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Test Code EGFRFF (FFPE), EGFRCS (Cytology Smear) EGFR Mutation Assay

Specimen Type

FFPE or Cytology Smear

Container

Block or slides

Preferred Volume

n/a

Offsite Collection Instructions

Slides/blocks labeled with two patient identifiers and a surgical pathology ID.

UCMC Collection Instructions

Formalin fixed tissue (paraffin block, unstained slides).  Sections should be at least 1cm2, and contain at least 40% tumor cells.

Availability

Monday -Friday, 9AM – 5PM

Turnaround Time

8-10 business days

STAT Availability

Not Available

Test Usage

Testing for EGFR mutations can aid in treatment decisions for patients who are candidates for TKI therapies. EGFR mutations have also been described in malignant mesothelioma

Test Methodology

EGFR gene is part of the OncoScreen ST2.0 NGS panel. The OncoScreen procedure is performed and data for EGFR gene only is analyzed.
 

The OncoScreen test is based on the Ion AmpliSeq Cancer Hotspot Panel (IACHP) v2 (Life Technologies). 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. It is then 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

Reporting: Mutations with known or possible pathogenic or clinical significance are reported. Variants of unknown significance are reported as such.

CPT Code

81235

STAT Turnaround Time

n/a

Critical Results

None.

Test Limitations

  • This test will not detect mutations in areas 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, 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 allelic under-sampling or drop-out.

Reference Range

Interpretive report will be provided.

Test Includes

This is no longer a Molecular Diagnostics standalone test!
 

This is a next-generation sequencing assay for detection of somatic mutations located within mutational hotspot regions of the EGFR (Epidermal Growth Factor Receptor) gene, exons 3, 7, 15, 18, 19, 20, and 21.EGFR is a proto-oncogene located on chromosome 7p12. Mutations in the EGFR occur in 10-40% of non-small cell lung cancers (NSCLC).

Fee Code

79809

Synonyms

EGFR