Liquid biopsy as an option for predictive testing and prognosis in patients with lung cancer

Efficacy of liquid biopsy for genetic mutations determination in non-small cell lung cancer: a systematic review on literatures

BACKGROUND

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality worldwide and is often diagnosed at advanced stages, limiting treatment options. This systematic review aims to evaluate the efficacy of liquid biopsy in detecting genetic mutations in NSCLC, focusing on its sensitivity, specificity, clinical utility, and potential to guide personalized treatment strategies.

METHODS

A systematic search was conducted in PubMed, Scopus, Embase, Web of Science, and Cochrane Library to identify relevant studies published between 1990 and September 2024. Eligible studies included comparative analyses of liquid biopsy techniques for NSCLC diagnosis, prognosis, progression, or treatment response. This review adheres to the PRISMA 2020 guidelines and assesses study quality using the QUADAS framework.

RESULTS

A total of 30 studies were included. Digital droplet PCR (ddPCR) demonstrated the highest sensitivity, detecting low-frequency mutations such as EGFR T790M at levels as low as 0.01%. Next-generation sequencing (NGS) provided comprehensive mutational profiling, revealing tumor heterogeneity and co-existing mutations but required high-quality plasma samples. The cobas EGFR Mutation Test, while less sensitive than ddPCR, remains widely used due to its clinical accessibility. Emerging methods, including extracellular vesicle analysis, show promise but require further validation. Additionally, liquid biopsy effectively identified non-EGFR mutations, such as KRAS, ALK, and MET amplifications, expanding its clinical applicability.

CONCLUSION

Liquid biopsy is a transformative tool in NSCLC management, offering a minimally invasive approach for mutation detection, disease monitoring, and treatment guidance. Future research should focus on multicenter trials and emerging technologies to enhance clinical integration and broaden applicability across different cancer types.

Discriminating Benign from Malignant Lung Diseases Using Plasma Glycosaminoglycans and Cell-Free DNA

We aimed to investigate the use of free glycosaminoglycan profiles (GAGomes) and cfDNA in plasma to differentiate between lung cancer and benign lung disease, in a cohort of 113 patients initially suspected of lung cancer. GAGomes were analyzed in all samples using the MIRAM® Free Glycosaminoglycan Kit with ultra-high-performance liquid chromatography and electrospray ionization triple quadrupole mass spectrometry. In a subset of samples, cfDNA concentration and NGS-data was available. We detected two GAGome features, 0S chondroitin sulfate (CS), and 4S CS, with cancer-specific changes. Based on the observed GAGome changes, we devised a model to predict lung cancer. The model, named the GAGome score, could detect lung cancer with 41.2% sensitivity (95% CI: 9.2-54.2%) at 96.4% specificity (95% CI: 95.2-100.0%, n = 113). When we combined the GAGome score with a cfDNA-based model, the sensitivity increased from 42.6% (95% CI: 31.7-60.6%, cfDNA alone) to 70.5% (95% CI: 57.4-81.5%) at 95% specificity (95% CI: 75.1-100%, n = 74). Notably, the combined GAGome and cfDNA testing improved the sensitivity, compared to cfDNA alone, especially in ASCL stage I (55.6% vs 11.1%). Our findings show that plasma GAGome profiles can enhance cfDNA testing performance, highlighting the applicability of a multiomics approach in lung cancer diagnostics.

Circulating tumour DNA analysis for early detection of lung cancer: a systematic review

Background

Circulating tumor DNA (ctDNA) analysis has been applied in cancer diagnostics including lung cancer. Specifically for the early detection purpose, various modalities of ctDNA analysis have demonstrated their potentials. Such analyses have showed diverse performance across different studies.

Methods

We performed a systematic review of original studies published before 1 January 2023. Studies that evaluated ctDNA alone and in combination with other biomarkers for early detection of lung cancer were included.

Results

The systematic review analysis included 56 original studies that were aimed for early detection of lung cancer. There were 39 studies for lung cancer only and 17 for pan-cancer early detection. Cancer and control cases included were heterogenous across studies. Different molecular features of ctDNA have been evaluated, including 7 studies on cell-free DNA concentration, 17 on mutation, 29 on methylation, 5 on hydroxymethylation and 8 on fragmentation patterns. Among these 56 studies, 17 have utilised different combinations of the above-mentioned ctDNA features and/or circulation protein markers. For all the modalities, lower sensitivities were reported for the detection of early-stage cancer.

