Advanced Lab Testing in Lung Cancer

April 15, 2016

The most important marker to test is epidermal growth factor receptor (EGFR). EGFR is the second most common oncogenic driver in lung cancer, present in 15% of adenocarcinoma cases, but the most common mutation to be actionable with an approved drug.

In the Clinic


When I meet a new patient, I begin my counseling by describing the nature of cancer. When discussing advanced laboratory testing it is easy to lose sight of the fact that the mutations we discuss are not simply laboratory markers, but rather the very reason that once healthy normal body cells convert into cancer cells. In lung cancer, the ability to evaluate driver mutations has greatly advanced practice. The Lung Cancer Mutation Consortium looked at data from almost 1,000 patients who underwent molecular testing. Survival was superior for those who had an oncogenic driver mutation and received targeted therapy compared with those who had no oncogenic driver, or who did not receive targeted therapy directed at the driving mutation.[1]

In my practice, the most important marker to test is epidermal growth factor receptor (EGFR). EGFR is the second most common oncogenic driver in lung cancer, present in 15% of adenocarcinoma cases, but the most common mutation to be actionable with an approved drug. More than a dozen studies have shown that progression-free survival (PFS) is superior with EGFR tyrosine kinase inhibitors (TKIs) as first-line therapy for stage IV disease compared with chemotherapy.[2] Although these agents are not free from toxicity, they tend to be more tolerable than cytotoxic chemotherapy for many patients. Even more important for some patients is having the option to take a pill rather than visiting the infusion room every 3 weeks; they can spend more time on the things that matter to them. The median duration of disease control with the three agents that are approved for first-line use (erlotinib, gefitinib, and afatinib) is about 10 months. At the time of acquired resistance, 50% to 60% of cases are caused by the T790M mutation, which is actionable with the US Food and Drug Administration (FDA)–approved third-generation EGFR TKI osimertinib,[3] offering a median PFS of an additional 10 months.

EML4/ALK and ROS1 are gene rearrangements. EML4/ALK is present in 4% of adenocarcinomas, and ROS1 is present in 2%. Both are treatable with the drug crizotinib (EML4/ALK has FDA approval; ROS1 has compendia listing). In the case of EML4/ALK, randomized data show a superior PFS of approximately 11 months in both first- and second-line settings compared with chemotherapy.[4,5] In addition, ceritinib and alectinib, two second-line ALK inhibitors, have FDA approval.[6,7]

Programmed death ligand 1 (PD-L1) is not a mutation, but rather an immuno-oncologic target. Randomized studies showed superior survival and a favorable toxicity profile for nivolumab, a programmed death 1 (PD-1) inhibitor, compared with docetaxel for the second-line treatment of both squamous and nonsquamous cell lung cancer.[8,9] Nivolumab is administered every 2 weeks and PD-L1 testing is not required. Pembrolizumab is also a PD-1 inhibitor and is given every 3 weeks; positive testing via immunohistochemistry is required. PD-L1 testing is controversial and the negative predictive value of testing may be too poor to make the marker clinically useful other than to meet the requirements for pembrolizumab use when every-3-week dosing is preferred.

Other molecular markers are useful for clinical trial selection. There are many active clinical investigations that hold promise for many targets such as BRAF, HER2, MET, RET, and NTRK; even KRAS may one day be actionable.[10]

In the Clinic


Multiple factors can affect the ability to characterize a patient’s tumor for the purpose of supporting targeted therapy decisions. There are a variety of lab tests that can determine whether tumors have gene alterations that are targets for therapy. EGFR mutations span 4 exons of the gene and are often classified using Sanger sequencing and/or real-time polymerase chain reaction (PCR)-based assays. Although Sanger sequencing detects all changes within this region, it has a lower limit of detection of approximately 20% mutant allele fraction (40% malignant nuclei within the sample) that requires a relatively pure tumor sample. Real-time PCR allows for more sensitive detection of mutations, but is restricted to a selected set of alterations.[11] Detection of EML4/ALK and ROS1 gene rearrangements involving large segments of chromosomes are most commonly evaluated with the use of fluorescence in situ hybridization (FISH), which necessitates a set of slides separate from those used for DNA extraction. Next-generation sequencing (NGS) assays can simultaneously characterize multiple gene targets. Because of the customizability of NGS assays, they are offered at hospitals, academic medical centers, and commercial laboratories. All of these assays are able to detect single nucleotide change mutations (eg, EGFR L858R) and short insertions and deletions (eg, EGFR exon 19 deletions). A subset of clinically offered tests is able to detect gene rearrangements.[12]

Although it is appealing to obtain a comprehensive genomic profile for all patients, resource availability should be a significant consideration. Insurance coverage for tumor profiling is highly variable among providers. When coverage does exist, it is often limited to individual gene testing. For this reason, our institution offers a lower-cost limited NGS panel for EGFR mutation characterization, paired with FISH analysis for EML4/ALK and ROS1. This allows us to capture the majority of actionable alterations while reducing the potential financial burden on patients.

The amount of tissue available for testing can also affect decision making. Diagnostic specimens are often obtained through small biopsies and/or needle aspirates. Because tissues must go through multiple processing steps, each of which contributes to loss of some specimen, it is important to collaborate with pathologists. We have a standing protocol where all biopsies for suspected lung cancer are processed as though they will require molecular testing to conserve tissue. For needle aspirate procedures, we have validated the slides used for on-site adequacy evaluation for DNA extraction. This helps overcome the paucity of disease that may be found on subsequent aspirate passes due to factors such as hemodilution. Finally, molecular laboratories may have stored residual DNA from prior testing (many as paraffin blocks retained in the surgical pathology department) that can be used for further testing. Such solutions can only be implemented with appropriate collaboration and consultation across departments.

Future directions of genomic profiling include the use of circulating cell-free DNA (cfDNA). Widespread cfDNA testing already exists in the prenatal arena, where it has been used to screen for fetal genetic abnormalities in a noninvasive, highly reproducible manner.[13] Studies have shown that cfDNA may serve as a useful biomarker to monitor disease,[14] and additional work is underway to determine whether results can be used to guide therapy in a more generalized manner.

Financial Disclosure:The authors have no significant financial interest or other relationship with the manufacturers of any products or providers of any service mentioned in this article.


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