreated specimens. Supplementary Figure 5: Persistence of TP53 mutations in post-treated radical prostatectomy (RP) specimens. Supplementary Figure 6: Representative copy number plots from targeted sequencing of diagnostic biopsies and RP specimens from the untreated arm. Supplementary Figure 7: Pearson's correlation comparing the Nanostring platform (x axis) and RNA-seq (y axis) performed in 13 matched cases. Supplementary Figure 8: Scatterplots showing Pearson correlation between Nanostring data obtained from matched FFPE and fresh/frozen tissue in 7 patients. Supplementary Figure 9: Gene expression of PTEN (y axis) relative to genomic status (PTEN deletion or wild type (WT). Supplementary Figure 10: Left: Correlation of TMPRSS2-ERG fusion transcript expression (x axis) and ERG gene expression (y axis). Right: ERG expression vs. TMPRSS2-ERG fusion status with positive defined as normalized count> 50. Supplementary Figure 11: Principal component analysis plotted using the Biological Coefficient of Variation (BCV) distance as part of the edgeR package. Supplementary Figure 12: Unsupervised analysis of expression of all genes within the panel in radical prostatectomies from treated (green) and untreated (yellow) arms. Red= high expression; blue= low expression.