UPMC Oncomine Plus

Test Description

The UPMC Oncomine Plus assay is a targeted Next-Generation Sequencing assay that analyzes > 500 genes for mutations, copy number variations, and gene fusions and provides assessment of sample Tumor Mutation Burden (TMB) and Microsatellite Instability (MSI) status. UPMC Oncomine Plus assay assists in diagnosis, prognostication, and treatment of adult and pediatric solid tumors.

Oncomine Advantage

• Large Pan-Cancer Panel
• Small Sample Size
• Fast Turnaround Time

Test Details

• Amplification-based NGS sequencing of DNA and mRNA
• Uses commercial Oncomine Comprehensive Assay Plus and v3 panel from ThermoFisher Scientific to sequence clinically relevant regions of genes for SNV and indel mutations, copy number alterations, and targeted gene fusions in > 500 cancer-associated genes
• Calculation of sample tumor mutation burden (TMB)
• Assessment of sample MSI status
• Can be performed on small tumor biopsies
• Aids in prognostication and treatment of many solid tumors
• Offers a fast turnaround time (10-14 days)

Genes Assayed by Oncomine

Full-length (>95% CDS coverage) genes for mutations and Copy Number Variation (CNV)

ACVR1B, ACVR2A, AMER1, APC, ARHGAP35, ARID1A, ARID2, ARID5B, ASXL1, ASXL2, ATM, ATR, ATRX, AXIN1, AXIN2, B2M, BAP1, BARD1, BCL2, BCOR, BLM, BRCA1, BRCA2, BRIP1, CASP8, CBFB, CD274, CD276, CDC73, CDH1, CDK12, CDKN1A, DKN1B, CDKN2A, CDKN2B, CDKN2C, CHEK1, CHEK2, CIC, CREBBP, CTCF, CTLA4, CUL3, CUL4A, CUL4B, CYLD, DAXX, DDX3X, DICER1, DNMT3A, DPYD, ELF3, ENO1, EP300, EPCAM, EPHA2, ERCC2, ERCC4, ERRFI1, ETV6, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FAT1, FBXW7, FGF23, FGF3, FGF4, FUBP1, GATA3, GNA13, GPS2, H3-3B, HDAC2, HDAC9, HNF1A, ID3, INPP4B, JAK1, JAK2, JAK3, KDM5C, KDM6A, KEAP1, KMT2A, KMT2B, KMT2C, KMT2D, LARP4B, LATS1, LATS2, MAGOH, MAP2K4, MAP3K1, MAP3K4, MAPK8, MCL1, MEN1, MGA, MLH1, MLH3, MRE11, MSH2, MSH3, MSH6, MTAP, MUTYH, NBN, NCOR1, NF1, NF2, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NRAS, PALB2, PARP1, PARP2, PARP3, PARP4, PBRM1, PCBP1, PDCD1, PDCD1LG2, PGD, PHF6, PIK3R1, PIM1, POLD1, POLE, POT1, PPM1D, PPP2R2A, PRDM1, PRKAR1A, PTCH1, PTEN, RAD50, RAD51B, RAD51C, RAD51D, RAD52, RAD54L, RASA1, RASA2, RB1, RBM10, RNASEH2A, RNASEH2B, RNASEH2C, RNF43, RPA1, RPL22, RUNX1, SDHA, SDHB, SDHD, SETD2, SLX4, SMAD2, SMAD4, SMARCA4, SMARCB1, SOCS1, SOX9, SPEN, STAG2, STK11, SUFU, TBX3, TCF7L2, TET2, TGFBR2, TNFAIP3, TP53, TSC1, TSC2, USP9X, VHL, WT1, XRCC2, XRCC3, ZMYM3, ZRSR2

Hotspot genes for mutations and Copy Number Variation (CNV)

