Table 2.
Validation of the AMP-FPS fusion transcript assay.
| Nr | Diagnosis | Pre-detected genetic abnormality | Primary detection method | Sequencing platfom | Histotype-specific fusion detected | Other passing filters fusions |
|---|---|---|---|---|---|---|
| 28 | Askin Tumor | EWSR1-ERG | RT-qPCR | Illumina | EWSR1-ERG | EWSR1-unl-ERG |
| 29 | Congenital Fibrosarcoma | ETV6-NTRK3 | RT-qPCR | Illumina | ETV6-NTRK3 | NFD |
| 30 | Dermatofibrosarcoma Protuberans | COL1A1-PDGFB | FISH | Thermo | COL1A1-PDGFB | NFD |
| 31 | Dermatofibrosarcoma Protuberans | COL1A1-PDGFB | RT-qPCR | Illumina | COL1A1-PDGFB | NFD |
| 32 | Ewing Sarcoma | EWSR1 | FISH | Thermo | EWSR-FLI1 | NFD |
| 33 | Ewing Sarcoma | EWSR1 | FISH | Thermo | EWSR-FLI1 | NFD |
| 34 | Ewing Sarcoma | EWSR1 | FISH | Thermo | EWSR1-PATZ1 | NFD |
| 35 | Ewing Sarcoma | EWSR1 | FISH | Thermo | EWSR-FLI1 | NFD |
| 36 | Ewing Sarcoma | EWSR1 | FISH | Thermo | EWSR-FLI1 | NFD |
| 37 | Ewing Sarcoma | EWSR1-FLI1 | RT-qPCR | Illumina | EWSR1-FLI1 | FXR2-CAMTA1 |
| 38 | Ewing Sarcoma | EWSR1-FLI1 | RT-qPCR | Illumina | EWSR1-FLI1 | NFD |
| 39 | Ewing Sarcoma | EWSR1-FLI1 | RT-qPCR | Illumina | EWSR1-FLI1 | NFD |
| 40 | Ewing Sarcoma | EWSR1-ERG | RT-qPCR | Illumina | EWSR1-ERG | EWSR1-unl-EWSR1-ERG; FUS-ERG; EWSR1-ERG-EWSR1; |
| 41 | Ewing Sarcoma | EWSR1-FLI1 | FISH | Illumina | EWSR1-FLI1 | EWSR1-FLI1-EWSR1 |
| 42 | Ewing Sarcoma | EWSR1 | FISH | Thermo | EWSR1-FLI1 | NFD |
| 43 | Ewing Sarcoma | EWSR1-FLI1 | RT-qPCR | Thermo | EWSR1-FLI1 | NFD |
| 44 | Ewing Sarcoma | EWSR1-FLI1 | RT-qPCR | Thermo | EWSR1-FLI1 | NFD |
| 45 | Ewing Sarcoma | EWSR1-FLI1 | RT-qPCR | Thermo | EWSR1-FLI1 | NFD |
| 46 | Ewing Sarcoma | EWSR1-FLI1 | RT-qPCR | Thermo | EWSR1-FLI1 | NFD |
| 47 | Ewing Sarcoma | EWSR1-FLI1 | RT-qPCR | Thermo | EWSR1-FLI1 | NFD |
| 48 | Ewing Sarcoma | EWSR1-FLI1 | RT-qPCR | Thermo | EWSR1-FLI1 | NFD |
| 49 | Ewing Sarcoma | EWSR1-FLI1 | RT-qPCR | Thermo | EWSR1-FLI1 | NFD |
| 50 | Ewing Sarcoma | EWSR1-FLI1 | RT-qPCR | Illumina | EWSR1-FLI1 | NFD |
| 51 | Ewing Sarcoma | EWSR1 | FISH | Illumina | EWSR1-FLI1 | NFD |
| 52 | Ewing Sarcoma | FUS | FISH | Thermo | FUS-ERG | NFD |
| 53 | Ewing-like Sarcoma | BCOR-CCNB3 | RT-qPCR | Illumina | BCOR-CCNB3 | NFD |
| 54 | Ewing-like Sarcoma | CIC-DUX4 | RT-qPCR | Illumina | CIC-DUX4 | NFD |
| 55 | Extraskeletal Myxoid Chondrosarcoma | NR4A3 | FISH | Illumina | EWSR1-NR4A3 | NFD |
| 56 | Extraskeletal Myxoid Chondrosarcoma | EWSR1 | FISH | Illumina | EWSR1-NR4A3 | NFD |
| 57 | Extraskeletal Myxoid Chondrosarcoma | EWSR1-NR4A3 | RT-qPCR | Illumina | EWSR1-NR4A3 | NFD |
