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FusionPlex® Solid Tumor Panel [UWMC Clinical Genomics Laboratory]

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General Information

Lab Name
Lab Code
894
Epic Name
Order using "UW Genetics and Solid Tumor Test Request"

See tip sheet for more information (internal link).
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. This test can also be ordered for a single gene or a subset of 2-10 genes, chosen by the ordering clinician based on clinical and pathological findings. Testing is performed by UWMC - Montlake DLMP Clinical Genomics Laboratory.

Epic Ordering:

  • Test Name: FusionPlex.
  • Order Code: LABFUSIONPLEX.
  • For orders submitted electronically via Epic, a separate requisition form is not required.
Forms & Requisitions

Outside Providers: CGL Neoplasia Test Request Form

Providers with access to the UW implementation of Epic (i.e., FHCC, HMC, UWMC, UWNW) may order this test using the order "UW Genetics and Solid Tumor Test Request." See tip sheet for more information (internal link).

Synonyms
Archer, LABFUSIONPLEX
Components

Interpretation

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.

Reference Range
Interferences and 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%).

Ordering & Collection

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

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.

FFPE Tumor Block:

  • Please send curls or slides if possible. Contact lab if block is the only option.

Fresh Frozen Tumor Tissue:

  • 50-150mg (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.

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. We can only accept RNA isolated in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the College of American Pathologists and/or the Centers for Medicare and Medicaid Services.
Forms & Requisitions

Outside Providers: CGL Neoplasia Test Request Form

Providers with access to the UW implementation of Epic (i.e., FHCC, HMC, UWMC, UWNW) may order this test using the order "UW Genetics and Solid Tumor Test Request." See tip sheet for more information (internal link).

Handling Instructions

Outside Laboratories:

  • Sample collection kits are available upon request. Kits include a biohazard bag with absorbent material, a test requisition, and FedEx shipping materials. Contact the lab at (206) 616-4062 to request a kit.
  • A completed request form must accompany all orders.
  • Samples are accepted Monday-Friday.
  • Ship sample to:
    • Clinical Genomics Laboratory
    • University of Washington Health Sciences Building
    • Room H-561
    • 1959 NE Pacific St
    • Seattle, WA 98195
Quantity
Requested: Varies; refer to Collection information.
Minimum: Varies; refer to Collection information.

Processing

Receiving Instructions

Hold samples at room temperature. If sample was frozen when received, keep frozen until pick up.

  • Call UWMC - Montlake DLMP Cytogenetics and Genomics Laboratory at (206) 598-4489 for pick up. Cytogenetics is staffed on weekends to accept samples.
  • If no answer or after hours, call (206) 598-4488 to leave message.
Misc Sendout

Performance

Lab Department
Frequency
Performed every other week. TAT: 2-3 weeks if insurance pre-authorization is approved.
Available STAT?
Yes
Performing Location(s)
Pathology Clinical Genomics Laboratory
206-598-8684
Other Locations/Notes

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

Ph: (206) 616-4062

Billing & Coding

Billing Comments

CPT code: 81455

Prior Insurance Authorization: Contact gpab@uw.edu for details