Conclusions

The systematic review suggested the clinical utility of ctDNA analysis for early detection of lung cancer, alone or in combination with other biomarkers. Future validation with standardised testing protocols would help integration into clinical care.

Values of circulating tumor DNA for non-small cell lung cancer patients receiving neoadjuvant therapy, progress and challenges: a narrative review

Background and Objective

The value of circulating tumor DNA (ctDNA) in neoadjuvant therapy (NAT) for lung cancer remains controversial. Therefore, we conducted a review to further investigate the role of ctDNA in non-small cell lung cancer (NSCLC) patients undergoing NAT for individualized management.

Methods

A search of online databases (PubMed, Embase, Web of Science, Science Direct, and Cochrane Library) was conducted to evaluate the value of ctDNA in predicting relapse, risk stratification, and efficacy of NAT in NSCLC. Only articles published in English within the last 25 years, between January 1st, 1998 and November 30th, 2023, were included. Additionally, the application of ctDNA in NSCLC is briefly reviewed.

Key Content and Findings

ctDNA is a non-invasive and dynamic method that plays an important role in future treatment guidance. Additionally, ctDNA successfully predicted the effect of neoadjuvant immunotherapy before surgery, and positive testing was strongly correlated with a lower major pathological response or complete pathological response rate. Sequential testing of ctDNA may serve as a secondary indicator to guide the adjustment of treatment programs. However, the application of this method has been limited by false negative results, a lack of objective indicators, and high costs. These issues must be addressed by researchers.

Conclusions

ctDNA has strong potential in NAT, based on positive preliminary studies. However, its widespread use is limited by the high cost of testing. Further research is needed to explore its value in risk stratification and treatment guidance in the future.

AutoCancer as an automated multimodal framework for early cancer detection

Current studies in early cancer detection based on liquid biopsy data often rely on off-the-shelf models and face challenges with heterogeneous data, as well as manually designed data preprocessing pipelines with different parameter settings. To address those challenges, we present AutoCancer, an automated, multimodal, and interpretable transformer-based framework. This framework integrates feature selection, neural architecture search, and hyperparameter optimization into a unified optimization problem with Bayesian optimization. Comprehensive experiments demonstrate that AutoCancer achieves accurate performance in specific cancer types and pan-cancer analysis, outperforming existing methods across three cohorts. We further demonstrated the interpretability of AutoCancer by identifying key gene mutations associated with non-small cell lung cancer to pinpoint crucial factors at different stages and subtypes. The robustness of AutoCancer, coupled with its strong interpretability, underscores its potential for clinical applications in early cancer detection.

Liquid biopsy in non-small cell lung cancer: a meta-analysis of state-of-the-art and future perspectives

Introduction: To date, tissue biopsy represents the gold standard for characterizing non-small-cell lung cancer (NSCLC), however, the complex architecture of the disease has introduced the need for new investigative approaches, such as liquid biopsy. Indeed, DNA analyzed in liquid biopsy is much more representative of tumour heterogeneity. Materials and methods: We performed a meta-analysis of 17 selected papers, to attest to the diagnostic performance of liquid biopsy in identifying EGFR mutations in NSCLC. Results: In the overall studies, we found a sensitivity of 0.59, specificity of 0.96 and diagnostic odds ratio of 24,69. Since we noticed a high heterogeneity among different papers, we also performed the meta-analysis in separate subsets of papers, divided by 1) stage of disease, 2) experimental design and 3) method of mutation detection. Liquid biopsy has the highest sensitivity/specificity in high-stage tumours, and prospective studies are more reliable than retrospective ones in terms of sensitivity and specificity, both NGS and PCR-based techniques can be used to detect tumour DNA in liquid biopsy. Discussion: Overall, liquid biopsy has the potential to help the management of NSCLC, but at present the non-homogeneous literature data, lack of optimal detection methods, together with relatively high costs make its applicability in routine diagnostics still challenging.

A comparative study on ctDNA and tumor DNA mutations in lung cancer and benign cases with a high number of CTCs and CTECs

BACKGROUND

Liquid biopsy provides a non-invasive approach that enables detecting circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) using blood specimens and theoretically benefits early finding primary tumor or monitoring treatment response as well as tumor recurrence. Despite many studies on these novel biomarkers, their clinical relevance remains controversial. This study aims to investigate the correlation between ctDNA, CTCs, and circulating tumor-derived endothelial cells (CTECs)  while also evaluating whether mutation profiling in ctDNA is consistent with that in tumor tissue from lung cancer patients. These findings will help the evaluation and utilization of these approaches in clinical practice.

