Genetics of Non-Small Cell Lung Cancer

Updated: Aug 22, 2022
Author: Maurie Markman, MD, MS; Chief Editor: Keith K Vaux, MD 

Practice Essentials

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 are widely accepted as standard practice.[1, 2, 3]  However, new tyrosine kinase inhibitors (TKIs) (ie, amivantamab, mobocertinib) that target the exon 20 mutation gained accelerated approval from the FDA in 2021. 

The role of human EGFR2 (HER2), a member of the ERBB family of tyrosine kinase receptors, has been studied for NSCLC. The first HER2-directed therapy (ie, trastuzumab deruxtecan) received accelerated approval from the FDA for NSCLC in August 2022. 

EGFR is expressed on the cell surface of a substantial percentage of NSCLCs. Initial studies with the EGFR tyrosine kinase inhibitors (TKIs) gefitnib (Iressa) and erlotinib (Tarceva) demonstrated biologic and clinical activity in only a relatively limited subset of lung cancers.[4] 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.[5] By contrast, the exon 20 T790M mutation is associated with acquired resistance to TKI therapy.[6]  

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,[7] researchers identified EGFR mutations in 50.5% of surgically resected lung adenocarcinomas. Mutations were associated with the micropapillary predominant subtype and the presence of the lepidic pattern (formerly known as bronchioloalveolar carcinoma).[8] 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.[1]

KRAS mutations are also predominantly 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.[9] Most importantly, 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]  KRAS G12C accounts for approximately 50% of KRAS mutations in NSCLC, and approximately 14% of patients with NSCLC have a KRAS G12C mutation.[11]  

Fusion between echinoderm microtubule-associated proteinlike 4 (EML4) and ALK is seen in approximately 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], brigatinib [Alunbrig]) is indicated.[12, 13, 14]

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.[15]

Rearranged during transfection (RET), kinase alterations, which include fusions and activating point mutation, lead to overactive RET signaling and uncontrolled cell growth. Selpercatinib is a kinase inhibitor for wild-type and mutated RET isoforms.[16]

To see complete information, please see the Medscape Reference article Non-Small Cell Lung Cancer.


Targeting the Genetic Mutations

Targeting EGFR

Gefitinib was the first EGFR-TKI evaluated in a phase III trial. In July 2015, gefitinib 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.[17]

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.[18]

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.[19, 20] 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 versus 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 and other clinical trial data showing improved progression-free-survival with erlotinib in patients with EGFR mutations,[21, 22] 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. In 2018, the indication for first-line use in metastatic NSCLC was expanded to include 3 additional nonresistant EGFR mutations (ie, L861Q, G719X, S768I).[23] 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, as compared to 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), as compared to 6.9 months for those in the comparator arm.[24]

The frontline indication for afatinib was expanded to include the treatment of patients with metastatic non–small cell lung cancer (NSCLC) whose tumors harbor uncommon EGFR alterations in L861Q, G719X, and/or S768I.

Approval is based on a pooled analysis of 3 studies from the LUX-Lung clinical trial program (phase II LUX-Lung 2 study and phase III studies LUX-Lung 3 and LUX-Lung 6) that examined afatinib in NSCLC patients whose tumors have EGFR mutations, including L861Q, G719X, or S768I. This analysis showed that afatinib was active in these EGFR mutations based on objective response rate, duration of response, disease control, progression-free survival, and overall survival.[25]

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.[26, 27]

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.[28]

Finally, the EGFR mutation T790M is found in approximately half of patients with acquired resistance EGFR-TKIs.[29] However, discontinuation of treatment can lead to a more rapid progression of disease regardless of T790M mutation status.[30] 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.[31]  

Amivantamab and mobocertinib are kinase inhibitors indicated for the treatment of adults with locally advanced or metastatic non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) exon 20 insertion mutations whose disease has progressed on or after platinum-based chemotherapy. Each gained accelerated FDA approval in 2021. Amivantamab is administered as an IV infusion, whereas mobocertinib is administered orally. 

