Lung cancer is the leading cause of cancer-related mortality in the United States. Diagnosis typically involves a combination of imaging studies, cytologic or histopathologic specimen evaluation, and subsequent immunohistochemistry (IHC) and genetic analysis. More than 80% of lung cancer cases are classified as non-small cell lung cancers (NSCLCs), and adenocarcinoma is the most common NSCLC subtype in nonsmokers. Adenocarcinoma is characterized by a prevalence of oncogenic driver (EGFR, ALK, ROS1, and BRAF) genetic alterations, which if present may influence prognosis and predict response to targeted therapies. Guidelines recommend IHC and/or molecular analysis to identify actionable targets and guide subsequent therapy selection.
Quick Answers for Clinicians
Although cell-free/circulating tumor DNA testing has generally high specificity, it has low sensitivity (with a false-negative rate of up to 30%) and should not be used in place of tissue-based testing, if tissue is available. Cell-free/circulating tumor DNA testing is appropriate when invasive tissue sampling is not an option for a given patient or when the tissue sample is insufficient for molecular analysis. Negative cell-free/circulating tumor DNA testing results should be confirmed by tissue-based analysis whenever possible.
RET gene rearrangements, ERBB2 mutations, high-level MET amplifications or MET exon 14 skipping mutations, and tumor mutational burden (TMB) are emerging predictive biomarkers. Currently, evaluating these biomarkers is not considered part of routine care. However, broad molecular profiling to identify rare targets (such as these) for which effective drugs may be available is strongly advised, and in that context, including these biomarkers is appropriate and encouraged.
Testing for NTRK gene fusions can be considered to detect rare driver alterations to determine the potential for effective therapy; NTRK gene fusions can be detected by fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), next generation sequencing (NGS), and polymerase chain reaction (PCR) assays.
Indications for Testing
Individuals with advanced or metastatic disease should undergo:
- Biomarker testing to identify oncogenic driver mutations for which effective drugs may be available
- PD-L1 IHC testing to assess whether PD-L1 inhibitor therapy is an option
Predictive and Prognostic Biomarker Testing
Several oncogenic driver alterations, including EGFR, ALK, ROS1, and BRAF, may inform treatment selection in lung cancer and are considered predictive biomarkers. KRAS oncogenetic mutations are prognostic biomarkers and confer a poor prognosis and predict lack of benefit from EGFR tyrosine kinase inhibitor (TKI) therapy.
Testing for the presence of genetic mutations or alterations is recommended for the following NSCLCs: adenocarcinoma, large cell, and NSCLC not otherwise specified (NOS); such testing should also be considered for squamous cell carcinoma. At a minimum, the National Comprehensive Cancer Network (NCCN) recommends that EGFR, BRAF, ALK, and ROS1 testing be performed, but also encourages the use of broad molecular profiling when available. This method of testing may identify rare driver mutations, such as NTRK gene fusions and RET rearrangements, for which effective therapy might be available. PD-L1 testing should also be performed to guide immunotherapy selection.
Large Cell Lung Cancer
|Squamous Cell Carcinoma|
PD‑L1 expression by IHC
|Consider EGFR and ALK testing in individuals who have never smoked, in small biopsy specimens, or in cases of mixed histology
Consider ROS1 and BRAF testing in small biopsy specimens or in cases of mixed histology
PD-L1 expression by IHC
|aBroad molecular profiling is strongly encouraged to identify other driver mutations for which effective therapy might be available.|
Epidermal growth factor receptor (EGFR) mutations occur in approximately 10% of NSCLC adenocarcinomas in the U.S. and are observed more frequently in nonsmokers. The two most common EGFR mutations, exon 19 deletions and exon 21 point mutations (L858R), account for approximately 90% of EGFR-mutated NSCLC cases and are associated with responsiveness to EGFR TKI therapy. However, there are many other less common EGFR mutations that are also sensitizing, and patients should be tested for these, as well. DNA mutational analysis is the preferred method for determining EGFR status; IHC is not recommended.
ALK Gene Rearrangements
Anaplastic lymphoma kinase (ALK) gene rearrangements are present in roughly 5% of patients with NSCLC. The presence of an ALK gene rearrangement correlates with responsiveness to ALK TKIs. The U.S. Food and Drug Administration (FDA)-approved IHC assay (D5F3 clone) is an adequate standalone test to detect ALK alterations, although secondary confirmation is encouraged. Fluorescence in situ hybridization (FISH) is also widely used for ALK gene rearrangement detection. Next generation sequencing (NGS) methodologies may detect ALK rearrangements, if appropriately designed.
