RNA-based Tests
List of RT-PCR tests available in the laboratory.
CAP recommends using neoplastic cellularity as the number of neoplastic cells or nuclei compared to the overall or toal number of cells or nuclei.
RNA is extracted from tumor-rich tissue region or from the whole FFPE sections, and is converted to cDNA. PCR is performed using specific primers from exons across different documented fusion points from the corresponding partner genes of the chimeric transcripts. The identities of the specific PCR products in agarose gel electrophoresis are confirmed by Sanger sequencing. DNA integrity is checked across PCR products of sizes 153, 247, 323 and 429 bp.
Click here to see common fusion transcripts (adapted from Archer FusionPlex Sarcoma Kit website).
References databases:
1. Atlas of Genetics and Cytogenetics in Oncology and Haematology
2. Catalogue of Somatic Mutations in Cancer COSMIC
Please order the test through the desktop little fox.
| Diseases | Tests |
|---|---|
| Alveolar rhabdomyosarcoma |
PAX3::FOXO1 PAX7::FOXO1 |
| Angiomatoid fibrous histiocytoma |
EWSR1::ATF1 EWSR1::CREB1 |
| BCOR::CCNB3 Fusion Positive Sarcomas | BCOR exon 15-CCNB3 exon 5 |
| Clear cell sarcoma |
EWSR1::ATF1 EWSR1::CREB1 |
|
Congenital/infantile fibrosarcoma Mammary analogue secretory carcinoma Secretory CA Breast |
ETV6::NTRK3 |
|
Dermatofibrosarcoma Protuberans Giant cell fibroblastoma |
COL1A1::PDGFB COL1A2::PDGFB COL6A3::PDGFD EMILIN2::PDGFD TNC::PDGFD |
| Desmoplastic small round-cell tumour | EWSR1::WT1 |
| Epithelioid hemangioendothelioma | WWTR1::CAMTA1 |
| Ewing sarcoma |
EWSR1::FLI1 EWSR1::ERG |
| Extraskeletal myxoid chondrosarcoma | EWSR1::NR4A3 |
| Myxoid liposarcoma |
EWSR1::DDIT3 FUS::DDIT3 |
| Papillary glioneuronal tumors | SLC44A1::PRKCA |
| Pilocytic Astrocytoma | KIAA1549::BRAF |
| RAF1 fusion related soft tissue sarcoma | MAP4::RAF1 |
| Soft tissue angiofibroma | AHRR::NCOA2 |
| Synovial sarcoma |
SS18::SSX1 SS18::SSX2 SS18::SSX4 |
| Lung cancers/ other | Tests |
|---|---|
| ALK (ALK receptor tyrosine kinase) |
CLTC::ALK DCTN1::ALK EAV::ALK EML4::ALK KIF5B::ALK KLC1::ALK NPM::ALK RANBP2::LK STRN::ALK TFG::ALK TPM3::ALK |
| MET (MET proto-oncogene, receptor tyrosine kinase) | exon 14 skipping |
| RET (ret proto-oncogene) |
CCDC6::RET CUX1::RET KIAA1217::RET KIAA1468::RET KIF5B::RET MPRIP::RET NCOA4::RET PRKAR1A::RET RUFY2::RET TRIM33::RET |
| ROS1 (ROS proto-oncogene 1, receptor tyrosine kinase) |
CCDC6::ROS1 CD74::ROS1 CLTC::ROS1 EZR::ROS1 FIG::ROS1 LIMA1::ROS1 LRIG3::ROS1 MSN::ROS1 SDC4::ROS1 SLC34A::ROS1 TFG::ROS1 TMEM106B::ROS1 TPM3::ROS1 WNK1::ROS1 ZCCHC8::ROS1 |
