Sign in →

Test Code LAB3886 FusionPlex Solid Tumor Panel

Clinical System Name

FusonPlex-Solid Tumor

Synonyms

Archer; LABFUSIONPLEX;

Description

Solid tumors (e.g. sarcomas, lung cancers, thyroid cancers, head and neck cancers, renal cell carcinomas, mammary gland tumors, prostate cancers, brain tumors) frequently have chromosome rearrangements and gene fusions that are important in establishing a diagnosis, predicting prognosis, and guiding therapy choices. The FusionPlex® Solid Tumor Panel is based on next generation sequencing of RNA (cDNA) from solid tumor tissue to detect somatic oncogenic gene fusions involving any of 100 genes associated with solid tumors, without prior knowledge of the fusion partners or the breakpoints of the translocations. 

Sample Requirements

Specimen Type: FFPE Tumor Block or Slides, Fresh or Frozen Tumor Tissue, Extracted RNA

Container: Sterile Container

 

FFPE Tumor Block:

  • Curls or slides preferred. Contact lab if block is the only option.

FFPE Tumor Slides:

  • If tumor content is <70% send 10 unstained 10μm FFPE slides.
    • Send one image of an H&E stained slide that has the area of tumor marked.
  • If tumor content is >70% send 10 x 10μm curls in two 1.5 mL tubes (5 per tube).
    • Send one H&E stained slide for QC.
  • Include a copy of corresponding surgical pathology report.
  • Mail slides in a protected mailing container at room temperature and protect from excessive heat.

Extracted RNA:

  • 1 microgram (minimum), suspended in water.
  • Store at -20°C.
  • Ship on minimum of 10 lb of dry ice in insulated container by overnight courier.

Fresh Frozen Tumor Tissue:

  • 50 - 150 mg (0.15 - 2.0 cm3) fresh tissue snap-frozen.
  • Store at -20°C.
  • Ship on minimum of 10 lb of dry ice in insulated container by overnight courier.

Processing Instructions

Reject due to: See specimen type.

Spin: N

Aliquot: N

Temp: RT. If sample is received frozen, maintain and send on dry ice.

 

Storage location:

Specimen Type Temperature Storage Instructions
FFPE Blocks, Curls, Slides RT RT Sendouts Bin
Extracted RNA -20°C or -70°C -20°C CPA Freezer, Sendouts Rack
Fresh Frozen Tumor Tissue -20°C or -70°C -20°C CPA Freezer, Sendouts Rack

 

Off-site collection: Contact Send Outs team prior to collection.

Stability

Specimen Type Temperature Time
FFPE Blocks, Curls, Slides RT  
Extracted RNA -20°C or -70°C  
Fresh Frozen Tumor Tissue -20°C or -70°C  

Availability

STAT Performed TAT
N Performed every other week. 3 w

 

Performing Laboratory

University of Washington Medical Center
Department of Laboratory Medicine

Clinical Genomics Laboratory
University of Washington Health Sciences Building
Room H-561
1959 NE Pacific St, NW220
Seattle, WA 98195
 

Phone Number: (206) 616-4062

Clinical Genomics Lab: (206) 598-8684

Department

Department: Send Outs

Phone: (206) 987-2563

CPT Codes

81456
88381 

Methodology

Method: Total nucleic acid (TNA) is extracted from the sample using standard procedures. First- and second-strand complementary DNA (cDNA) synthesis is performed. A library of DNA fragments is constructed for targeted capture of cDNA from fusion genes using a custom designed FusionPlex® BBI Solid Tumor panel and reagent kit (ArcherDX, Boulder, CO). The library is quantitated using quantitative PCR and normalized for next generation sequencing. Paired-end sequencing of the enriched library is performed using Mid Output v2 (Illumina) chemistry on a NextSeq sequencer according to the manufacturer’s recommended protocol (Illumina, Inc. San Diego, CA). FASTQ files with base call and quality information of minimum 4.5 million paired-end sequence reads are processed using Archer Analysis software to annotate gene fusions and variants found within these genes. Human Genome build GRCh37 (hg19) is used. Additional details about this assay are available.

Limitations: The FusionPlex Solid Tumor Panel test does not detect gene fusions located outside the targeted gene regions. This test is also has limited ability to detect low-level mosaicism (<10%).

Special Instructions

UWMC Clinical Genomics Page

Requisition

Send Out Instructions

Reference Test Name: FusionPlex® Solid Tumor Panel [UWMC Clinical Genomics Laboratory]
Reference Test Number: 894
Instructions: Send out Monday - Friday with the UW courier.