Why molecular profiling matters: Non-small cell lung cancer (NSCLC) is the most common lung cancer type, and most patients still receive chemotherapy that works the same way for everyone. Molecular profiling identifies specific genetic mutations in individual tumors, allowing treatments matched to each patient's cancer biology.
Scope of this review: This PRISMA-compliant systematic review analyzed 75 clinical studies published through 2025, covering molecular biomarkers, targeted therapies, immunotherapy, and liquid biopsy applications in early-stage and locally advanced NSCLC.
Key questions addressed: How do specific mutations (EGFR, ALK, KRAS, MET) predict treatment response? What is the role of ctDNA in detecting minimal residual disease? How should neoadjuvant and adjuvant therapies be sequenced for maximum benefit?
Clinical significance: Despite advances in surgical techniques, recurrence rates after resection of early-stage NSCLC remain high. Identifying and treating molecular residual disease is the next frontier in improving cure rates.
EGFR mutations: EGFR is mutated in 15-30% of NSCLC adenocarcinomas (predominantly exon 19 deletions and L858R point mutations). Third-generation EGFR inhibitor osimertinib has become the standard adjuvant therapy for resected EGFR-mutant NSCLC, reducing recurrence risk by more than 80% in the ADAURA trial.
ALK rearrangements: ALK gene fusions, present in 3-7% of NSCLC, drive tumor growth through constitutive kinase activation. The ALINA trial established alectinib as the preferred adjuvant treatment for resected ALK-positive NSCLC, with a 3-year event-free survival rate of 88%.
KRAS G12C mutations: KRAS was long considered undruggable, but G12C-specific inhibitors like sotorasib and adagrasib have changed the landscape. KRAS G12C is found in about 13% of NSCLC and is more common in former smokers. Clinical trials are now exploring these agents in earlier disease stages.
MET amplification and exon 14 skipping: MET alterations, found in 3-5% of NSCLC, are actionable with agents like tepotinib and capmatinib. Accurate MET testing using next-generation sequencing (NGS) panels is now part of standard molecular workup.
What is ctDNA: Circulating tumor DNA (ctDNA) is DNA shed by cancer cells into the bloodstream. Unlike tissue biopsies, blood-based ctDNA tests can be performed repeatedly, offering a non-invasive window into tumor dynamics before, during, and after treatment.
Minimal residual disease (MRD) detection: After surgical resection of NSCLC, a positive ctDNA test indicates that residual cancer cells persist even when imaging is negative. This concept of molecular residual disease (MRD) is a powerful predictor of relapse - patients with detectable ctDNA after surgery have dramatically worse outcomes.
Landmark studies: Multiple studies now show that ctDNA-based MRD detection precedes radiographic recurrence by weeks to months. The TRACERx study demonstrated that early detection of ctDNA dynamics predicts which patients will relapse.
Implications for adjuvant therapy: ctDNA-guided treatment decisions - where MRD-positive patients receive adjuvant therapy while MRD-negative patients are spared toxicity - are being tested in prospective trials. This approach promises to personalize adjuvant treatment intensity.
The neoadjuvant paradigm: Giving immunotherapy (checkpoint inhibitors) before surgery - called neoadjuvant therapy - allows assessment of tumor response, treatment of micrometastatic disease early, and in some cases converts inoperable tumors to resectable ones.
CheckMate-816 trial: This landmark trial showed that nivolumab (anti-PD-1) combined with chemotherapy before surgery achieved a pathologic complete response (pCR) in 24% of patients vs. 2.2% with chemotherapy alone. pCR is strongly associated with long-term survival benefit.
KEYNOTE-671 trial: Pembrolizumab plus chemotherapy as neoadjuvant therapy, followed by adjuvant pembrolizumab, significantly improved event-free survival in resectable NSCLC. This trial established the concept of perioperative immunotherapy - spanning both the pre- and post-surgical periods.
Selecting candidates: Not all patients benefit equally. PD-L1 expression and tumor mutational burden (TMB) help identify likely responders, though these biomarkers are imperfect. Research is ongoing to identify better predictors of neoadjuvant immunotherapy response.
Osimertinib in EGFR-mutant NSCLC: The ADAURA trial demonstrated that three years of adjuvant osimertinib after resection of EGFR-mutant NSCLC reduced recurrence risk by 83% in stage II-IIIA disease. Osimertinib penetrates the blood-brain barrier, reducing brain metastases - a common site of EGFR NSCLC recurrence.
Alectinib in ALK-positive NSCLC: The ALINA trial established alectinib as adjuvant therapy for resected ALK-positive NSCLC, achieving 88% 3-year event-free survival vs. 19% for chemotherapy. These results support routine ALK testing in all resected NSCLC.
Immunotherapy in the adjuvant setting: Atezolizumab (anti-PD-L1) was studied as adjuvant therapy in PD-L1-positive NSCLC (IMpower010 trial). While showing disease-free survival benefit in PD-L1-high subgroups, its role is being refined as perioperative approaches gain prominence.
Choosing the right adjuvant approach: For patients without targetable mutations, adjuvant chemotherapy remains standard for stage II-III NSCLC. The field is moving toward MRD-guided decisions where ctDNA results determine who receives adjuvant therapy after surgery.
What NGS tests: Next-generation sequencing (NGS) simultaneously analyzes hundreds or thousands of genes in a tumor biopsy. This comprehensive approach can identify not only common mutations (EGFR, KRAS) but also rare actionable alterations (NTRK fusions, RET rearrangements) that would be missed by single-gene tests.
Recommended testing approach: Major guidelines now recommend upfront comprehensive NGS testing for all patients with advanced NSCLC, and increasingly for resected early-stage disease. This ensures that patients with rare mutations receive matched targeted therapies.
Liquid biopsy NGS: Blood-based ctDNA NGS can detect driver mutations in patients where tissue biopsy is insufficient or not feasible. While tissue remains the gold standard, liquid biopsy has high specificity and can be repeated over time to track molecular evolution.
Timing and challenges: A major practical challenge is turnaround time - NGS results can take 2-3 weeks, potentially delaying urgent treatment decisions. Rapid NGS platforms and parallel testing workflows are being developed to address this.
Perioperative immunotherapy trials: Multiple ongoing trials are testing perioperative checkpoint inhibitor strategies - combining neoadjuvant and adjuvant immunotherapy around surgery - to maximize the window of treatment effect and reduce relapse.
ctDNA-adaptive treatment trials: Prospective trials like MERMAID-1 and MERMAID-2 are testing whether MRD-guided adjuvant therapy - starting or escalating treatment based on post-surgical ctDNA positivity - improves outcomes over standard approaches.
Emerging targets: Beyond established targets, new targets including HER2, BRAF, RET, and NTRK are being evaluated in early-stage disease. As precision oncology expands, more patients will have targetable alterations that can guide treatment.
Integrating AI and multi-omics: The future of NSCLC risk stratification will likely integrate genomics, transcriptomics, imaging-based radiomics, and AI-based prediction models to create individualized treatment plans that optimize outcomes while minimizing unnecessary therapy.