Oncoplex Select Cancer Gene Panel

General Information

Lab Name

Lab Code

OPS

Epic Ordering

Oncoplex Select Cancer Gene Panel

Description

OncoPlex Select panels are tumor-specific somatic panels that detect mutations in up to 50 genes related to cancer treatment, prognosis, or diagnosis. The OncoPlex Select panels are designed to detect somatic mutations in tumors/cancer, and are not designed to detect germline (heritable) mutations.

The test uses next-generation "deep" sequencing to detect most classes of mutations, including single nucleotide variants, small insertions and deletions (indels), gene amplifications, and selected gene fusions. Complete sequencing of all coding exons is available for most but not all genes in each panel.

Microsatellite instability (MSI) status and total mutation burden (TMB) are reported for relevant cancer cases.

Please note that UW-OncoPlex™ is intended for solid tumors. For testing related to myeloid and lymphoid disorders, please order Heme Gene Panel by NGS [HCAPA]. For testing related to acute myeloid leukemias and myelodysplastic syndromes, please order Myeloid Gene Panel by NGS [HCAPMY].

For information on the complete UW-OncoPlex™ Panel, see UW OncoPlex Cancer Gene Panel [OPX].

For information about ordering individual genes on the panel, see UW-Oncoplex™ Single Gene [OPG].

The following panel(s) are currently available to providers within the UWMC system (OncoPlex Select is not yet available to providers outside of the UWMC system):

OncoPlex Select-Gyn:

AKT1, ARID1A, ARID1B, ATM, BARD1, BRAF, BRCA1, BRCA2, BRIP1, CCND1, CCNE1, CD274, CDK12, CHEK1, CHEK2, CTNNB1, DICER1, EPCAM, ERBB2, ESR1, FBXW7, KMT2C, KRAS, MET, MLH1, MSH2, MSH6, MTOR, MYC, MYCN, NBN, NF1, NRAS, NTRK fusions, PALB2, PIK3CA, PIK3R1, PMS2, POLD1, POLE, PTEN, RAD51B, RAD51C, RAD51D, RB1, SMARCA4, STK11, TP53

OncoPlex Select-Neuro:

ALK, APC, ATRX, BAP1, BRAF, C19MC, CDKN2A, CDKN2B, CTNNB1, DICER1, EGFR, FGFR1, FGFR2, FGFR3, FGFR4, H3-3A (H3F3A), H3-3B (H3F3B), H3C2 (HIST1H3B), IDH1, IDH2, MAP2K1, MET, MLH1, MSH2, MSH6, MYB, MYC, MYCN, NF1, NF2, NTRK1, NTRK2, NTRK3, PDGFRA, PIK3CA, PMS2, PTCH1, PTEN, ROS1, SMARCA4, SMARCB1, SMARCE1, SMO, SUFU, TERT, TP53, TSC1, TSC2, ZFTA (aka c11orf95), YAP1

Forms & Requisitions

Requisition Form and Ordering Instructions:

1. Fill out a Genetics Requisition Form
2. Check "UW-Oncoplex™ Cancer Single Gene"3. Please indicate the gene(s) requested in clinical history space provided
Genetics Preauthorization Form (preauthorization is only done for providers who are external to the UW system, orders coming from outside institutions where direct patient billing (non-institutional) billing is allowed).

Synonyms

brain tumor, endometrial cancer panel, glioblastoma, glioma, gynecologic oncology, high-grade glioma, low-grade glioma, neuro oncology, neuropathology, OncoPlex, ovarian cancer panel, paired tumor panel, precision medicine, somatic panel, subpanel, tumor panel

Components

Code	Name
OPSPAN	Oncoplex Select Panel
OPSRE	Oncoplex Select Result
OPSIN	Oncoplex Select Interpretation
OPSCH	Oncoplex Select Tested Sample
OPSMT	Oncoplex Select Methods
OPSDI	Oncoplex Select Director

Interpretation

Method

Next-generation sequencing. Test genes are sequenced on an Illumina instrument to detect single nucleotide variants, small insertions and deletions, gene amplifications, and selected translocations

Reference Range

See individual components

Guidelines

Genetics and Solid Tumor Diagnostic Testing

Ordering & Collection

Specimen Type: Formalin-Fixed Paraffin Embedded Tumor Tissue (FFPE), Purified DNA, Peripheral Blood, cultured cells from skin biopsy, skin biopsy (direct), saliva, purified DNA from peripheral blood or cultured cells
Collection: 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

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.
Forms & Requisitions: Requisition Form and Ordering Instructions:

1. Fill out a Genetics Requisition Form
2. Check "UW-Oncoplex™ Cancer Single Gene"3. Please indicate the gene(s) requested in clinical history space provided
Genetics Preauthorization Form (preauthorization is only done for providers who are external to the UW system, orders coming from outside institutions where direct patient billing (non-institutional) billing is allowed).
Handling Instructions: • 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).

Attach a copy of the pathology report for the tumor sample being submitted. Included the flow cytometry report for leukemia (AML) samples.

For Outside Laboratory:

Ship at room temperature.

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

Processing

Processing: 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: 2 days; Refrigerated: 7 days

Performance

LIS Dept Code

Genetics (GEN)

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 Brian Shirts, MD, PhD Abbye McEwen, MD, PhD Colin Pritchard, MD, PhD Vera Paulson, MD, PhD Eric Konnick, MD, MS He Fang, PhD

Frequency

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

Available STAT?

Billing & Coding

CPT codes
Billing Comments: For additional test/billing information, see following page: UW-OncoPlex™ Select Cancer Gene Panel Billing
LOINC: 51967-8
Interfaced Order Code: UOW5563