METHODS

104 participants (49 with lung cancer and 31 with benign lesions) underwent CTCs and CTECs detection using integrating subtraction enrichment and immunostaining-fluorescence in situ hybridization (SE-iFISH) strategy. The circulating cell-free DNA (cfDNA) concentration was measured and the mutational profiles of ctDNA were examined by Roche AVENIO ctDNA Expanded Kit (targeted total of 77 genes) by next generation sequencing (NGS) in 28 patients (20 with lung cancer and 8 with benign lesions) with highest numbers of CTCs and CTECs. Mutation validation in matched tumor tissue DNA was then performed in 9 patients with ctDNA mutations using a customized xGen pan-solid tumor kit (targeted total of 474 genes) by NGS.

RESULTS

The sensitivity and specificity of total number of CTCs and CTECs for the diagnosis of NSCLC were 67.3% and 77.6% [AUC (95%CI): 0.815 (0.722-0.907)], 83.9% and 77.4% [AUC (95%CI): 0.739 (0.618-0.860)]. The concentration of cfDNA in plasma was statistically correlated with the size of the primary tumor (r = 0.430, P = 0.022) and CYFRA 21-1 (r = 0.411, P = 0.041), but not with the numbers of CTCs and CTECs. In this study, mutations were found to be poorly consistent between ctDNA and tumor DNA (tDNA) in patients, even when numerous CTCs and CTECs were present.

CONCLUSION

Detection of CTCs and CTECs could be the potential adjunct tool for the early finding of lung cancer. The cfDNA levels are associated with the tumor burden, rather than the CTCs or CTECs counts. Moreover, the poorly consistent mutations between ctDNA and tDNA require further exploration.

The Contribution of Mediastinal Transbronchial Nodal Cryobiopsy to Morpho-Histological and Molecular Diagnosis

(1) Background: endobronchial ultrasound-guided mediastinal transbronchial cryo-node biopsy, previously assisted by fine-needle aspiration, is a novel technique of particular interest in the field of lung cancer diagnosis and is of great utility for extrathoracic tumor metastases, lymphomas, and granulomatous diseases. An integrated histological and molecular diagnosis of small samples implies additional difficulty for the pathologist. Additionally, emerging tumor biomarkers create the need to search for new approaches to better manage the tissue sample; (2) Methods: An analytical observational study of 32 mediastinal node cryobiopsies is carried out in 27 patients (n = 27). Statistical analysis using the t-student and Wilcoxon signed-rank tests for paired data is performed with SPSS 26 and R Statistical software. The significance level is established at p < 0.05; (3) Results: cryobiopsies were valid for diagnosis in 25 of 27 patients, with a maximum average size of 3.5 ± 0.7 mm. A total of 18 samples (66.67%) were positive for malignancy and 9 (33.33%) were benign. The tumor percentage measured in all neoplastic samples was greater than 30%. The average DNA and RNA extracted in nine non-small cell lung cancer cases was 97.2 ± 22.4 ng/µL and 26.6 ± 4.9 ng/µL, respectively; (4) Conclusions: the sample size obtained from an endobronchial ultrasound-guided mediastinal transbronchial cryo-node biopsy facilitates the morphological and histo-architectural assessment of inflammatory and neoplastic pathology. It optimizes molecular tests in the latter due to more tumor cells, DNA, and RNA.

The Impact of Liquid Biopsies Positive for EGFR Mutations on Overall Survival in Non-Small Cell Lung Cancer Patients

In recent years, non-small cell lung cancer treatment has been revolutionized. EGFR tyrosine kinase inhibitors and our improved understanding of its alterations have driven new diagnostic strategies. Liquid biopsies have emerged as a useful tool in these contexts, showing potential utility in early diagnosis combined with low-dose CT scans, as well as potential in monitoring treatment response and predicting the development of patients. We studied the circulating tumor DNA (ctDNA) of 38 EGFR-mutated non-small cell lung cancer patients at diagnosis in different moments of their disease by liquid biopsy techniques. Our results show that mean overall survival was significantly lower when a liquid biopsy was positive for the detection of EGFR mutations compared with wild-type patients in their liquid biopsy in both univariate (29 ± 4 vs. 104 ± 19 months; p = 0.004) and multivariate analysis (p = 0.008). Taking this into consideration, liquid biopsies could be key to improving the control of this disease.