Mobocertinib’s approval was based on results from the phase I/II EXCLAIM open-label trial of 114 patients treated with mobocertinib 160 mg once daily. Investigator-assessed overall response rate was 35% (95% CI: 26, 45), with a median duration of response (DOR) of 11.2 months, of which 63% of these patients had observed responses lasting longer than 6 months.[32]

Targeting KRAS

KRAS G12C accounts for approximately 50% of KRAS mutations in NSCLC, and approximately 14% of patients with NSCLC have a KRAS G12C mutation.[11]    

In May 2021, the FDA approved sotorasib (Lumakras), the first KRAS G12C inhibitor. It is indicated for KRAS G12C-mutated locally advanced or metastatic NSCLC in adults who have received 1 or more prior systemic therapies. Sotorasib forms an irreversible, covalent bond with the unique cysteine of KRAS G12C, locking the protein in an inactive state that prevents downstream signaling without affecting wild-type KRAS. 

Accelerated approval was supported by the CodeBreak 100 phase 2 trial, with 124 patients who had measurable disease at baseline being evaluated. An objective response was observed in 46 patients (37.1%), including 4 who had a complete response and 42 who had a partial response. Disease control occurred in 100 patients (80.6%), and median overall survival was 12.5%.[33]   

Adagrasib also gained accelerated approval from the FDA in December 2022 that is contingent on results from a phase 3 confirmatory trial. Accelerated approval was supported by evidence from the KRYSTAL-1 phase 2 trial. Among 112 patients with measurable disease at baseline, 48 (42.9%) had a confirmed objective response. The median duration of response was 8.5 months and the median progression-free survival was 6.5 months. As of January 15, 2022 (median follow-up, 15.6 months), the median overall survival was 12.6 months. Additionally, 33 patients with previously treated, stable CNS metastases, the intracranial confirmed ORR was 33.3%. 

Although meta-analyses indicate that patients with KRAS mutations have a lowered response rate to EGFR-TKIs, most of the trials evaluated were small, and it is unclear whether mutation status predicts reduced progression-free or overall survival.[34] Subgroup analysis of data from clinical trials evaluating EGFR-TKIs and cetuximab also showed no independent association between KRAS mutation status and survival.[35, 36]

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.[1]

Targeting ALK

The benefit of testing for ALK rearrangements was demonstrated in phase I and phase II trials of the ALK inhibitor crizotinib (Xalkori).[12, 13] 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.[12, 13]

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.[37] 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.

A second ALK tyrosine kinase inhibitor, ceritinib (Zykadia), gained accelerated approval from the FDA in 2014 for patients with ALK-positive metastatic NSCLC whose disease had progressed or who were intolerant to crizotinib, which was based on a blinded independent review committee (BIRC)–assessed ORR of 44% of 163 patients in a single-arm trial. 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.[14]

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.[38]

In May 2017, ceritinib was granted approval for patients with metastatic NSCLC whose tumors are anaplastic lymphoma kinase (ALK)–positive as detected by an FDA-approved test. This approval also included use as first-line treatment. Approval was based on data from ASCEND-4, a randomized, multicenter, open-label, active-controlled trial conducted in patients with untreated ALK-positive NSCLC. All patients were required to have evidence of ALK-rearrangement identified by the VENTANA ALK (D5F3) test performed through central laboratory testing.

ASCEND-4 randomized 376 patients (1:1) to receive either ceritinib (N=189) 750 mg orally once daily until disease progression or platinum-pemetrexed doublet chemotherapy (N=187). Patients in the chemotherapy arm received pemetrexed (500 mg/m2) with either cisplatin (75 mg/m2) or carboplatin (AUC 5-6) on day 1 of every 21-day cycle for up to 4 cycles, followed by pemetrexed maintenance therapy. Results demonstrated improved PFS as assessed by BIRC, with a hazard ratio (HR) of 0.55 (P< 0.0001). The estimated median PFS was 16.6 months in the ceritinib arm and 8.1 months in the chemotherapy arm. Confirmed ORR was 73% and 27% in the ceritinib and chemotherapy arms, respectively. Estimated median response durations were 23.9 months and 11.1 months in the ceritinib and chemotherapy arms, respectively. Overall survival data are immature.[39]