| 58 | Extraskeletal Myxoid Chondrosarcoma | TAF15-NR4A3 | RT-qPCR | Illumina | TAF15-NR4A3 | NFD |
| 59 | Extraskeletal Myxoid Chondrosarcoma | EWSR1-NR4A3 | RT-qPCR | Illumina | EWSR1-NR4A3 | NFD |
| 60 | Extraskeletal Myxoid Chondrosarcoma | EWSR1-NR4A3 | RT-qPCR | Illumina | EWSR1-NR4A3 | NFD |
| 61 | Extraskeletal Myxoid Chondrosarcoma | EWSR1-NR4A3 | RT-qPCR | Illumina | EWSR1-NR4A3 | NFD |
| 62 | Extraskeletal Myxoid Chondrosarcoma | EWSR1-NR4A3 | RT-qPCR | Illumina | EWSR1-NR4A3 | NFD |
| 63 | Extraskeletal Myxoid Chondrosarcoma | EWSR1-NR4A3 | RT-qPCR | Illumina | EWSR1-NR4A3 | NFD |
| 64 | Extraskeletal Myxoid Chondrosarcoma | NR4A3 | FISH | Illumina | EWSR1-NR4A3 | NFD |
| 65 | Extraskeletal Myxoid Chondrosarcoma | EWSR1-NR4A3 | RT-qPCR | Illumina | EWSR1-NR4A3 | NFD |
| 66 | Myoepitelial carcinoma (soft tissue) | EWSR1 | FISH | Illumina | EWSR1-ATF1 | NFD |
| 67 | Myoepithelioma (soft tissue) | EWSR1 | FISH | Illumina | EWSR1-ATF1 | NFD |
| 68 | Myxoid Liposarcoma | FUS-DDIT3 | RT-PCR | Thermo | FUS-DDIT3 | NFD |
| 69 | Myxoid Liposarcoma | FUS-DDIT3 | RT-qPCR | Illumina | FUS-DDIT3 | NFD |
| 70 | Myxoid Liposarcoma | FUS-DDIT3 | FISH | Thermo | FUS-DDIT3 | NFD |
| 71 | Myxoid Liposarcoma | FUS-DDIT3 | FISH | Illumina | FUS-DDIT3 | NFD |
| 72 | Myxoid Liposarcoma | FUS-DDIT3 | FISH | Illumina | FUS-DDIT3 | NFD |
| 73 | Nodular Fascitis | USP6 | FISH | Thermo | MYH9-USP6 | NFD |
| 74 | Rhabdomyosarcoma, alveolar | PAX3-FOXO1 | RT-PCR | Thermo | PAX3-FOXO1 | NFD |
| 75 | Rhabdomyosarcoma, alveolar | PAX3-FOXO1 | RT-PCR | Thermo | PAX3-FOXO1 | NFD |
| 76 | Rhabdomyosarcoma, alveolar | PAX3-FOXO1 | RT-PCR | Thermo | PAX3-FOXO1 | NFD |
| 77 | Rhabdomyosarcoma, alveolar | PAX3-FOXO1 | RT-qPCR | Illumina | PAX3-FOXO1 | NFD |
| 78 | Rhabdomyosarcoma, alveolar | PAX3-FOXO1 | RT-qPCR | Illumina | PAX3-FOXO1 | NFD |
| 79 | Rhabdomyosarcoma, alveolar | PAX3-FOXO1 | RT-qPCR | Illumina | PAX3-FOXO1 | NFD |
| 80 | Rhabdomyosarcoma, alveolar | PAX3-FOXO1 | RT-qPCR | Illumina | PAX3-FOXO1 | NFD |
| 81 | Rhabdomyosarcoma, alveolar | PAX3-FOXO1 | RT-qPCR | Illumina | PAX3 - FOXO1 | FOXO1-PAX3 |
| 82 | Rhabdomyosarcoma, alveolar | PAX3-FOXO1 | RT-qPCR | Illumina | PAX3-FOXO1 | NFD |
| 83 | Rhabdomyosarcoma, splindle cell | SRF-NCOA2 | RT-qPCR | Illumina | SRF- NCOA2 | NFD |
| 84 | Sarcoma NOS | EWSR1 | FISH | Illumina | EWSR1-FLI1 | NFD |
| 85 | Solitary Fibrous Tumor | STAT6 | IHC | Thermo | NAB2-STAT6 | NFD |
| 86 | Synovial Sarcoma | SS18-SSX2 | RT-qPCR | Illumina | SS18-SSX2 | SS18-SSX4;SS18-SSX1; complex SS18-SSX2 fusions |
