TABLE 1.
List of samples for benchmarking.
| Sample ID | Tumor type | Expected fusion | Fusion positive/negative | Confirmed method |
|---|---|---|---|---|
| pos_S1 | Pilocytic astrocytoma (WHO Grade I) | KIAA1549-BRAF | positive | RT-PCR with Sanger sequencing |
| pos_S2 | High grade astrocytoma consistent with glioblastoma small cell type, IDH-wildtype | EGFR-SEPT14 | positive | RT-PCR with Sanger sequencing |
| pos_S3 | Granular cell astrocytoma | EGFR-EGFR (EGFRvIII) | positive | RT-PCR with Sanger sequencing |
| pos_S4 | Anaplastic astrocytoma, IDH-mutant | EWSR1-FLI1 | positive | RT-PCR |
| pos_S5 | Pilocytic astrocytoma | FAM131B-BRAF | positive | RT-PCR with Sanger sequencing |
| pos_S6 | Glioblastoma, IDH-wildtype | FGFR3-TACC3 | positive | RT-PCR with Sanger sequencing |
| pos_S7 | Glioblastoma, IDH-mutant | MN1-MOB3B | positive | RT-PCR with Sanger sequencing |
| pos_S8 | Pilocytic astrocytoma | SRGAP3-RAF1 | positive | CMA |
| pos_S9 | Anaplastic ependymoma (WHO grade III) | C11ORF95-RELA | positive | RT-PCR with Sanger sequencing |
| pos_S10 | Pilocytic astrocytoma | PDE4B-NTRK2 | positive | RT-PCR with Sanger sequencing |
| pos_S11 | Pleomorphic xanthoastrocytoma | QKI-RAF1 | positive | RT-PCR with Sanger sequencing |
| pos_S12 | Solitary fibrous tumor | NAB2-STAT6 | positive | RT-PCR with Sanger sequencing |
| pos_S13 | Negative sample spiked in with fusion oligos | SRGAP3-RAF1 | positive | Specific synthetic oligonucleotide design |
| KIAA1549-BRAF | ||||
| MYB-QKI | ||||
| FAM131B-BRAF | ||||
| PVT1-MYC | ||||
| FGFR1-TACC1 | ||||
| DDX31-GFI1B | ||||
| SLC44A1-PRKCA | ||||
| MYB-ESR1 | ||||
| PTPRZ1-MET | ||||
| TPM3-NTRK1 | ||||
| MYB-PCDHGA1 | ||||
| FGFR1-FGFR1 (E9-E19) | ||||
| pos_S14 | Negative cell line with insilico spiked in fusions | FGFR3-FAM184B | positive | Insilico spike in |
| MET-ST7 | ||||
| NTRK1-TPR | ||||
| ZSCAN21-MET | ||||
| ATG7-RAF1 | ||||
| MET-PTPRZ1 | ||||
| ETV6-NTRK3 | ||||
| PACRG-QKI | ||||
| KIAA1549-BRAF | ||||
| TFG-MET | ||||
| FN1-FGFR1 | ||||
| NTRK2-VCL | ||||
| FGFR3-TACC3 | ||||
| KIAA1549-BRAF | ||||
| QKI-RAF1 | ||||
| QKI-NTRK2 | ||||
| NAB2-STAT6 | ||||
| EGFR-EGFR | ||||
| KIF21B-NTRK1 | ||||
| YAP1-FAM118B | ||||
| C11orf95-RELA | ||||
| PDE4B-NTRK1 | ||||
| EWSR1-FLI1 | ||||
| FAM131B-BRAF | ||||
| FGFR1-TACC1 | ||||
| MYB-QKI | ||||
| SRGAP3-RAF1 | ||||
| neg_S1 | CNS negative | None | negative | CNS negative |
| neg_S2 | CNS negative | None | negative | CNS negative |
| neg_S3 | CNS negative | None | negative | CNS negative |
| neg_S4 | CNS negative | None | negative | CNS negative |
| neg_S5 | CNS negative | None | negative | CNS negative |
| neg_S6 | CNS negative | None | negative | CNS negative |
| neg_S7 | CNS negative | None | negative | CNS negative |
| neg_S8 | CNS negative | None | negative | CNS negative |
| neg_S9 | CNS negative | None | negative | CNS negative |