A1CF, ABCB1, ABL1, ABL2, ABRAXAS1, ACSM2B, ACVR1, ADAM18, ADAMTS12, ADAMTS2, AKT1, AKT2, AKT3, ALK, ANO4, AR, ARAF, ARID1B, ARMC4, AURKA, AURKC, AXL, BCL2L12, BCL6, BMPR2, BRAF, BRINP3, BTK, C6, C8A, C8B, CACNA1D, CALR, CANX, CARD11, CASR, CBL, CCND1, CCND2, CCND3, CCNE1, CD79B, CDH10, CDK4, CDK6, CHD4, CIITA, CNTN6, CNTNAP4, CNTNAP5, COL11A1, CSF1R, CSMD3, CTNNB1, CTNND2, CYP2C9, CYP2D6, DCAF4L2, DCDC1, DDR1, DDR2, DOCK3, DSC1, DSC3, EGFR, EIF1AX, EMSY, ERAP1, ERAP2, ERBB2, ERBB3, ERBB4, ESR1, EZH2, FAM135B, FAS, FGF19, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, FLT4, FOXA1, FOXL2, FYN, GALNT17, GATA2, GLI1, GLI3, GNA11, GNAQ, GNAS, GPR158, GRID2, H3-3A, H3C2, HCN1, HLA-A, HLA-B, HRAS, IDH2, IGF1R, IKBKB, IL7R, KCND2, KCNH7, KDR, KEL, KIR3DL1, KIT, KLF5, KLHL13, KRAS, LRRC7, MAP2K1, MAP2K2, MAP2K7, MAPK1, MARCO, MAX, MDM2, MDM4, MECOM, MED12, MEF2B, MET, MITF, MPL, MTOR, MTUS2, MYC, MYCL, MYCN, MYD88, NFE2L2, NOL4, NRXN1, NT5C2, NTRK1, NTRK2, NTRK3, OR10G8, OR2G6, OR2L13, OR2L2, OR2L8, OR2M3, OR2T3, OR2T33, OR2T4, OR2W3, OR4A15, OR4C15, OR4C6, OR4M1, OR4M2, OR5D18, OR5F1, OR5L1, OR5L2, OR6F1, OR8H2, OR8I2, OR8U1, ORC4, PAK5, PDE1A, PDE1C, PDGFRA, PDGFRB, PDIA3, PIK3C2B, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R2, PLCG1, PLXDC2, PMS1, PMS2, POM121L12, PPFIA2, PPP2R1A, PPP6C, PRDM9, PRKACA, PSMB10, PSMB8, PSMB9, PTPN11, PTPRT, PXDNL, RAC1, RAD51, RAF1, RARA, RBP3, RECQL4, REG1A, REG1B, REG3A, REG3G, RET, RHEB, RICTOR, RIT1, ROS1, RPS6KB1, RPTOR, RUNDC3B, RUNX1T1, SDHC, SETBP1, SF3B1, SLC15A2, SLC8A1, SLCO1B3, SMC1A, SMO, SOS1, SPOP, SRC, STAT1, STAT3, STAT5B, STAT6, SYT10, TAP1, TAP2, TERT, TMEM132D, TNFRSF14, TOP1, TP63, TPMT, TPP2, TPTE, TRHDE, TRIM48, TRIM51, TRRAP, TSHR, U2AF1, USP8, XPO1, YAP1, YES1, ZFHX3, ZNF217, ZNF429

Hotspot genes for mutation only

ATP1A1, AURKB, BCR, BMP5, CD163, CUL1, CYSLTR2, DGCR8, DROSHA, E2F1, EPAS1, ERCC5, FGF7, FOXO1, H1-4, H2BC5, HIF1A, HLA-C, IDH1, IL6ST, IRF4, IRS4, KCNJ5, KLF4, KNSTRN, KRTAP21-1, KRTAP6-2, MYOD1, NLRC5, NSD2, NUP93, NYAP2, PAX5, PCDH17, PTPRD, RGS7, RHOA, RPL10, RPL5, RPTN, SH3RF2, SIX1, SIX2, SNCAIP, SOX2, SRSF2, SYT16, TAF1, TAPBP, TGFBR1, TOP2A, UGT1A1, WAS, ZBTB20, ZIM3, ZNF479, ZNF536

Targeted gene fusions involving

AKT2, ALK, AR, AXL, BRAF, BRCA1, BRCA2, CDKN2A, EGFR, ERBB2, ERBB4, ERG, ESR1, ETV1, ETV4, ETV5, FGFR1, FGFR2, FGFR3, FGR, FLT3, JAK2, KRAS, MDM4, MET, MYB, MYBL1, NF1, NOTCH1, NOTCH4, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, PDGFRA, PDGFRB, PIK3CA, PPARG, PRKACA, PRKACB, PTEN, RAD51B, RAF1, RB1, RELA, RET, ROS1, RSPO2, RSPO3, TERT

Background

The UPMC Oncomine Plus assay is a targeted comprehensive NGS panel designed to detect multiple alterations across a wide spectrum of tumor types. These alterations include Single Nucleotide Variants (SNVs), Insertions/Deletions (indels), Copy Number (CN) alterations, and targeted Gene Fusions across > 500 of the most relevant cancer-associated genes.

Specimen Requirements

Paraffin Embedded Tissue Sections

• Tissue should be fixed in formalin and not exposed to decalcification solution. The paraffin block should contain no less than 3 mm area of tumor.
• Slides should be prepared by histology using a specific protocol for cutting molecular sections to avoid contamination of the tissue sections.
• One H&E and 6 unstained sections are required. Ten unstained sections or more are required if the tissue is small. Please call the lab if you have questions.
• Slides should be properly labeled with a block label that matches the surgical pathology specimen number on the surgical pathology report.
• Slides should be sent ambient temperature in proper storage containers (plastic slide boxes) to protect them during shipment.
• A surgical pathology and/or cytology report and completed requisition form must accompany all specimens.

Turnaround Time

10-14 Business days

Billing Information

For insurance or institutional prices, please call.