UW OncoPlex Cancer Gene Panel

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General Information

Lab Name
UW OncoPlex Cancer Gene Panel
Lab Code
OPX
ORCA Name
(Contact Lab For Information)
Description

UW-OncoPlex is a multiplexed mutation assay for tumor tissue that assesses mutations >350 genes related to cancer treatment, prognosis, or diagnosis (listed below).

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.

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

This test is designed to detect somatic mutations in cancer, and is not designed to detect germline (heritable) mutations.

To request testing for one individual gene in the panel, see information for UW-OncoPlex Single Gene UW-OncoPlex Single Gene [OPG].

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
Forms & Requisitions

Requisition Form and Ordering Instructions:

  1. Fill out a Genetics Requisition Form
  2. Check "UW-Oncoplex Cancer Gene Panel"
  3. Please eneter 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).

Synonyms
ABL1, ABL2, ACVR1, AKT1 , AKT2, AKT3, ALK, ANGPTL1, ANKRD26, APC, AR, ARAF, ARID1A, ARID1B, ASXL1, ASXL2, ATM, ATR, ATRX, AURKA, AURKB, AXIN2, AXL, BABAM1, BAK1, BAP1, BARD1, BCL2, BCL2L11, BCOR, BCORL1, BCR, BIRC3, BMPR1A, BRAF, BRCA1, BRCA2, BRIP1, BTK, C11orf95, CALR , CARD11, CBL, CBLB, CBLC, CCND1, CCND2, CCNE1, CD19, CD274, CD33, CD74, CDC27, CDH1, CDK12, CDK4, CDK6, CDK8, CDK9, CDKN1A, CDKN2A, CDKN2B, CEBPA, CHD1, CHEK1, CHEK2, CREBBP, CRLF2, CRX, CSF1R, CSF3R, CTCF, CTNNA1, CTNNB1, CUX1, DAXX, DDR2, DDX41, DEPDC5, DICER1, DNAJB1, DNMT3A, DOCK7, DPYD, EBF1, EGFR, EIF3E , ELF1, EML4 , EP300, EPAS1, EPCAM, EPHA3, EPHA5, EPHB2, EPHB6, ERBB2, ERBB3, ERBB4, ERCC2, ERG, ESR1, ESR2, ETV6, EZH2, FAM175A, FANCA, FANCB, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FBXW7, FGFR1, FGFR2, FGFR3, FGFR4, FH, FKBP1A, FLT1, FLT3, FLT4, FOXA1, FOXR2, GAB2, GALNT12, GATA1, GATA2, GATA3, GEN1, GLI1, GLTSCR1, GLTSCR2, GNA11, GNAQ, GNAS, GREM1, GRIN2A, GRM3, H3F3A, H3F3B, HDAC4, HDAC9, HIF1A, HIST1H3B, HNF1A, HRAS, HSPH1, ID3, IDH1, IDH2, IGF1R, IKZF1, IL7R, JAK1, JAK2, JAK3, KDM6A, KDR, KIF5B, KIT, KLF4, KMT2A, KMT2C, KMT2D, KRAS, MAP2K1 (MEK1), MAP2K2 (MEK2), MAP2K4, MAPK1, MAX, MC1R, MCL1, MDM2, MDM4, MED12, MEGF6, MEN1, MET, MIOS, MITF, MLH1, MLH3, MN1, MPL, MRE11A, MSH2, MSH6, MSLN, MTAP, MTOR, MUTYH, MYB, MYC, MYCL1, MYCN, MYD88, MYOD1, NAB2, NAT2, NBN, NF1, NF2, NKX2-1, NOTCH1, NOTCH2, NOTCH3, NPM1, NPRL2, NPRL3, NR4A3, NRAS, NT5C2, NTHL1, NTRK1, NTRK2, NTRK3, NUDT15, PAK1, PALB2, PAX5, PBRM1, PDCD1LG2, PDGFRA, PDGFRB, PHF6, PHOX2B, PIK3CA, PIK3CB, PIK3R1, PLCG2, PLK1, PLK2, PLK3, PLK4, PML, PMS2, POLD1, POLE, PPM1D, PRKAR1A, PRPF40B, PRPS1, PTCH1, PTEN, PTPN11, PTPRD, QKI, RAC1, RAD21, RAD51B, RAD51C, RAD51D, RAF1, RARA, RB1, RECQL, RELA, RET, RHEB, RICTOR, RINT1, RIT1, ROR1, ROS1, RPL10, RPS14, RPS15, RPS20, RPTOR, RRM1, RRM2, RSPO2, RSPO3, RUNX1, SAMD9L, SDHA, SDHB, SDHC, SDHD, SETBP1 , SETD2, SF1, SF3B1, SH2B3, SHH, SLX4, SMAD2, SMAD3, SMAD4, SMARCA4, SMARCB1, SMC1A, SMC3, SMO, SPOP, SPRY4, SRC, SRP72, SRSF2, STAG2, STAT5B, STAT6, STK11, SUFU, SUZ12, TACC3, TACSTD2, TCF3, TERC, TERT, TET1, TET2, TET3, TFE3, TFG, TGFBR2, TLX1, TMPRSS2, TP53, TP73, TRAF7, TRRAP, TSC1, TSC2, TTYH1, TYMS, U2AF1, U2AF2, VHL, WRN, WT1, XRCC2, YAP1, ZBTB16, ZRSR2, microsatellite instability, multigene panel, next-generation sequencing, precision medicine panel, precision oncology panel, total mutation burden, TMB
Components

Interpretation

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 6)

ALK fusions (including ALK-EML4, ALK-KIF5B, ALK-TFG, ALK-C2orf44) 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) NTRK3-ETV6 fusions PML-RARA 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.

Total Mutation Burden Analysis

Total 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
Guidelines

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
  2. Check "UW-Oncoplex Cancer Gene Panel"
  3. Please eneter 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 Acute Myeloid Luekemia (AML) and chronic lymphocitic leukemia (CLL).

Quantity
requested: Amounts as noted above
minimum: Amounts as noted above

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: 3 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: 206-598–0304
Lab email: genelab@uw.edu

Supervisor

Robert Livingston, PhD bobl@uw.edu

Genetic Counselors

Angela Jacobson, MS, LGC agibson@uw.edu
Ginger Tsai, MS, LGC, gjtsai@uw.edu

Faculty

Colin C. Pritchard, MD, PhD
Brian H. Shirts, MD, PhD
Christina Lockwood, PhD, DABCC
Stephen Salipante, MD, PhD
Eric Konnick, MD, MS
Karen Stephens, PhD, FACMG
Jonathan F. Tait, MD, PhD
Vera Paulson, MD, PhD

Frequency
Results within 4-6 weeks, from sample receipt in laboratory.
Available STAT?
No

Billing & Coding

CPT codes
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

LOINC
51967-8