ROS1 Gene Rearrangements
ROS proto-oncogene 1 (ROS1) gene rearrangements are more common in patients who are negative for EGFR mutations, KRAS mutations, and ALK rearrangements. The presence of a ROS1 gene rearrangement correlates with responsiveness to ROS1 TKIs. FISH is often used to detect ROS1 rearrangements, but may not detect the FIG-ROS1 variant. IHC testing is also available, but has lower specificity than other methodologies. Therefore, positive IHC results should be confirmed molecularly or cytogenetically. NGS methodologies may detect ROS1 rearrangements, if appropriately designed.
BRAF mutations at amino acid position 600 (BRAF V600E) have been associated with responsiveness to combined therapy with oral inhibitors of BRAF and MEK. The American Society of Clinical Oncology (ASCO) and NCCN recommend BRAF testing in all patients with advanced lung adenocarcinoma, irrespective of clinical characteristics. Testing methodologies include polymerase chain reaction (PCR), NGS, and Sanger sequencing. IHC, although available, is not a preferred approach.
The presence of a KRAS mutation, considered a prognostic biomarker, suggests poor survival for patients with NSCLC and is associated with reduced responsiveness to EGFR TKI therapy. EGFR, KRAS, ROS1, and ALK genetic alterations do not usually overlap. Therefore, the presence of a KRAS mutation suggests that patients may not benefit from further testing. Targeted therapy is not currently available for patients with KRAS mutations, though immune checkpoint inhibitors appear to be effective.
PD-L1 Expression Testing
Testing for PD-L1 expression levels by IHC is recommended before first-line treatment in patients with metastatic NSCLC to assess whether PD-1 or PD-L1 inhibitors are a treatment option. Refer to the PD-L1 Testing topic for the most up-to-date testing recommendations.
Therapy Resistance Testing
Patients can develop resistance to therapy. For example, the EGFR T790M mutation is associated with acquired resistance to EGFR TKI therapy. Therefore, patients with an underlying EGFR sensitizing mutation who have been treated with an EGFR TKI should undergo high-sensitivity testing for EGFR T790M. The presence of a T790M mutation suggests that a patient may benefit from third-generation EGFR TKI therapy. If there is no evidence of a T790M mutation, testing for alternate mechanisms of resistance, such as MET or ERBB2 amplification, may be considered to direct patients to alternative therapies. There is currently insufficient evidence to support routine secondary ALK mutation testing in patients who have relapsed after initial response to ALK inhibitor therapy.
ARUP Laboratory Tests
Polymerase Chain Reaction/Pyrosequencing
Immunohistochemistry/Fluorescence in situ Hybridization
Polymerase Chain Reaction
Polymerase Chain Reaction
Test Fact Sheet(s)
NCCN Clinical Practice Guidelines in Oncology: non-small cell lung cancer, version 3.2019. National Comprehensive Cancer Network. [Accessed: Jul 2019]Online
Kalemkerian GP, Narula N, Kennedy EB, et al. Molecular Testing Guideline for the Selection of Patients With Lung Cancer for Treatment With Targeted Tyrosine Kinase Inhibitors: American Society of Clinical Oncology Endorsement of the College of American Pathologists/International Association for the Study of Lung Cancer/Association for Molecular Pathology Clinical Practice Guideline Update. J Clin Oncol. 2018; 36 (9): 911-919.PubMed
Biswas A, Leon ME, Drew P, et al. Clinical performance of endobronchial ultrasound-guided transbronchial needle aspiration for assessing programmed death ligand-1 expression in nonsmall cell lung cancer. Diagn Cytopathol. 2018;46(5):378-383.
Mollaoglu G, Jones A, Wait SJ, et al. The Lineage-Defining Transcription Factors SOX2 and NKX2-1 Determine Lung Cancer Cell Fate and Shape the Tumor Immune Microenvironment. Immunity. 2018;49(4):764-779.e9.
Vaughn CP, Costa JL, Feilotter HE, et al. Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach: a multi-institutional research study. BMC Cancer. 2018;18(1):828.