Deeper understanding of the pathobiology of non-small cell lung cancer (NSCLC) has led to the development of small molecules that target genetic mutations known to play critical roles in the progression to metastatic disease. Mutations in epidermal growth factor receptor (EGFR), KRAS, and anaplastic lymphoma kinase (ALK) are mutually exclusive in patients with NSCLC, and the presence of one mutation in lieu of another can influence response to targeted therapy. Therefore, testing for these mutations and tailoring therapy accordingly is widely accepted as standard practice. [1, 2, 3]
EGFR is expressed on the cell surface of a substantial percentage of NSCLCs. Initial studies with the EGFR tyrosine kinase inhibitors (TKIs) gefitinib (Iressa) and erlotinib (Tarceva) demonstrated biologic and clinical activity in only a relatively limited subset of lung cancers.  Further investigation demonstrated that the highest response rates to these TKIs were seen in patients with somatic mutations within the EGFR-TK domain, particularly exon 19 deletion, exon 21 L858R, and exon 18 G719X.  By contrast, the exon 20 T790M mutation is associated with acquired resistance to TKI therapy. 
In general, activating EGFR mutations are more commonly observed in patients with adenocarcinomas and no prior history of smoking, as well as in females and those of Asian descent. Based on the new adenocarcinoma classification proposed by the International Association for the Study of Lung Cancer, American Thoracic Society, and European Respiratory Society,  Korean researchers identified EGFR mutations in 50.5% of surgically resected lung adenocarcinomas in their center. Mutations were associated with the micropapillary predominant subtype and the presence of the lepidic pattern (formerly known as bronchioloalveolar carcinoma).  These data support estimates from clinical trial evidence that activating EGFR mutations are seen in approximately 50% of Asians and 10% of non-Asians.
Use of the EGFR-TKIs gefitinib, erlotinib, and afatinib is limited to patients with adenocarcinomas who have known activating EGFR mutations. As discussed below, activity of the EGFR monoclonal antibody cetuximab seems to be independent of EGFR mutation status. It is unclear how the presence of an acquired EGFR mutation such as T790M should influence therapeutic decisions. 
KRAS mutations are also predominately found in adenocarcinomas, and are seen in approximately 25% of cases. However, they are less common among those of Asian descent and are more common in smokers.  Most important, patients with KRAS mutations seem to have a poorer prognosis and seem to be resistant to EGFR-TKIs, although the extent to which this might influence treatment selection remains somewhat unclear. [9, 10]
Finally, fusion between echinoderm microtubule-associated proteinlike 4 (EML4) and ALK is seen in approximately in 2-7% of patients with NSCLC adenocarcinomas. This and other ALK rearrangements are more common in nonsmokers or light smokers and in those with adenocarcinomas. Because EGFR and ALK mutations are mutually exclusive, patients with ALK rearrangements are not thought to benefit from EGFR-targeting TKIs. Instead, treatment with an ALK inhibitor (crizotinib [Xalkori], ceritinib [Zykadia]) is indicated. [11, 12, 13]
ROS-1 gene alterations, thought to lead to abnormal cells, have been identified in various cancers, including NSCLC. ROS-1 gene alterations are present in approximately 1% of patients with NSCLC. 
To see complete information, please see the Medscape Reference article Non-Small Cell Lung Cancer.
Targeting the Genetic Mutations
Gefitinib was the first EGFR-TKI evaluated in a phase III trial. Initially, results demonstrated that only approximately 10% of patients responded well to the therapy, and no survival benefit was conferred.  However, patients were not prospectively stratified according to mutation status. Follow-up analysis of tissue samples identified activating EGFR mutations in 8 of 9 responders, whereas no mutations were seen in 7 patients who did not respond to gefitinib therapy,  suggesting that the drug could provide a benefit in appropriately selected patients. Nevertheless, the lack of a significant clinical benefit in the trial overall led to withdrawal of gefitinib from the market in the United States.
