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Test Code NGPLSM OncoPlus, Universal Cancer Mutation Analysis Panel (NGS), Bone Marrow

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.

Specimen Type

Bone Marrow

Container/Tube

Lavender Top (EDTA)

Offsite Collection Instructions

Bone Marrow samples collected in EDTA (lavender top)
transported at room temperature to UCM
Lab Services Center.

Preferred Volume

2 mL

UCMC Collection Instructions

Bone Marrow samples collected in EDTA (lavender top),
stored at room temperature or refrigerator. Samples should be
sent
no later than 48 hours from the time of collection to
UCM Lab
Services Center at ambient temperature.

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.

Critical Results

None

Additional Information

  • Appropriate specimens 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.

?�

Synonyms

CNV

copy number

cancer

mutation

panel

NGS

NextGen

Sequencing

Gene

Specimen Minimum Volume

200 uL

Day(s) Performed

Monday – Friday, 8:00am – 5:00pm

STAT DAY(S) AND TIME(S) PERFORMED

Not Available

CPT

81455

Method Name

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).  

Reference Values

None

Specimen and Container/Tube

Bone Marrow

Pediatric Volume

200 uL

Clinical Indications

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
.

Transport Instructions

Bone Marrow?�samples collected in EDTA (lavender top)
transported at room temperature to UCM
Lab Services Center.

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).?�?�

Synonyms/Key Search Words

CNV

copy number

cancer

mutation

panel

NGS

NextGen

Sequencing

Gene