Fig. 4

Expression of clinically relevant genes in breast cancer, and comparison to IHC. (a) Scatter plot of the expression levels of a set of 701 differentially expressed genes in the METABRIC dataset, between normal and tumor samples, as measured on T1 FFPE sample by RiboZero (orange; left) or mRNA-seq (purple; middle) vs. their mRNA-seq derived expression in the T1 FF sample. At the right we compare the expression of these genes on the T1 FFPE sample alone, as measured by mRNAs-seq (x-axis) and RiboZero (y-axis). (b) Same as (a) for PAM50 genes (“intrinsic subtype”). ESR1 (Estrogen Receptor) is indicated in the scatter plots. (c) Comparison between the expression levels of Estrogen Receptor (ESR1) as measured by the different RNA-seq protocols on T1-T6 (mRNA-seq in purple, RiboZero in orange, diamond for FF samples, circles for ~ 4 years old FFPE samples, and stars for ~ 10 years old FFPE samples), relative to IHC levels. (d) Chromosomal view of ESR1 with the reads mapped to this location (from IGV). Data shown for T1 FF sample, done with the mRNA-seq protocol; T1 FFPE sample, done with mRNA-seq protocol, and T1 FFPE sample done with RiboZero protocol. For each panel a histogram of the mapped reads to this genomic location is presented. At the bottom the gene model and the chromosomal location are shown