In July 2015, gefitinib returned to the United States market following restricted availability. It was approved by the FDA as first-line treatment of patients with metastatic NSCLC whose tumors have EGFR exon 19 deletions or exon 21 (L858R) substitution mutations ,as detected by an FDA-approved test. Approval as first-line treatment for metastatic NSCLC is based on data from the IFUM (IRESSA Follow-Up Measure) clinical trial, which showed an overall response rate (ORR) of about 50%, with a median duration of response of 6 months. 
The IFUM results were supported by the most recent analysis of the IPASS (IRESSA Pan-ASia Study) study, which assessed gefitinib versus carboplatin/paclitaxel as a first-line treatment in these patients. The subset population consisted of 186 of 1217 patients (15%) determined to be EGFR positive by the same clinical trial assay used in IFUM, and they had radiographic scans available for a retrospective assessment. IPASS showed an ORR of 67% and a median duration of response of 9.6 months in gefitinib-treated patients, versus a 41% ORR with a median duration of response of 5.5 months for the carboplatin/paclitaxel group. Mean progression-free survival (PFS) was 10.8 months in the gefitinib group versus 5.4 months for the carboplatin/paclitaxel patients. 
Data from a phase III study of gefitinib conducted in Asia more clearly indicated that EGFR mutation status could influence the choice of first-line treatment options. [18, 19] In this study, known as the Iressa Pan-Asia Study, or IPASS, previously untreated never-smokers and light ex-smokers with advanced NSCLC adenocarcinomas were randomized to gefitinib vs carboplatin/paclitaxel. Patients who were positive for an activating EGFR mutation demonstrated significantly longer progression-free survival when treated with gefitinib than with carboplatin-paclitaxel, whereas patients who were negative for the mutation had significantly longer progression-free survival with carboplatin-paclitaxel; overall survival rates did not differ between the groups.
Based on these data as well as on other clinical trial data showing improved progression-free-survival with erlotinib in patients with EGFR mutations, [20, 21] current guidelines recommend testing all patients with metastatic NSCLC adenocarcinomas for the presence of activating EGFR mutations, and to use an EGFR-TKI as first-line therapy in patients with adenocarcinoma and a known EGFR mutation. [1, 2]
In May 2013, erlotinib was approved for first-line treatment of NSCLC whose tumors have EGFR exon 19 deletions or exon 21 (L858R) substitution mutations. Until that time, the official indication was second- or third-line use in advanced NSCLC. First-line use includes the use of the cobas EGFR Mutation Test, a companion diagnostic for erlotinib.
Afatinib (Gilotrif) is a tyrosine kinase inhibitor that was approved in the United States in July 2013 for first-line treatment of patients with metastatic NSCLC whose tumors have EGFR exon 19 deletions or exon 21 (L858R) substitution mutations as detected by the diagnostic companion test, therascreen EGFR RGQ PCR Kit. Approval was based on data from the LUX-Lung 3 trial, comparing afatinib to chemotherapy with pemetrexed/cisplatin. Results showed the afatinib group’s progression-free survival (PFS) was 11.1 months compared with 6.9 months for those treated with pemetrexed/cisplatin. Additionally, patients with tumors expressing the 2 most common EGFR mutations (Del19 or L858R) taking afatinib lived over a year without tumor progression (PFS of 13.6 mo) compared with 6.9 months for those in the comparator arm. 
In contrast to the clear link between EGFR mutation status and EGFR-TKI response, the presence of EGFR mutations does not appear to predict response to treatment with the EGFR monoclonal antibody cetuximab. Data from the phase III First-Line Erbitux in Lung Cancer (FLEX) trial, which randomized patients to cisplatin/vinorelbine with or without cetuximab, showed that the presence of a mutation was not predictive of response to treatment. However, post hoc analysis showed that high expression of EGFR proteins on immunohistochemistry (IHC) was predictive of response to cetuximab plus chemotherapy vs chemotherapy alone. [23, 24]
An ongoing study evaluating the use of carboplatin and paclitaxel with or without bevacizumab and/or cetuximab in patients with metastatic or recurrent NSCLC will examine prospectively whether high EGFR protein expression can be used as a predictor of treatment response to cetuximab. Until then, the potential benefit of EGFR protein expression by IHC or EGFR gene amplification by fluorescence in situ hybridization (FISH) remains unclear. Cetuximab is FDA-approved for colorectal cancer and for head and neck cancer. It is not yet approved by the FDA for NSCLC.
