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Test Code NGPLSF OncoPlus, Universal Cancer Mutation Analysis Panel (NGS), (FFPE)

Specimen Handling and Transport Instructions

UCMC Onsite Instructions: Collect specimen per standard collection procedure and send to laboratory immediately. Specimens must be receieved within 72 hours.
UCMC Offsite and UC MedLab Outreach Instructions: Collect specimen per standard collection procedure and send to laboratory immediately. Specimens must be receieved within 72 hours.

Rejection Criteria

• Common specimen rejected situations include: incorrect specimen type, insufficient volume, missing or incomplete specimen identifiers, incorrect specimen transport, or specimens outside stability limits.
• Specimens received >72 hours will be rejected
• Specimens fixed or decalcified in mercury-based fixatives such as B5 will be rejected

Turnaround Time

Routine Turnaround Time: 21 days
STAT Turnaround Time: not available

CPT Codes

88381, 81445

Specimen

Specimen Type: Tumor Tissue
Preferred Specimen: FFPE Slides
Other Acceptable Specimens: not applicable

Appropriate specimens (FFPE) should contain >20% tumor cells and enough total cells to produce adequate DNA yield (typically >50,000 total cells). Specimens with less than 20% tumor cells may be tested at the discretion of the attending molecular pathologist.

Volume

Preferred Volume: >10 slides
Minimum Volume: 10 slides

Unstained slides containing formalin-fixed, paraffin embedded tissue are acceptable. At least 10 microtome sections of 5 micron thickness should be submitted for testing

Specimen Stability

Storage Temperature

Stability

Room temperature

(20 - 25°C)

 72 hours

Refrigerated

(2 - 10°C)

not acceptable

Frozen

(-20°C)

 not acceptable

Collection Instructions

Collect specimen per standard laboratory collection procedures.

Clinical Indications

The test is intended for any hematological (blood or bone marrow) or solid tumor (formalin-fixed paraffin-embedded) samples, provided the malignant cell proportion is greater than 20%. The mutation detects point mutations and insertions and deletions of DNA up to 60 bp. Additional analytics specialized for FLT3 internal tandem duplication mutations allow detection of these anomalies up to 100 bp. Ancillary findings are also produced and reported, including microsatellite instability (MSI) and tumor mutational burden (TMB).

This is a comprehensive assay for solid tumor and hematological malignancy specimens to determine appropriate therapies. It also can be useful for diagnosis, prognosis, clinical trials selection and for translational research.

Methodology

Next Generation Sequencing

Synonyms/Key Search Words

DNA OncoPlus, NGS, cancer, DNAOP

Additional Information

Genes analyzed for mutations and insertions/deletions (154): ABL1, AKT1, ALK, APC, ARID1A, ARID2, ASXL1, ATM, ATR, ATRX, AXL, B2M, BAP1, BCOR, BCORL1, BIRC3, BLM, BRAF, BRCA1, BRCA2, BTK, CALR, CBL, CBLB, CCND1, CCND2, CCND3, CDH1, CDK4, CDK6, CDKN2A, CEBPA, CHEK1, CHEK2, CSF1R, CSF3R, CTCF, CTNNA1, CTNNB1, CUX1, CXCR4, DAXX, DDR2, DDX3X, DDX41, DICER1, DNMT3A, EGFR, EP300, EPHA3, EPHA5, ERBB2, ERBB3, ERBB4, ERCC3, ESR1, ETV6, EZH2, FANCA, FAT3, FBXW7, FGFR1, FGFR2, FGFR3, FH, FLT3, FOXL2, GATA1, GATA2, GNA11, GNAQ, GNAS, GRIN2A, H3F3A, HIST1H3B, HIST1H3C, HNF1A, HRAS, IDH1, IDH2, IKZF1, ITPKB, JAK2, KDM6A, KDR, KIT, KMT2A, KRAS, MAP2K1, MAPK1, MDM2, MET, MLH1, MLH3, MPL, MRE11A, MSH2, MSH6, MTOR, MYC, MYCN, MYD88, NBN, NF1, NF2, NFE2L2, NOTCH1, NOTCH2, NPM1, NRAS, PALB2, PBRM1, PDGFRA, PDGFRB, PHF6, PIK3CA, PIK3CB, PIK3R1, PLCG2, POLE, POT1, PPP2R1A, PTCH1, PTEN, PTPN11, RAD21, RAD51, RB1, RET, RUNX1, SDHB, SDHC, SDHD, SETBP1, SF3B1, SMAD4, SMARCB1, SMC1A, SMC3, SMO, SRSF2, STAG2, STAT3, STAT5B, STK11, TERT (promoter only), TET2, TP53, TSC1, TSC2, U2AF1, VHL, WT1, ZRSR2

Genes analyzed for copy number variations (143 gene subset): ABL1, AKT1, ALK, APC, ARID1A, ARID2, ASXL1, ATM, ATR, AXL, B2M, BAP1, BIRC3, BLM, BRAF, BRCA1, BRCA2, CALR, CBL, CBLB, CCND1, CCND2, CCND3, CDH1, CDK4, CDK6, CDKN2A, CEBPA, CHEK1, CHEK2, CSF1R, CSF3R, CTCF, CTNNA1, CTNNB1, CUX1, CXCR4, DAXX, DDR2, DDX41, DICER1, DNMT3A, EGFR, EP300, EPHA3, EPHA5, ERBB2, ERBB3, ERBB4, ERCC3, ESR1, ETV6, EZH2, FANCA, FAT3, FBXW7, FGFR1, FGFR2, FGFR3, FH, FLT3, FOXL2, GATA2, GNA11, GNAQ, GNAS, GRIN2A, H3F3A, HIST1H3B, HIST1H3C, HNF1A, HRAS, IDH1, IDH2, IKZF1, ITPKB, JAK2, KDR, KIT, KMT2A, KRAS, MAP2K1, MAPK1, MDM2, MET, MLH1, MLH3, MPL, MRE11A, MSH2, MSH6, MTOR, MYC, MYCN, MYD88, NBN, NF1, NF2, NFE2L2, NOTCH1, NOTCH2, NPM1, NRAS, PALB2, PBRM1, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PIK3R1, PLCG2, POLE, POT1, PPP2R1A, PTCH1, PTEN, PTPN11, RAD21, RAD51, RB1, RET, RUNX1, SDHB, SDHC, SDHD, SETBP1, SF3B1, SMAD4, SMARCB1, SMC3, SMO, SRSF2, STAT3, STAT5B, STK11, TERT, TET2, TP53, TSC1, TSC2, U2AF1, VHL, WT1

Genes reported for fusions/translocations: ALK, RET, and ROS1

Last Review Date

6/1/2022