| 87 | Synovial Sarcoma | SS18 | FISH | Illumina | SS18-SSX1 | SS18-SSX4; SS18-SSX4-SS18 |
| 88 | Synovial Sarcoma | SS18 | FISH | Thermo | SS18-SSX1 | NFD |
| 89 | Synovial Sarcoma | SS18-SSX1 | RT-qPCR | Illumina | SS18-SSX1 | NFD |
| 90 | Synovial Sarcoma | SS18-SSX1 | RT-qPCR | Thermo | SS18-SSX1 | NFD |
| 91 | Synovial Sarcoma | SS18-SSX1 | RT-qPCR | Thermo | SS18-SSX1 | SS18-SSX2 |
| 92 | Synovial Sarcoma | SS18-SSX1 | RT-qPCR | Thermo | SS18-SSX1 | SS18-SSX4 |
| 93 | Synovial Sarcoma | SS18-SSX1 | RT-qPCR | Thermo | SS18-SSX1 | SS18-SSX4 |
| 94 | Synovial Sarcoma | SS18 | FISH | Illumina | SS18-SSX1 | SS18-SSX4-SS18 |
| 95 | Synovial Sarcoma | SS18-SSX2 | RT-qPCR | Illumina | SS18-SSX2 | NFD |
| 96 | Synovial Sarcoma | SS18 | FISH | Illumina | SS18-SSX1 | SS18-SSX4 |
| 97 | Synovial Sarcoma | SS18-SSX1 | RT-qPCR | Thermo | SS18-SSX1 | SS18-SSX4 |
| 98 | Clear Cell Sarcoma | EWSR1 | FISH | Thermo | EWSR1-CREB1 | NFD |
| 99 | Endometrial Stromal Sarcoma | BCOR | FISH | Thermo | NFD | NFD |
| 100 | Extraskeletal Myxoid Chondrosarcoma | NR4A3 | FISH | Illumina | NFD | NFD |
| 101 | Myoepithelioma (soft tissue) | EWSR1 | FISH | Illumina | NFD | NFD |
| 102 | Myxoid Fibrosarcoma | FUS | FISH | Illumina | NFD | NFD |
| 103 | Myxoid Liposarcoma | DDIT3 | FISH | Illumina | NFD | NFD |
| 104 | Nodular Fasciitis | USP6 | FISH | Thermo | NFD | NFD |
| 105 | Rhabdomyosarcoma, alveolar | FOXO1 | FISH | Thermo | NFD | NFD |
| 106 | Sarcoma NOS | BCOR | FISH | Thermo | NFD | NFD |
| 107 | Solitary Fibrous Tumor | EWSR1 | FISH | Illumina | NFD | NFD |
| 108 | Undifferentiated round cell, Ewing-Like Sarcoma | CIC | FISH | Illumina | NFD | NFD |
| 109 | Lipoblastoma | PLAG1 neg | FISH | Illumina | NFD | NFD |
| 110 | Myxoid Fibrosarcoma | EWSR1, FUS neg | FISH | Thermo | NFD | NFD |
| 111 | Myxoid Fibrosarcoma | EWSR1, FUS neg | FISH | Thermo | NFD | NFD |
| 112 | Myxoid Fibrosarcoma | 12q13-15 amp | FISH | Thermo | NFD | NFD |
| 113 | Rhabdomyosarcoma, alveolar | FOXO1 neg | FISH | Thermo | NFD | NFD |
| 114 | Rhabdomyosarcoma, embryonal | FOXO1 neg | FISH | Illumina | NFD | NFD |
| 115 | Rhabdomyosarcoma, embryonal | FOXO1 neg | FISH | Illumina | NFD | NFD |
| 116 | Rhabdomyosarcoma, embryonal | FOXO1 neg | FISH | Illumina | NFD | NFD |
| 117 | Sarcoma NOS | EWSR1 neg | FISH | Illumina | CIC-DUX4 | NFD |
| 118 | Small Round Cell Tumor | EWSR1, BCOR, FUS, CIC neg | FISH | Thermo | NFD | NFD |
| 119 | Undifferentiated Sarcoma | EWSR1 neg | FISH | Illumina | CIC-DUX4 | NFD |
| 120 | Undifferentiated Sarcoma | 12q13-15 amp | FISH | Thermo | NFD | NFD |