Necitumumab (Portrazza) is a monoclonal antibody that targets EGFR. It was approved in the United States in November 2015 for first-line treatment of metastatic squamous NSCLC in combination with gemcitabine and cisplatin. 
Finally, the EGFR mutation T790M is found in approximately half of patients with acquired resistance EGFR-TKIs.  However, discontinuation of treatment can lead to a more rapid progression of disease regardless of T790M mutation status.  Because the presence of this mutation should not necessarily preclude continued use of EGFR-TKIs, the clinical relevance of routine testing in patients demonstrating treatment resistance is unknown. The first EGFR inhibitor that targets T790M, osimertinib (Tagrisso), was approved in the United States in November 2015. It is indicated for metastatic epidermal growth factor receptor (EGFR) T790M mutation–positive non-small cell lung cancer (NSCLC), as detected by an FDA approved test, in patients who have progressed during or after EGFR TKI therapy. 
No prospective trials have been conducted to demonstrate the potential value of testing for KRAS mutations and to tailor therapy accordingly.
Although meta-analyses indicate that patients with KRAS mutations have a lowered response to EGFR-TKIs, most of the trials evaluated were small and it is unclear whether mutation status predicts reduced progression-free or overall survival.  Subgroup analysis of data from clinical trials evaluating EGFR-TKIs and cetuximab also showed no independent association between KRAS mutation status and survival. [30, 31]
Nevertheless, despite the lack of definitive data demonstrating the benefit of KRAS mutation testing, the presence of mutations does seem to be associated with primary resistance to EGFR-TKI therapy. Testing can be considered to help in determining whether a patient might be a candidate for a TKI. 
The benefit of testing for ALK rearrangements was demonstrated in phase I and phase II trials of the ALK inhibitor crizotinib. [11, 12] Results from these trials formed the basis of crizotinib’s accelerated approval in the United States along with a companion diagnostic to evaluate ALK rearrangements on FISH.
In these trials, patients with the EML4-ALK fusion, nearly all of whom had progressed despite at least 1 prior line of therapy, showed response rates of approximately 50% to 60% crizotinib. Response duration was 42-48 weeks. [11, 12]
Because phase III trials are still underway and survival data are not yet available, researchers conducted a retrospective, nonrandomized analysis comparing patients enrolled in the 2 trials with historical controls to estimate the clinical benefit of crizotinib therapy.  In patients who received crizotinib as second-line therapy, the 1-year overall survival rate was 70% and the 2-year overall survival rate was 55%. By contrast, ALK -positive matched controls had a 1-year survival of 44% and a 2-year survival of 12%, whereas ALK -negative controls had a 1-year survival of 47% and a 2-year survival of 32%. These data suggest that the presence of the ALK gene fusion itself does not confer a poorer outcome but that the use of crizotinib in ALK -positive patients can improve outcomes.
Based on these data, testing for ALK rearrangement is recommended in patients with metastatic NSCLC adenocarcinoma and the ALK inhibitor crizotinib is recommended for ALK-positive patients.
In April 2014, the FDA approved a second ALK tyrosine kinase inhibitor, ceritinib (Zykadia). It is indicated for ALK-positive, metastatic NSCLC in patients who have progressed on or are intolerant to crizotinib. The FDA granted ceritinib breakthrough-therapy designation, priority review, and orphan product designation because of preliminary clinical evidence that the drug may offer a substantial improvement over available therapies. Early-stage results showed that ceritinib was highly active in patients with advanced, ALK-rearranged NSCLC, including those who experienced disease progression during crizotinib treatment, regardless of the presence of resistance mutations in ALK. 
