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Test Code NGPLSC OncoPlus, Universal Cancer Mutation Panel (NGS), Cytology Smear (CS)

Important Note

Starting on 01/09/2017, the University of Chicago Molecular Pathology Laboratory launched an updated version of the OncoPlus universal cancer mutation analysis panel. This is a Next Generation Sequencing assay designed to interrogate over 1,200 solid tumor and hematological malignancy related genes via analysis of Peripheral Blood, Bone Marrow, Formalin-Fixed Paraffin-Embedded and Cytology Smear specimens. 28 additional genes were added to the previously 119 clinically reported genes.

In addition, this updated panel version allows:

  • The detection and reporting of copy number variations (CNVs) for 136 genes.
  • The detection and reporting of lung cancer-related gene fusions in ALK, RET, and ROS1.

Test includes

  • Detection of mutations, insertions and deletions for 147 clinically reported genes.
  • Detection and reporting of copy number variations (CNVs) for 136 genes.
  • Detection and reporting of lung cancer-related gene fusions in ALK, RET, and ROS1.

Specimen Type

Cytology Smear

Container

Cytology Smear slides

Preferred Volume

N/A

Mimimum Volume

N/A

Offsite Collection Instructions

Formalin-fixed, paraffin embedded tissue:

  • 0.5x0.5 cm total area (5 micron tissue) with >20% tumor cells (typically >50,000 total cells) is required to yield sufficient total DNA.
  • Immediate on-site adequacy assessment is performed by a pathologist and tumor-rich areas are selected for testing.
  • Slides received from outside laboratories must be received labeled with two patient identifiers and a surgical pathology ID.
  • Specimens with less than 20% tumor cells may be tested at the discretion of the attending molecular pathologist.

UCMC Collection Instructions

Cytology smears: immediate on-site adequacy assessment is performed by a pathologist and tumor-rich areas are selected for testing.

Availability

Monday – Friday, 8:00am – 5:00pm

Turnaround Time

14-20 business days

STAT Availability

Not Available

Test Usage

The OncoPlus panel is a universal cancer mutation, next generation sequencing (NGS) assay that has the capability to cover more than 1,200 cancer-related genes for personalized assessments of both solid tumors and hematological malignancies. 

 

  • 147 genes shown below are clinically reportable for mutations, insertions and deletions:

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, 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, MET, MLH1, MLH3, MPL, MRE11A, MSH2, MSH6, MTOR, 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, STK11, TERT, TET2, TP53, TSC1, TSC2, U2AF1, VHL, WT1, and ZRSR2.

 

  • Genes reported for copy number gains and losses (136):

ABL1, AKT1, ALK, APC, ARID1A, ARID2, ASXL1, ATM, ATR, AXL, B2M, BAP1, BIRC3, BLM, BRAF, BRCA1, BRCA2, CALR, CBL, CBLB, CCND1, CCND2, CCND3, CDH1, 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, MET, MLH1, MLH3, MPL, MRE11A, MSH2, MSH6, MTOR, 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, STK11, TERT, TET2, TP53, TSC1, TSC2, U2AF1, VHL, and WT1.

 

  • Genes reported for fusions/translocations:

ALK, RET, and ROS1.

Test Methodology

The test procedure involves DNA extraction and quantity/quality assessment, fragmentation and library preparation, followed by pooled capture targeting the desired genomic loci. Next generation sequencing (NGS) is performed on the HiSeq 2500 system (Illumina) and downstream analysis for quality control and detection of mutations is performed via custom-design bioinformatics pipelines on a HIPAA-compliant high performance computing system within the Center for Research Informatics (CRI).  

Critical Results - Reference range

None

Reporting - Test Limitations

  • An interpretive report will be provided including mutations (and now copy numbers and fusions) listed according to interpreted pathogenicity, along with interpretative summaries. 
  • This test is intended for the detection of single-nucleotide mutations and insertions/deletions up to 60 bp in size.  Internal tandem duplications of the FLT3 gene are detected at larger sizes (largest size tested = 102 bp). 
  • Copy number changes will be reported at levels greater than 2X or less than 0.6X.
  • The assay is intended for performance on specimens with >20% tumor cells and adequate overall tissue.
  • Mutational assay sensitivity is 10% mutant allelic fraction (MAF). 
  • False-negative results of all types may occur when there is a lower than adequate tumor cell burden. 

Additional Information

  • 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.
  • Specimens fixed or decalcified in mercury-based fixatives such as B5 are unacceptable. Other fixatives will be accepted at the discretion of the laboratory director.
  • Unstained slides containing formalin-fixed, paraffin embedded tissue are acceptable. At least 10 microtome sections of 5 micron thickness should be submitted for testing. 

CPT Code

81455

Synonyms

fusion

ALK/RET/ROS1

CNV

copy number

cancer

mutation

panel

NGS

NextGen

Sequencing

Gene