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Test Code NGFFPE (FFPE), NGSCS ( Cytology Smear) OncoScreen ST2.0

Specimen and Container/Tube

FFPE or
Cytology Smear

Turnaround Time

n/a

Test Includes

OncoScreen ST2.0 tests hot spot regions of 50 commonly
mutated
genes in cancer. The genes are:ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A,
CSF1R, CTNNB1, EGFR, ERB2, ERBB4, EZH2,
FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A,
HRAS, IDH1,
IDH2, JAK2, JAK3,
KDR,
KIT,
KRAS,
MET,
MLH1, MPL,
NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA,
PTEN, PTPN11,
RB1, RET,
SMAD4, SMARCB1, SMO,
SRC, STK11,
TP53, VHL.

Specimen Type

FFPE or
Cytology Smear

Preferred Volume

n/a

Offsite Collection Instructions

Formalin-fixed, paraffin embedded tissue:  

  • Total tumor area on slides = 0.1 cm2 total
    (include
    top and bottom H&E guide slides). 
  • Paraffin block acceptable.

UCMC Collection Instructions

  • FFPE
    tissues: a pathologist will
    review the respective case upon receiving a requisition to
    select
    the appropriate block for testing. Slides will be recut and
    evaluated, tumor-rich areas are selected for
    testing.  


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

STAT Turnaround Time

n/a

Test Usage

The OncoScreen ST2.0 assay is designed to sequence hot-spot
mutational regions of 50 clinically relevant genes that are
commonly mutated in cancer for the purpose of identifying
somatic
mutations (substitutions and
insertions/deletions). Mutations
in these 50 genes are linked to many types of cancers,
including
lung, colorectal, gastric, thyroid, ovarian cancer, melanoma
and
myeloid malignancies.Mutations with known clinical significance
and/or those deemed to be pathogenically related to the biology
of
each patient’s tumor are reported, and this personalized
mutational profile may be useful fordiagnosis, prognosis,
therapy
selection, clinical trials options and for translational
research.

Critical Results

None.

Test Limitations

  • This test will not detect mutations outside the targeted
    genomic regions.
  • Copy number alterations and translocations will not be
    detected.
  • This test is not intended to detect minimal residual
    disease.
  • Assay sensitivity is 5% mutant allele frequency (MAF), thus false-negative
    results may occur when
    there is a lower mutant allele burden.
  • Variants present at oligonucleotide binding sites may
    negatively interfere with hybridization (as with any PCR-based assay),
    potentially resulting in
    underestimation of a particular allele frequency.

Additional Information

  • Specimen requirements: Appropriate specimens contains
    >20%
    tumor cells and those with 10-20% tumor cells may be tested at
    the
    discretion of the attending molecular pathologist.
  • Reporting: Mutations with known or possible pathogenic or
    clinical significance are reported. Variants of unknown
    significance are reported as such.
  • List of exonic intervals covered by the Oncoscreen ST2.0
    Cancer
    Panel:


?�

Gene

Exon(s)

Gene

 Exon
(s)

Gene

 Exon
(s)

Gene

Exon(s)

ABL1

 ?�1-4 EZH2 1 JAK2 1 PTEN 1, 3-8

AKT1

 1, 2 FBXW7 ?�1-5 JAK3 ?�1-3 PTPN11 2

ALK

 1, 2 FGFR1 1, 2 KDR ?�1-9 RB1 9

APC

 ?�1-7 FGFR2 ?�1-4 KIT ?�1-9 RET ?�1-5

ATM

 ?�1-17 FGFR3 ?�1-5 KRAS ?�1-3 SMAD4 ?�1-9

BRAF

 1, 2 FLT3 ?�1-4 MET ?�1-6 SMARCB1 ?�1-4

CDH1

 ?�1-3 GNA11 1 MLH1 1 SMO ?�1-5

CDKN2A

 1, 2 GNAS 1, 2 MPL 1 SRC 1

CSF1R

 1, 2 GNAQ 1 NOTCH1 ?�1-3 STK11 ?�1-5

CTNNB1

 1 HNF1A 1, 2 NPM1 1 TP53 ?�1-8

EGFR

 ?�1-5 HRAS 2 NRAS ?�1-3 VHL ?�1-3

ERBB2

 ?�1-3 IDH1 1 PDGFRA ?�1-4 ?� ?�

ERBB4

 ?�1-8 IDH2 1 PIK3CA ?�1-11 ?� ?�

?�

?�

?�References:

1. Lander, E.S., et al., Initial sequencing and analysis of
the
human genome. Nature, 2001. 409(6822): p. 860-921.
2. Koboldt, D.C., et al., The next-generation sequencing
revolution
and its impact on genomics. Cell, 2013. 155(1): p. 27-38.
3. Shendure, J., et al., Next-generation DNA sequencing. Nat
Biotechnol, 2008. 26(10): p.
1135-45.
4. Hatem A1, Bozda? D, Toland AE, ??ataly?�rek ??V.
Benchmarking short sequence mapping tools. Bioinformatics. 2013
Jun
7;14:184. doi: 10.1186/1471-2105-14-184.
5. Tucker, T., et al., Massively parallel sequencing: the next
big
thing in genetic medicine. Am J Hum Genet, 2009. 85(2): p.
142-54.
6. Frampton, G.M., et al., Development and validation of a
clinical
cancer genomic profiling test based on massively parallel
DNA sequencing.
Nat Biotechnol, 2013.
31(11): p. 1023-31.
7. TruSeq Amplicon Cancer Panel Library Preparation Guide.
Illumina. April, 2012.
8. Green, R.C. et al. ACMG
Recommendations for Reporting of Incidental Findings in
Clinical
Exome and Genome Sequencing.Genet Med. 2013
Jul;15(7):565-74.?�

Fee Code

79800

Container/Tube

Slide

Specimen Minimum Volume

n/a

Day(s) Performed

Monday – Friday, 8:00am – 5:00pm

STAT DAY(S) AND TIME(S) PERFORMED

Not Available

CPT

81479

Method Name

This test is based on the Ion AmpliSeq Cancer Hotspot Panel
(IACHP) v2
(Life Technologies). The panel
covers “hotspots” in 50 oncogenes and tumor
suppressor
genes by using 206 primer pairs in a single tube multiplexed
PCR assay.
After DNA is
isolated and its quality and quantity
determined, a single multiplexed PCR is
performed using a single reaction containing the 207 Ion
AmpliSeq
Cancer Hotspot primer pairs. Then, it is cleaned up using Ampure
XP
beads and a library is constructed using KAPA HTP Library
Preparation Kit and Illumina compatible adapters. Through the
library construction, adapter oligonucleotides containing
unique
patient-specific “barcode” indexes and P5/P7
sequences
are ligated onto the amplicon PCR
products to make an Illumina compatible sequencing
library. All DNA samples for a given
run are processed in duplicate and in parallel, and then
following
a library quantitation, samples with different bar-code
sequences
are pooled and sequenced in a 2 × 152 bp MiSeq run.

Reference Values

An interpretive report will be provided.

Pediatric Volume

n/a

Clinical Indications

The OncoScreen ST2.0 assay is designed to sequence hot-spot
mutational regions of 50 clinically relevant genes that are
commonly mutated in cancer for the purpose of identifying
somatic
mutations (substitutions and
insertions/deletions).?�Mutations
in these 50 genes are linked to many types of cancers,
including
lung, colorectal, gastric, thyroid, ovarian cancer, melanoma
and
myeloid malignancies.Mutations with known clinical significance
and/or those deemed to be pathogenically related to the biology
of
each patient�??s tumor are reported, and this personalized
mutational profile may be useful fordiagnosis, prognosis,
therapy
selection, clinical trials options and for translational
research.

Transport Instructions

Formalin-fixed, paraffin embedded tissue:?�?�

  • Total tumor area on slides = 0.1 cm2 total
    (include
    top and bottom H&E guide slides).?�
  • Paraffin block acceptable.

Test Components

OncoScreen ST2.0 tests hot spot regions of 50 commonly
mutated
genes in cancer. The genes are:ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1,
CDKN2A,
CSF1R, CTNNB1, EGFR, ERB2, ERBB4, EZH2,
FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A,
HRAS, IDH1,
IDH2, JAK2, JAK3,
KDR,
KIT,
KRAS,
MET,
MLH1, MPL,
NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA,
PTEN, PTPN11,
RB1, RET,
SMAD4, SMARCB1, SMO,
SRC, STK11,
TP53, VHL.

Methodology

This test is based on the Ion AmpliSeq Cancer Hotspot Panel
(IACHP) v2
(Life Technologies). The panel
covers �hotspots�?� in 50 oncogenes and tumor
suppressor
genes by using 206 primer pairs in a single tube multiplexed
PCR assay.
After DNA is
isolated and its quality and quantity
determined, a single multiplexed PCR is
performed using a single reaction containing the 207 Ion
AmpliSeq
Cancer Hotspot primer pairs. Then, it is cleaned up using
Ampure
XP
beads and a library is constructed using KAPA HTP Library
Preparation Kit and Illumina compatible adapters. Through the
library construction, adapter oligonucleotides containing
unique
patient-specific �barcode�?� indexes and P5/P7
sequences
are ligated onto the amplicon PCR
products to make an Illumina compatible sequencing
library.?�All DNA samples for a
given
run are processed in duplicate and in parallel, and then
following
a library quantitation, samples with different bar-code
sequences
are pooled and sequenced in a 2 ?? 152 bp MiSeq run.