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

Specimen Type

FFPE or Cytology Smear

Container

Slide

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.

Availability

Monday – Friday, 8:00am – 5:00pm

Turnaround Time

10-15 business days

STAT Availability

Not Available

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.

Test 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.

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, Çatalyürek ÜV. 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. 

CPT Code

81479

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.

Reference Range

An interpretive report will be provided.

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.

STAT Turnaround Time

n/a

Minimum Volume

n/a

Fee Code

79800