Detection of KRAS mutation using plasma samples in non-small-cell lung cancer: a systematic review and meta-analysis

Background

The aim of this study was to investigate the diagnostic accuracy of KRAS mutation detection using plasma sample of patients with non-small cell lung cancer (NSCLC).

Methods

Databases of Pubmed, Embase, Cochrane Library, and Web of Science were searched for studies detecting KRAS mutation in paired tissue and plasma samples of patients with NSCLC. Data were extracted from each eligible study and analyzed using MetaDiSc and STATA.

Results

After database searching and screening of the studies with pre-defined criteria, 43 eligible studies were identified and relevant data were extracted. After pooling the accuracy data from 3341 patients, the pooled sensitivity, specificity and diagnostic odds ratio were 71%, 94%, and 59.28, respectively. Area under curve of summary receiver operating characteristic curve was 0.8883. Subgroup analysis revealed that next-generation sequencing outperformed PCR-based techniques in detecting KRAS mutation using plasma sample of patients with NSCLC, with sensitivity, specificity, and diagnostic odds ratio of 73%, 94%, and 82.60, respectively.

Conclusion

Compared to paired tumor tissue sample, plasma sample showed overall good performance in detecting KRAS mutation in patients with NSCLC, which could serve as good surrogate when tissue samples are not available.

Updates of liquid biopsy in oral cancer and multiomics analysis

Liquid biopsy is a method sampled from body fluids, such as blood, saliva, urine, pleural effusion, cerebrospinal fluid, and so on. It is minimally invasive and reproducible and therefore can build a dynamic, real-time monitoring of oral squamous cell carcinoma patient's conditions and treatment responses. Circulating tumor cells, circulating tumor DNA and exosomes are three main detection objects of liquid biopsy, having different detection methods and features involving cost, sensitivity, specificity and output. Blood and saliva are the options of liquid biopsy in oral cancer. Then we reviewed the studies of liquid biopsy in oral cancer, integrating multiomics analysis of these results. The multiomics analysis of genomics, transcriptomics, proteomics, metabolomics, and DNA methylation have shown potential for the early screening, diagnosis, staging, prognosis, personalized medicine therapy, and monitoring of recurrence (minimal residual disease). Besides, we concluded some problems to be solved, such as the lack of the standard of the measurement methods and procedures of samples, the insufficient connection among different omics, and how to improve the sensitivity and specificity. And we also put up rough assumptions to these problems. However, the analysis of multiomics of liquid biopsy in oral cancer still shows great clinical value in the diagnosis and treatment of oral squamous cell carcinoma.

Synggen: fast and data-driven generation of synthetic heterogeneous NGS cancer data

SUMMARY

Whole-exome and targeted sequencing are widely utilized both in translational cancer genomics and in the setting of precision medicine. The benchmarking of computational methods and tools that are in continuous development is fundamental for the correct interpretation of somatic genomic profiling results. To this aim we developed synggen, a tool for the fast generation of large-scale realistic and heterogeneous cancer whole-exome and targeted sequencing synthetic datasets, which enables the incorporation of phased germline single nucleotide polymorphisms and complex allele-specific somatic genomic events. Synggen performances and effectiveness in generating synthetic cancer data are shown across different scenarios and considering different platforms with distinct characteristics.

AVAILABILITY AND IMPLEMENTATION

synggen is freely available at https://bitbucket.org/CibioBCG/synggen/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Diagnostic accuracy of circulating free DNA testing for the detection of KRAS mutations in non-small cell lung cancer: A systematic review and meta-analysis

