Table 2.
FFPE tumor tissue characteristics.
| Sample | Clinical scenario | Pathology data | RNA conc | RIN | DV200 | No pre-amplification | Pre-amplification | Final resulta |
|---|---|---|---|---|---|---|---|---|
| MRD0033 | Resection at diagnosis | PAX3-FOXO1 | 322 | 1.1 | 52.46 | PAX3-FOXO1 | PAX3-FOXO1 | PAX3-FOXO1 |
| MRD0127 | Resection after chemotherapy | PAX3-FOXO1 | 86.4 | 1.6 | 56.13 | PAX3-FOXO1 | PAX3-FOXO1 | PAX3-FOXO1 |
| MRD0205 | Diagnostic biopsy | EWSR1-unknown | 9.32 | 1.1 | 8.25 | EWSR1-WT1 | EWSR1-WT1 | EWSR1-WT1 |
| MRD0270 | Diagnostic biopsy | EWSR1-WT1 | 5.92 | 1.6 | 6.46 | EWSR1-WT1 | EWSR1-WT1 | EWSR1-WT1 |
| MRD0124 | Biopsy of a third recurrence | BCOR-CCNB3 | too low | 1.8 | 37.04 | BCOR-CCNB3 | BCOR-CCNB3 | BCOR-CCNB3 |
| MRD0012 | Metastasectomy at progression | EWSR1-FLI1 | 472 | 1 | 29.44 | 0 | EWSR1-FLI1 | EWSR1-FLI1 |
| MRD0070 | Resection at diagnosis | EWSR1-ERG | 752 | 1.6 | 75.45 | 0 | EWSR1-ERG | EWSR1-ERG |
| MRD0090 | Diagnostic biopsy | EWSR1-WT1 | too low | 1.9 | 9.08 | 0 | EWSR1-WT1 | EWSR1-WT1 |
| MRD009 | Resection after chemotherapy | EWSR1-FLI1 | 492 | 1.2 | 31.4 | 0 | 0 | EWSR1-FLI1 |
| MRD004 | Resection after chemotherapy | EWSR1-FLI1 | 14.6 | 2.7 | 29.59 | 0 | 0 | EWSR1-FLI1 |
| MRD0011 | Diagnostic biopsy | EWSR1-ERG | 13.5 | 1.8 | 31.47 | 0 | 0 | 0 |
Clinical information, quality metrics describing the extracted RNA from each sample, and the multiplexed ddPCR results for each FFPE tumor biopsy sample profiled in this study.
aFinal results include the use of a second set of primers designed to target a short template for EWSR1-FLI1 and EWSR1-ERG.
RNA conc: RNA concentration; RIN: RNA integrity number; DV200: percentage of RNA fragments >200 nucleotides in size.