• Test Code:
  • Department:
  • Test Synonyms:
    EGFR Gene Mutation (Exons 18, 19, 20 & 21)FISH for ALK and ROS1 Gene Rearrangements
  • CPT Code(s):
    8389088368 88369

Activating mutations in EGFR are present in approximately 10-12% of non-small cell carcinomas of the lung (primarily adenocarcinomas).  Based on a number of phase II and III trials, most EGFR mutations predict a good response to treatment with EGFR inhibitors such as gefitinib and erlotinib.1 The exceptions are insertion mutations in exon 20 and the T790M substitution, which correlate with resistance to these drugs.
Gene rearrangements involving the ALK gene are present in approximately 5% of non-small cell carcinomas of the lung (primarily adenocarcinomas).  The most common of these is the EML4-ALK fusion, although other partner genes have been identified.   Activation of ALK kinase through these gene fusions contributes to tumor cell growth and can be inhibited by ALK inhibitors such as crizotinib.2

Gene fusions involving ROS1 are present in 1-2% of non-small cell lung carcinomas, primarily adenocarcinomas. Several partner genes (FIG, SLC34A2, CD74) have been identified. Resulting activation of ROS1 kinase activity appears to be a principal growth driver in these tumors. This kinase is sensitive to crizotinib, and patients with ROS1-fusion positive tumors have shown responses to this inhibitor.


Methodology for EGFR Mutations:

  1. Microscopic examination of the specimen and macrodissection of tumor-rich areas.
  2. DNA extraction and purification.
  3. PCR amplification of EGFR coding exons 18, 19, 20 & 21.
  4. Screening for mutations by one of two methods.
    1. Pyrosequencing of each exon
    2. Real-time PCR with high resolution melting curve analysis (HRM), to screen for deletions in exon 19 and insertions in exon 20. DNA sequencing is used to confirm any potential mutations identified by this approach.
  5. Estimated sensitivity: 20% mutant allele.
  6. Estimated specificity: 98% of EGFR mutations reported in non-small cell lung carcinoma.
Methodology for screening for ALK and ROS1 gene fusions:
  1. Fluorescence in-situ hybridization (FISH) is performed using an FDA-approved break-apart probe set for the ALK gene. This testing can be performed on sections of formalin-fixed, paraffin-embedded tissue.
  2. Fluorescence in-situ hybridization (FISH) is performed using a break-apart probe set for the ROS1 gene. This testing can be performed on sections of formalin-fixed, paraffin-embedded tissue.

Specimen Requirements:

  • A paraffin block or
  • 15 unstained sections of tumor (4-5 micron sections on positively-charged slides)

Contact Client Services for shipping materials and procedures at (855)535-1522

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES.  Please include detailed clinical information.

Test Performed (Days):

Mon - Fri

Turn Around Time:

7-10 days

Shipment Sensitivity Requirements:

  • Keep specimen cool during transit. Do not ship on dry ice.
  • Please use the cold pack provided in the KDL shipping kit.
  • Ship the specimen overnight express, using the FedEx priority overnight label provided. 
  • Contact Client Services for shipping materials and procedures at (855) 535-1522.


  1. Linardou H, Dahabreh IJ, Bafaloukos D, Kosmidis P, Murray S. Somatic EGFR mutations and efficacy of tyrosine kinase inhibitors in NSCLC. Nat Rev Clin Oncol. 2009 Jun;6(6):352-66.
  2. Kwak EL, Bang YJ, Camidge DR, Shaw AT, Solomon B, Maki RG, Ou SH, Dezube BJ, Jänne PA, Costa DB, Varella-Garcia M, Kim WH, Lynch TJ, Fidias P, Stubbs H, Engelman JA, Sequist LV, Tan W, Gandhi L, Mino-Kenudson M, Wei GC, Shreeve SM, Ratain MJ, Settleman J, Christensen JG, Haber DA, Wilner K, Salgia R, Shapiro GI, Clark JW, Iafrate AJ. Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. N Engl J Med. 2010 Oct 28;363(18):1693-703.

Additional Info:

The Knight Cancer Institute at Oregon Health & Science University is a pioneer in the field of precision cancer medicine. The institute's director, Brian Druker, M.D., helped prove it was possible to shut down just the cells that enable cancer to grow. This breakthrough has made once-fatal forms of the disease manageable and transformed how cancer is treated. The OHSU Knight Cancer Institute is the only National Cancer Institute-designated Cancer Center between Sacramento and Seattle – an honor earned only by the nation's top cancer centers. It is headquarters for one of the National Cancer Institute's largest research collaboratives, SWOG, in addition to offering the latest treatments and technologies as well as hundreds of research studies and clinical trials.

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