Kirsten rat sarcoma viral oncogene homolog (KRAS) gene encodes a GTPase that acts as a molecular switch for intracellular signal transduction, promoting cell growth and proliferation. Mutations in the KRAS gene represent important biomarkers for NSCLC targeted therapy. However, detection of KRAS mutations in tissues has shown some limitations. During the last years, analyses of circulating free DNA (cfDNA) has emerged as an alternative and minimally invasive, approach to investigate tumor molecular changes. Here, we assessed the diagnostic performance of cfDNA analysis, compared to tissues through a meta-analysis and systematic review of existing literature. From 561 candidate papers, we finally identified 40 studies, including 2,805 NSCLC patients. We extracted values relating to the number of true-positive, false-positive, false-negative, and true-negative. Pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio, each with 95% CI, were calculated. A summary receiver operating characteristic curve and the area under curve (AUC) were used to evaluate the overall diagnostic performance. The pooled sensitivity was 0.71 (95% CI 0.68–0.74) and the specificity was 0.93 (95% CI 0.92–0.94). The diagnostic odds ratio was 35.24 (95% CI 24.88–49.91) and the area under the curve was 0.92 (SE = 0.094). These results provide evidence that detection of KRAS mutation using cfDNA testing is of adequate diagnostic accuracy thus offering to the clinicians a new promising screening test for NSCLC patients.

NTRK Fusion in Non-Small Cell Lung Cancer: Diagnosis, Therapy, and TRK Inhibitor Resistance

Neurotrophic tropomyosin receptor kinase (NTRK) gene fusion has been identified as an oncogenic driver of various solid tumors, and it is rare in non-smalll cell lung cancer (NSCLC) with a frequency of approximately less than 1%. Next-generation sequencing (NGS) is of priority for detecting NTRK fusions, especially RNA-based NGS. Currently, the tropomyosin receptor kinase (TRK) inhibitors have shown promising efficacy and well tolerance in patients with NTRK fusion-positive solid tumors, regardless of tumor histology. The first-generation TRK inhibitors (larotrectinib and entrectinib) are recommended as the first-line treatment for locally advanced or metastatic NSCLC patients with positive NTRK fusion. However, TRK inhibitor resistance can eventually occur due to on-target or off-target mechanisms. Further studies are under investigation to overcome resistance and improve survival. Interestingly, NTRK fusion might be the mechanism of resistance to epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKI) in NSCLC patients with EGFR mutation. Regarding immunotherapy, the efficacy of immune checkpoint inhibitors in NSCLC patients harboring NTRK fusion has yet to be well described. In this review, we elucidate the function of NTRK genes, summarize the diagnostic techniques for NTRK fusions, and present clinical data for TRK inhibitors; we also discuss potential mechanisms of resistance to TRK inhibitors.

Biological and technical factors in the assessment of blood-based tumor mutational burden (bTMB) in patients with NSCLC

BACKGROUND

Patients treated with immunotherapy are at risk of considerable adverse events, and the ongoing struggle is to accurately identify the subset of patients who will benefit. Tumor mutational burden (TMB) has emerged as a promising predictive biomarker but requires tumor tissue which is not always available. Blood-based TMB (bTMB) may provide a minimally invasive assessment of mutational load. However, because of the required sequencing depth, bTMB analysis is costly and prone to false negative results. This study attempted to design a minimally sized bTMB panel, examined a counting-based method for bTMB in patients with stage I to IV non-small cell lung cancer (NSCLC) and evaluated both technical factors such as bTMB and tissue-based TMB (tTMB) cut-off, as well as sample-related factors such as cell-free DNA input mass which influence the correlation between bTMB and tTMB.

METHODS

Tissue, plasma, and whole blood samples collected as part of the LEMA trial (NCT02894853) were used in this study. Samples of 185 treatment naïve patients with stage I to IV NSCLC were sequenced at the Roche Sequencing Solutions with a custom panel designed for TMB, using reagents and workflows derived from the AVENIO Tumor Tissue and circulating tumor DNA Analysis Kits.

RESULTS

A TMB panel of 1.1 Mb demonstrated highly accurate TMB high calls with a positive predictive value of 95% when using a tTMB cut-off of 16 mut/Mb, corresponding with 42 mut/Mb for bTMB. The positive per cent agreement (PPA) of bTMB was relatively low at 32%. In stage IV samples with at least 20 ng of cfDNA input, PPA of bTMB improved to 63% and minimizing the panel to a subset of 577 kb was possible while maintaining 63% PPA.

CONCLUSION

Plasma samples with high bTMB values are highly correspondent with tTMB, whereas bTMB low results may also be the result of low tumor burden at earlier stages of disease as well as poorly shedding tumors. For advanced stages of disease, PPA (sensitivity) of bTMB is satisfactory in comparison to tTMB, even when using a panel of less than 600 kb, warranting consideration of bTMB as a predictive biomarker for patients with NSCLC eligible for immunotherapy in the future.