In November 2017, the FDA approved alectinib (Alecensa) for the frontline treatment of patients with ALK-positive metastatic NSCLC, a TKI that targets ALK and RET. In addition to granting this new indication, the FDA has also converted alectinib’s accelerated approval for patients with ALK-positive NSCLC who have progressed on crizotinib to a full approval. It is indicated for anaplastic lymphoma kinase (ALK)-positive, metastatic NSCLC in patients whose disease has progressed on crizotinib or who are intolerant to crizotinib. The NCCN guidelines lists alectinib as the preferred first-line treatment in ALK-positive metastatic NSCLC.[1]

Approval was primarily based on findings from the phase III ALEX study. In the trial, treatment-naive patients were randomly assigned to alectinib 600 mg PO BID or crizotinib 250 mg PO BID. Median PFS, as determined by an independent review committee, was 25.7 months in the alectinib arm versus 10.4 months in the crizotinib arm. The overall response rate (ORR) with alectinib was 79% versus 72% with crizotinib. The complete response rates were 13% versus 6%, respectively, and the partial response rate was 66% in both arms. Eighty-two percent of patients receiving alectinib had a response duration ≥6 months, with 64% and 37%, having response durations ≥12 months and ≥18 months, respectively. The corresponding rates in the crizotinib arm were 57%, 36%, and 14%.[40]

Brigatinib (Alunbrig) was granted accelerated approval by the FDA in April 2017 for ALK-positive metastatic NSCLC in patients who have progressed on or are intolerant to crizotinib.[41]

Lorlatinib (Lorbrena) gained accelerated FDA approval in November 2018 for ALK-positive metastatic NSCLC in patients who have progressed on crizotinib and at least 1 other ALK inhibitor, or alectinib or ceritinib as a first ALK inhibitor therapy.[42]

Targeting ROS-1

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.[43]

Entrectinib (Rozyltrek) was approved in August 2019 for metastatic NSCLC in adults whose tumors are ROS1-positive. Entrectinib and its major metabolite inhibit tropomyosin receptor tyrosine kinases (TRKs), proto-oncogene tyrosine-protein kinase ROS1 (ROS1), and anaplastic lymphoma kinase (ALK).

Approval of entrectinib for NSCLC was based on pooled analysis of 3 multicenter, single-arm, open-label trials (ALKA, STARTRK-1, STARTRK-2). Of the 51 patients with ROS1-positive confirmed NSCLC who were assessed, ORR was 78%, and 55% had a duration of response (DOR) of at least 12 months. Favorable results were also shown in patients with CNS metastases.[44, 45]

Targeting RET

Selpercatinib is the first targeted therapy to be approved by the FDA for tumors that have rearranged during transfection (RET) mutations. It is indicated for metastatic RET-fusion–positive NSCLC. 

Accelerated approval in May 2020 for NSCLC was based on the open-label LIBRETTO-001 phase I/II clinical trial (N = 144). Objective response rate (ORR) was 64% in treatment-experienced patients (N = 105) and 85% in treatment-naive patients (N = 39). The phase III confirmatory trial (LIBRETTO-431) is under way.[16]  

Targeting HER2 

Trastuzumab deruxtecan is the first HER2 -directed treatment approved by the FDA for unresectable or metastatic HER2-mutant NSCLC, based on the presence of activating HER2 (ERBB2) mutations in tumor or plasma specimens. 

Mutations in the gene encoding HER2 drive approximately 3% of nonsquamous NSCLCs and are associated with female sex, never-smoking history, and a poor prognosis, as well as with a slightly younger age and a higher incidence of brain metastases, when compared to NSCLC without HER2  mutations or with other mutations.[46]  


Genetic Testing

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 it 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.[47]

The cobas EGFR Mutation Test v2 is available for the detection of EGFR T790M mutations to determine if osimertinib should be considered for treatment.[48]

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.[49]

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.


Questions & Answers