Solid Tumors
GeneTrails Solid Tumor Fusion Gene Panel
-
Test Code:
4480 • LAB101830 • LAB103983 • LAB103996
-
Department:
Solid Tumors
-
Test Synonyms:
Solid Tumor Fusion Panel • Fusion gene • Gene fusion • AKT3 • ALK • BCOR • BRAF • C11orf95 • CIC • EGFR • ERBB4 • ERG • ETV6 • EWSR1 • FGFR1 • FGFR2 • FGFR3 • FGFR4 • FOSB • FUS • LTK • MAML2 • MET • MN1 • MYB • MYBL1 • NCOA2 • NOTCH1 • NOTCH2 • NRG1 • NTRK1 • NTRK2 • NTRK3 • NUTM1 • PAX3 • PDGFRA • PPARG • PRKCA • RAF1 • RET • ROS1 • RSPO2 • RSPO3 • THADA • YAP1 • YWHAE
-
CPT Code(s):
81445
Background:
In recent years an increasing number of gene fusions have been identified in solid tumors, many of them involving kinases that are targetable with specific therapies. Examples include fusions involving ALK (e.g. EML4-ALK) and ROS1 in non-small cell carcinoma, RET in thyroid carcinoma, BRAF in some types of glioma, and FGFR2 in cholangiocarcinoma.(1-6).
The GeneTrails® Solid Tumor Fusion Gene panel is designed to detect fusions involving the target genes listed and is agnostic with respect to fusion partners. The panel is performed using next-generation sequencing of tumor RNA (cDNA) and encompasses all fusions for which FDA-approved therapies are available, as well as targets for ongoing clinical trials. Control genes are included in the panel to assess specimen adequacy.
Genes covered by RNA (cDNA) sequencing:
| Fusion Genes |
| AKT3 | ALK | BCOR | BRAF | C11orf95 |
| CIC | EGFR | ERBB4 | ERG | ETV6 |
| EWSR1 | FGFR1 | FGFR2 | FGFR3 | FGFR4 |
| FOSB | FUS | LTK | MAML2 | MET |
| MN1 | MYB | MYBL1 | NCOA2 | NOTCH1 |
| NOTCH2 | NRG1 | NTRK1 | NTRK2 | NTRK3 |
| NUTM1 | PAX3 | PDGFRA | PPARG | PRKCA |
| RAF1 | RET | ROS1 | RSPO2 | RSPO3 |
| THADA | YAP1 | YWHAE | | |
| Housekeeping Genes |
| CIAO1 | COPA | MRPS14 | UBE3C |
|
Methodology:
The test is performed on RNA extracted from tumor-rich regions of formalin-fixed/paraffin embedded tissue. The RNA (cDNA) NGS library preparations are designed using custom
QiaSeq chemistry (Qiagen) that include unique molecular indices for the assessment of library
complexity. Sequencing is performed on Illumina NextSeq500/550/2000 instruments and the
data is analyzed through custom bioinformatics pipelines. The targeted RNA panel is designed
to detect fusions involving the genes listed above and is agnostic with respect to fusion
partners. EGFRvIII and splice variants causing MET exon 14 skipping are also tested. All of the
driver genes are known to play a role in cancer growth, and most of them are actionable with
one or more targeted therapies. The gene fusions can be detected to the range of
approximately 1-5% of input cells.
Specimen Requirements:
Blood: EDTA or ACD (Solution A or B):
- Adult: 5 mL
- Child: 2-3mL
- Infant: 1-2mL
Bone Marrow:
- 2-10 mL Yellow (ACD) or purple (EDTA) tube (unspun)
- Bone marrow aspirates or cores are acceptable if received in the lab within 24 hours (room temperature) or 4 days (refrigerated; never frozen).
- Frozen cell pellets of bone marrow-derived leukocytes (without red blood cells) are also acceptable.
Paraffin Blocks or Slides:
- A paraffin block, or
- 10 unstained sections of tumor (4-5 microns) (15 sections for small biopsies)
- Contact Client Services for shipping materials and procedures at 855-535-1522
Deliver to lab at shipping address above within 24 hours of collection; if sample cannot arrive within 24 hours, refrigerate until sample can be transported. If frozen pellets, freeze until shipped.
A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information.
Test Performed (Days):
Twice weekly
Turn Around Time:
10-17 calendar days
Shipment Sensitivity Requirements:
- Keep specimen cool during transit, but do not ship on dry ice.
- Please use the cold pack provided in the KDL shipping kit.
- Ship the specimen overnight express, using the FedEx priority overnight label provided.
- Contact Client Services for shipping materials and procedures at (855) 535-1522.
References:
- Shaw AT, et al. Ceritinib in ALK-rearranged non-small-cell lung cancer. N Engl J Med. 2014 Mar 27;370(13):1189-97.
- Shaw AT, et al. Crizotinib versus chemotherapy in advanced ALK-positive lung cancer. N Engl J Med. 2013 Jun 20;368(25):2385-94.
- Shaw AT, et al. Crizotinib in ROS1-rearranged non-small-cell lung cancer. N Engl J Med. 2014 Nov 20;371(21):1963-71.
- Elisei R, et al. Cabozantinib in progressive medullary thyroid cancer. J Clin Oncol. 2013 Oct 10;31(29):3639-46.
- Dimitriadis E, et a. BRAF alterations in pediatric low grade gliomas and mixed neuronal-glial tumor. J Neurooncol. 2013 Jul;113(3):353-8.
- Graham RP, et al. Fibroblast growth factor receptor 2 translocations in intrahepatic cholangiocarcinoma. Hum Pathol. 2014 Aug;45(8):1630-8
Additional Info: