284 Chapter 12 Figure 2. Distribution of well-known cancer genes related to MSS CRC. Additional Analyses Pathways, molecular functions, and biological processes were not significantly different between the three CRC subgroups. Also, after the additional inclusion of all identified variants of uncertain significance (VUSs), no significant differences were found between the subgroups. A detailed overview of all additional data analyses can be requested via the corresponding author. RNA Sequencing RNA sequencing was performed on 28 samples, divided as follows: M0 (n = 10), LM (n = 9), and PM (n = 9). Data analysis revealed no splice variants for the genes in the panel, whereas three samples (one M0 and two PM samples) showed gene fusion transcripts, which are summarized in Table 3. Interestingly, two gene fusions were identified which can be considered driving mutations, i.e., FAM198A-RAF1 and TARSL2-NTRK3. The NTRK3 fusion was confirmed via fluorescence in situ hybridization (FISH), using an NTRK3 break-apart probe (Figure 3). Table 3. Detailed output of RNA analysis. M Group Gene Pair Breakpoint 1 Breakpoint 2 Fusion Supporting Reads M0 TARSL2-NTRK3 Exon 18 chr15:102197123 Exon 14 chr15:88576274 19 PM FAM198A-RAF1 Exon not found chr3:43101459 Exon 3 chr3:12653448 85 PM RPS6KB1-HSF5 Exon 1 chr17:57970685 Exon 3 chr17:56544340 21 M0, no metastases; PM, peritoneal metastases.
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