| 121 | Undifferentiated Sarcoma | 12q13-15 amp | FISH | Thermo | NFD | HMGA2-LGR5 |
| 122 | Biphenotypic Sinonasal Sarcoma | nd | nd | Thermo | PAX3-MAML3§ | NFD |
| 123 | Biphenotypic Sinonasal Sarcoma | nd | nd | Thermo | PAX3-MAML3§ | NFD |
| 124 | Biphenotypic Sinonasal Sarcoma | nd | nd | Thermo | PAX3-MAML3§ | NFD |
| 125 | Dermatofibrosarcoma Protuberans | nd | nd | Thermo | COL1A1-PDGFB | NFD |
| 126 | Endometrial Stromal Sarcoma | nd | nd | Thermo | YWHAE-NUTM2B | NFD |
| 127 | Gastrointestinal Neuroectodermal Tumor | nd | nd | Thermo | EWSR1-CREB1 | SS18-PTRF |
| 128 | Inflammatory Myofibroblastic Sarcoma | nd | nd | Illumina | TPM4-ALK | NFD |
| 129 | Inflammatory Myofibroblastic Tumor | nd | nd | Thermo | TFG-ROS1 | NFD |
| 130 | Myoepithelioma (bone) | nd | nd | Illumina | FUS-NFATC2 | NFD |
| 131 | Myoepithelioma (soft tissue) | nd | nd | Illumina | TRPS1-PLAG1 | NFD |
| 132 | Sclerosing Epitheliodid Fibrosarcoma | nd | nd | Illumina | EWSR1-CREB3L2 | NFD |
| 133 | Sclerosing epitheliodid fibrosarcoma (soft tissue) | nd | nd | Illumina | FUS-CREB3L2 | NFD |
| 134 | Solitary Fibrous Tumor | nd | nd | Thermo | NAB2-STAT6 | NFD |
| 135 | Chondrosarcoma | nd | nd | Thermo | NFD | NFD |
| 136 | Endometrial Stromal Sarcoma | nd | nd | Thermo | NFD | NFD |
| 137 | Epithelioid Angiosarcoma | nd | nd | Illumina | NFD | NFD |
| 138 | Follicular Dendritic Cell Sarcoma | nd | nd | Thermo | NFD | NFD |
| 139 | Leiomyosarcoma | nd | nd | Illumina | NFD | NFD |
| 140 | Leiomyosarcoma | nd | nd | Thermo | NFD | NFD |
| 141 | Myoepithelioma (bone) | nd | nd | Illumina | NFD | NFD |
| 142 | Myxoid Fibrosarcoma | nd | nd | Thermo | NFD | NFD |
| 143 | Myxoinflammatory Fibroblastic Sarcoma | nd | nd | Illumina | NFD | NFD |
| 144 | Osteosarcoma | nd | nd | Illumina | NFD | NFD |
| 145 | Osteosarcoma | nd | nd | Illumina | NFD | NFD |
| 146 | Pleomophic Sarcoma | nd | nd | Thermo | NFD | NFD |
| 147 | Pleomophic Sarcoma | nd | nd | Thermo | NFD | NFD |
| 148 | Pleomophic Sarcoma | nd | nd | Thermo | NFD | NFD |
| 149 | Sarcoma NOS HG Myxoid | nd | FISH | Thermo | NFD | NFD |
| 150 | Undifferentiated Sarcoma | nd | nd | Illumina | NFD | NFD |
NFD, no histotype-specific fusion detected; nd, not done; amp, amplification; neg, negative; RT-PCR, reverse transcriptase-PCR; FISH, fluorescent in situ hybridization; RT-qPCR, reverse transcriptase-quantitative PCR; IHC, immunohistochemistry; unl, unaligned sequence. PAX3-MAML3§: fusion detected with a PAX3-customized AMP-FPS Panel. This sample scored negative with the standard AMP-FPS Panel.