UW OncoPlex Cancer Gene Panel

Interpretation

Guidelines

• Genetics and Solid Tumor Diagnostic Testing
• Gynecologic Oncology (GYNPTH) Pathways
• Next-Generation Sequencing Panels Preauthorization

Method

Next-generation sequencing.

The genes listed above are sequenced on an Illumina instrument to detect single nucleotide variants, small insertions and deletions, gene amplifications, and selected translocations

Gene Fusions and Rearrangements Detected*** (assay version 8)

ALK fusions (including EML4, KIF5B::ALK, TFG::ALK, C2orf44::ALK), BRAF fusions (common fusions only, including KIAA1549::BRAF), DNAJB1::PRKACA fusions, FGFR3 fusions, RET fusions (select fusions only), ROS1 fusions, NTRK1 fusions, NTRK2 fusions (select fusions only), ETV6::NTRK3 fusions, RSPO2 fusions (select fusions only), RSPO3 fusions (select fusions only), TMPRSS2 fusions (select fusions only).

***Some fusions involving the genes listed above are not detectable by this method

Microsatellite Instability Analysis

Microsatellite instability (MSI) status is reported for all relevant cancer cases. MSI is detected using methods described in Salipate et al. 2014.

Tumor Mutation Burden Analysis

Tumor mutation burden (TMB) is estimated based on the number of somatic coding mutations per Mb sequenced.

Reference Range

See individual components

Ref. Range Notes

No mutations detected

References

• Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 19997069
• Pritchard CC, et al. Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens. J Mol Diagn 2014, 16:56-67. 24189654
• Salipante SJ, Scroggins SM, Hampel HL, Turner EH, and Pritchard CC. Microsatellite instability detection by next generation sequencing. Clin Chem 2014, 60:1192-9. 24987110
• Kuo AJ, et al. Validation and implementation of a modular targeted capture assay for the detection of clinically significant molecular oncology alterations. Pract Lab Med. 2020 Feb 3;19:e00153. PMID: 32123717
• Perrone ME, et al. Validating cell-free DNA from supernatant for molecular diagnostics on cytology specimens. Cancer Cytopathol. 2021 Dec;129(12):956-965. PMID: 34265180

Ordering & Collection

Specimen Type

Tumor Tissue, Purified DNA, Bone Marrow, Peripheral Blood, accompanied by a PATHOLOGY REPORT for the tested tissue.

Collection

Requirements for Specimen Selection

• To ensure clinically relevant results, the most recent and/or metastatic sample is preferred to older specimens, provided sufficient tumor is present (see point 2).
• To ensure detection of all types of mutations there should be at least 10% tumor cells in the tissue area processed for DNA for mutation detection and 20% tumor cells for microsatellite instability evaluation. If there is more than one tissue block, please provide the block that has the greatest percentage of neoplastic nuclei.
• Tissue samples and pathology reports will be reviewed by directors upon receipt for acceptability prior to testing. Director consultation for tissue selection is available if needed (contact Genetics lab).

Specimen Types

Tissue samples

Send one of the following:

1. Slides: 1 slide at 4-micron thickness stained with hematoxylin-and-eosin (H&E) AND 10 unstained, non-baked slides at 10-micron thickness (a minimum of 5 unstained slides is acceptable). Unstained slides can be on charged or uncharged slides.
2. Tissue Blocks: Provide complete formalin-fixed tissue block containing tumor tissue. Tissue block will be returned at completion of testing.
3. Fresh/frozen tissue: 5 microgram tissue in cell culture medium or frozen tissue stored at -20C. Tumor percentage will not be determined prior to sequencing studies.

NOTE: In order to ensure that enough DNA is obtained, the minimum acceptable tissue area is 10 square millimeters when ten 10-micron slides are supplied (1 cubic millimeter of tissue).

Purified DNA

5 micrograms ANDa reference hematoxylin-and-eosin (H&E) stained slide and pathology report required.

Bone Marrow

1 to 2 mL Bone Marrow in LAVENDER TOP (EDTA) tube

Blood

6 mL blood in LAVENDER TOP (EDTA) tube.

Alternative specimens may be acceptable with approval (contact: 206-598-1149).

For ADD-ON after prior testing, contact Genetics lab.

Unacceptable samples

We cannot accept decalcified samples or tissue samples treated with fixatives other than formalin.

Quantity:

Requested:

• Tissue: 10 unstained slides (10-micron thickness) plus one H&E-stained slide.
• Extracted DNA: 5 microgram Bone Marrow: 2 mL
• Blood: 6 mL

Minimum:

• Tissue: 5 unstained slides (10-micron thickness) plus one H&E-stained slide.
• Extracted DNA: 100-250 nanograms Bone Marrow: 1 mL
• Blood: 3 mL

Forms & Requisitions

Requisition Form and Ordering Instructions:

1. Fill out a Genetics Requisition 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).

2. Check "UW-OncoPlex™ Cancer Gene Panel"

3. Please enter any prior molecular testing results in the clinical history space provided

Genetics Preauthorization Form (preauthorization is only done for providers who are external to the UW system).

Handling Instructions

Please attach a copy of the pathology report for the tumor sample being submitted. Please include the flow cytometry report for appropriate hematologic malignancy samples, such as those for acute myeloid leukemia (AML) or chronic lymphocytic leukemia (CLL).

Quantity

Requested: Amounts as noted above
Minimum: Amounts as noted above

Processing

Receiving Instructions

Tissue: Hold slides or tissue blocks at room temperature.

Outside Laboratory: Ship at room temperature.

Stability: unstained slides or tissue blocks stable at room temperature for at least 2 years.

Purified DNA: Refrigerate DNA specimens. Frozen is acceptable.

Blood or Bone Marrow: Refrigerate whole blood and/or bone marrow

Unacceptable Conditions: Frozen or clotted specimens

Stability (collection to initiation of testing): Ambient: 3 days; Refrigerated: 7 days

Misc Sendout

Performance

Lab Department

Genetics(GEN)

Frequency

Typical Turnaround: 4 weeks *Turn around times may vary based on factors such as tissue acquisition and insurance preauthorization.

Available STAT?

No

Performing Location(s)

UW-MT	Genetics Attention: Genetics Lab Clinical lab, Room NW220 University of Washington Medical Center 1959 NE Pacific Street Seattle, WA 98195 Tel: 206-598–6429 M–F (7:30 AM–4:00 PM) Fax: 206-616-4584 Lab email: cgateam@uw.edu Tel (EXOME only): 206-543-0459	Faculty Jillian Buchan, PhD, FACMG Runjun Kumar, MD, PhD Regina Kwon, MD, MPH Christina Lockwood, PhD, DABCC, DABMGG Abbye McEwen, MD, PhD Colin Pritchard, MD, PhD Vera Paulson, MD, PhD Eric Konnick, MD, MS He Fang, PhD

Billing & Coding

LOINC

51967-8

Interfaced Order Code

UOW5573

Billing Comments

For additional test/billing information, see following page: UW-OncoPlex™ Cancer Gene Panel Billing.

For pricing information, contact Client Support Services 206-520-4600 or 800-713-5198.

We offer insurance pre-authorization services (preauthorization is only done for providers who are external to the UW system).

Email: ngsbill@uw.edu or call 1-855-320-4869 for more information.

Genetics Preauthorization Form