• Test Code:
    4480
  • Department:
  • Test Synonyms:
    Fusion geneGene fusionALKROS1
  • 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 20 target genes listed below. The panel is performed using next-generation sequencing of tumor RNA, and is useful for finding clinically actionable fusions that are not routinely screened by FISH. Control genes are included on the panel to assess specimen adequacy. The assay has high sensitivity (to the level of approximately 1%, or 1 positive cell in 100).

Fusion genes

AKT3 

ALK

BRAF

CD74

EFGR

EML4

ERBB4

ERG

ETV6

FGFR1

FGFR2

FGFR3

MET

NOTCH1

NOTCH2

NRG1

NTRK1

NTRK2

NTRK3

NUTM1

PDGFRA

RAF1

RET

ROS1

housekeeping genes

HMBS

ITGB7

LMNA

MYC

TDP

 

Methodology:

  1. Microscopic examination of the specimen and macrodissection of tumor-rich areas
  2. ​Nucleic extraction and purification
  3. Next-generation RNA sequencing

Estimated sensitivity: at least 15% mutant allele; estimated specificity >99%

Specimen Requirements:

  • 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.

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES.  Please include detailed clinical information.

Test Performed (Days):

Mon - Fri

Turn Around Time:

14-17 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:

  1. Shaw AT, et al. Ceritinib in ALK-rearranged non-small-cell lung cancer. N Engl J Med. 2014 Mar 27;370(13):1189-97. 
  2. Shaw AT, et al. Crizotinib versus chemotherapy in advanced ALK-positive lung cancer. N Engl J Med. 2013 Jun 20;368(25):2385-94.
  3. Shaw AT, et al. Crizotinib in ROS1-rearranged non-small-cell lung cancer. N Engl J Med. 2014 Nov 20;371(21):1963-71.
  4. Elisei R, et al. Cabozantinib in progressive medullary thyroid cancer J Clin Oncol. 2013 Oct 10;31(29):3639-46.
  5. Dimitriadis E, et a. BRAF alterations in pediatric low grade gliomas and mixed neuronal-glial tumor. J Neurooncol. 2013 Jul;113(3):353-8.
  6. Graham RP, et al. Fibroblast growth factor receptor 2 translocations in intrahepatic cholangiocarcinoma Hum Pathol. 2014 Aug;45(8):1630-8
  7. A Multiplexed Amplicon Approach for Detecting Gene Fusions by Next-Generation Sequencing. Beadling C, Wald AI, Warrick A, Neff TL, Zhong S, Nikiforov YE, Corless CL, Nikiforova MN.J Mol Diagn. 2016 Mar;18(2):165-75. PMID: 26747586​.

Additional Info:

The Knight Cancer Institute at Oregon Health & Science University is a pioneer in the field of precision cancer medicine. The institute's director, Brian Druker, M.D., helped prove it was possible to shut down just the cells that enable cancer to grow. This breakthrough has made once-fatal forms of the disease manageable and transformed how cancer is treated. The OHSU Knight Cancer Institute is the only National Cancer Institute-designated Cancer Center between Sacramento and Seattle – an honor earned only by the nation's top cancer centers. It is headquarters for one of the National Cancer Institute's largest research collaboratives, SWOG, in addition to offering the latest treatments and technologies as well as hundreds of research studies and clinical trials.

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