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UW-OncoPlex - Cancer Gene Panel

Questions: 1-800-256-0893

Background

UW-OncoPlex is a multiplexed gene sequencing panel that detects mutations in tumor tissue in 234 cancer-related genes (listed in the methods below). The panel includes genes related to cancer treatment, prognosis, and diagnosis. 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. In addition, microsatellite instability status is reported for colorectal cancers. UW-OncoPlex will be ordered as "full panel" or "add-on". The add-on test will be selected by the lab when one or more components of the UW-OncoPlex panel is also ordered (e.g. EGFR mutations + UW-OncoPlex) or has already been done.

Methods (assay version 4)

The following genes are sequenced on an Illumina instrument to detect single nucleotide variants, small insertions and deletions, gene amplifications, and selected translocations: ABCB1*, ABCC4*, ABCG2*, ABL1, ABL2, AKT1, AKT2, AKT3, ALK**, APC, AR, ASXL1, ATM, ATRX (NEW), AURKA, AURKB, AXL (NEW), BAK1, BAP1, BARD1 (NEW), BCL2, BCL2L11, BCOR, BCR*, BRAF**, BRCA1, BRCA2, BRIP1 (NEW), CALR (NEW), CBL, CBLB, CCND1, CCNE1, CDH1, CDK4, CDK6, CDK8, CDKN1A (NEW), CDKN2A, CEBPA, CHD1 (NEW), CHEK1, CHEK2, CREBBP, CRLF2, CSF1R, CTNNB1, CYP1B1*, CYP2C19*, CYP2C8*, CYP2D6*, CYP3A4*, CYP3A5*, DAXX (NEW), DDR2, DEPDC5 (NEW), DNAJB1 (NEW), DNMT3A, DOCK7 (NEW), DPYD, EGFR, EIF3A, EML4*, EPHA3, EPHA5, EPHB2, EPHB6, ERBB2, ERBB3, ERBB4, ERCC2*, ESR1*, ESR2*, ETV6, EZH2, FAM175A (NEW), FBXW7, FCGR1A, FCGR2A, FCGR3A*, FGFR1, FGFR2, FGFR3, FGFR4, FLT1, FLT3, FLT4, FOXA1, GAB2, GATA1, GATA2, GATA3, GLI1 (NEW), GNA11, GNAQ, GNAS, GRIN2A, GRM3, GSTP1*, H3F3A (NEW), HDAC4, HIF1A, HNF1A, HRAS, HSPH1*, IDH1, IDH2, IGF1R, IKZF1, IL7R, ITPA*, JAK1, JAK2, JAK3, KDM6A, (UTX), KDR, KIF5B*, KIT, KRAS, LRP2*, MAN1B1*, MAP2K1, MAP2K2, MAP2K4, MAPK1, MC1R, MCL1, MDM2, , MDM4, MED12, MEN1, MET, MIOS (NEW), MITF, MLH1**, MLH3 (NEW), MLL (KMT2A)**, MPL, MRE11A, MSH2**, MSH6**, MTAP (NEW), MTHFR*, MUTYH, MYC, MYCL1, MYCN, NBN (NEW), NF1, NF2, NKX2-1, NOTCH1, NOTCH2, NPM1, NPRL2 (NEW), NPRL3 (NEW), NQO1*, NRAS, NRP2*, NTRK1 (NEW), PAK1 (NEW), PALB2 (NEW), PAX5, PBRM1, PDGFRA, PDGFRB, PHF6 (NEW), PIK3CA, PIK3R1, PLK1 (NEW), PLK2 (NEW), PLK3 (NEW), PLK4 (NEW), PML*, PMS2, POLD1 (NEW), POLE (NEW), PRPF40B, PTCH1, PTEN, PTPN11, PTPRD, RAD51C (NEW), RAD51D (NEW), RAF1, RARA**, RB1, RET, RICTOR, ROS1**, RPS14, RUNX1, SF1, SF3B1, SHH (NEW), SLC19A1*, SLC22A2*, SLCO1B3*, SMAD2, SMAD3, SMAD4, SMARCA4, SMARCB1, SMO, SOD2*, SPOP, SPRY4, SRC, SRSF2, STK11, SUFU (NEW), SULT1A1*, SUZ12, TACC3 (NEW), TACSTD2 (NEW), TET2, TFG*, TGFBR2, TMPRSS2*, TP53, TPMT*, TRRAP, TSC1, TSC2, TYMS*, TYR, U2AF1, (U2AF35), U2AF2, (U2AF65), UGT1A1*, UMPS*, VHL, WT1, ZBTB16 (NEW), and ZRSR2.

*Selected regions only sequenced, **Selected introns sequenced in addition to all coding regions

Gene Fusions and Rearrangements Detected (assay version 4)

Microsatellite Instability Analysis

Microsatellite instability (MSI) status is reported for all colorectal cancer cases. MSI is detected using methods described in Salipate et al. 2014 Clin Chem. (2014) 60:1192-9.

Turnaround Time

6 weeks

Shipping Address

Acceptable Specimens

Tissue samples (FFPE): Send EITHER (a) slides, OR (b) tissue block: (a) Instructions for slide specimens: 1 slide at 4-micron thickness stained with hematoxylin-and-eosin 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. Note: Sections should contain as much tumor tissue as possible. (b) Instructions for tissue block specimen: Provide complete tissue block containing tumor tissue. If there is more than one tissue block, please provide the block that has the greatest amount of tumor tissue. Tissue block will be returned at completion of testing. Ship at room temperature.

Purified DNA: (Reference hematoxylin-and-eosin stained slide and pathology report required): 5 ug minimum. Ship specimen refrigerated for overnight delivery.

Blood: 6 mL blood in LAVENDER TOP (EDTA) tube. Ship specimen refrigerated for overnight delivery. Specimen can be held for up to 24 hours before shipping if refrigerated.

Bone Marrow: 1 to 2 mL Bone Marrow in LAVENDER TOP (EDTA) tube. Ship specimen refrigerated for overnight delivery. Specimen can be held for up to 24 hours before shipping if refrigerated.

For further details regarding specimen collection, handling and transport, see the Laboratory Medicine Online Test Guide for OPX

Requisition Form

CPT Codes & Pricing

CPT coding

For pricing information, contact Reference Laboratory Services at 1-800-256-0893

Reference Range

No mutation detected.

Further Information

For further information:

References

  1. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. (2010) 11:31-46.

  2. Pritchard CC, Salipante SJ, Koehler K, Smith C, Scroggins S, Wood B, Wu D, Lee MK, Dintzis S, Adey A, Liu Y, Eaten KD, Martins R, Stricker K, Margolin K, Hoffman N, Churpek J, Tait JF, King MC, Walsh T. Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens. The Journal of Molecular Diagnostics (2014) 16:56-67.

  3. Salipante SJ, Scroggins SM, Hampel HL, Turner EH, Pritchard CC. Microsatellite instability detection by next generation sequencing. Clin Chem. (2014) 60:1192-9.

2014-10-18 16:22