Ceritinib was shown to overcome crizotinib resistance mutations in a preclinical trial. In vitro and in vivo models of acquired resistance to crizotinib were evaluated, including cell lines established from biopsies of crizotinib-resistant NSCLC patients. Results revealed that ceritinib overcame crizotinib resistance mutations, in particular, ALK-harboring L1196M, G1269A, I1171T, and S1206Y mutations. 
The FDA granted accelerated approval of alectinib, a TKI that targets ALK and RET, in December 2015. It is indicated for anaplastic lymphoma kinase (ALK)–positive, metastatic non-small cell lung cancer (NSCLC) in patients who have progressed on, or are intolerant to, crizotinib. 
In March 2016, the FDA expanded use of crizotinib to include patients with metastatic NSCLC whose tumors harbor a ROS-1 gene mutation. Study results showed crizotinib exhibited marked antitumor activity in this population, with an objective response rate of 66% by an independent radiology review. There was 1 complete response and 32 partial responses. The median duration of response was 18.3 months. 
Testing for activating EGFR mutations in exons 18 through 21 is recommended in all patients with advanced NSCLC adenocarcinoma to help determine whether an EGFR-TKI should be considered. Routine testing for KRAS mutations is not recommended, but can be considered as a way to help determine whether a patient might be resistant to treatment with an EGFR-TKI. No clear guidelines suggest whether to test for EGFR T790M mutations in patients with acquired resistance to EGFR-TKIs because the clinical significance of mutation status relative to treatment continuation remains unknown.
The current standard for EGFR and KRAS mutation testing is polymerase chain reaction (PCR) analysis of formalin-fixed paraffin-embedded specimens or fresh-frozen biopsy. The clinical relevance of FISH or IHC testing for EGFR amplification is unknown.
In May 2013, erlotinib was approved for first-line treatment of NSCLC tumors that have EGFR exon 19 deletions or exon 21 (L858R) substitution mutations. Until that time, the official indication was second- or third-line use in advanced NSCLC. First-line use includes the use of the cobas EGFR Mutation Test, a companion diagnostic for erlotinib.
The safety and effectiveness of the cobas EGFR Mutation Test was established with clinical data from the EURTAC study and showed progression-free survival in patients with NSCLC who had specific types of EGFR mutations (exon 19 deletions or exon 21 [L858R] substitution mutations) for 10.4 months when they received erlotinib treatment, compared with 5.4 months for those who received standard therapy. 
The cobas EGFR Mutation Test v2 is available for the detection of EGFR T790M mutations to determine if osimertinib should be considered for treatment. 
In July 2013, afatinib was approved for first-line treatment of NSCLC in patients with metastatic NSCLC with tumors that have EGFR exon 19 deletions or exon 21 (L858R) substitution mutations as detected by the diagnostic test, therascreen EGFR RGQ PCR Kit.
Testing for ALK rearrangements to determine potential benefit from crizotinib is recommended in all patients with advanced NSCLC adenocarcinoma using the Vysis ALK Break Apart FISH Probe Kit on formalin-fixed paraffin-embedded tissue specimens.
As of March 2016, there are no FDA-approved tests for detecting ROS-1 mutation. In clinical trials, the ROS-1 status of NSCLC tissue samples was determined by laboratory-developed break-apart FISH (96%) or RT-PCR (4%) clinical trial assays. For assessment by FISH, ROS-1 positivity required that ≥15% of a minimum of 50 evaluated nuclei contained a ROS-1 gene rearrangement. 
Regardless of current recommendations, any decision to test for genetic mutations should be individualized for each patient and should take into account considerations such as: (a) the time available before the management decision must be made and the potential delay in obtaining genetic test results; (b) third-party payment for the test; (c) the relative toxicities of alternative therapeutic options in this specific patient; and (d) the availability and quality of the clinical laboratory that will be performing the test.