Liquid Biopsies in Lung Cancer
Abstract
:Simple Summary
Abstract
1. Introduction
2. Methodology (Figure 1)
2.1. Cell Free DNA (cfDNA) and Circulating Tumor DNA (ctDNA)
2.1.1. Sample Collection and Preparation Timeline
2.1.2. Collecting Tubes
EDTA Tubes | Preservative Tubes | |
---|---|---|
Advantages | Inexpensive and easily available Broad experience with use Better than heparin or citrate for anticoagulation [20] Transport to external laboratory not required | PAXgene® Blood DNA tubes (Qiagen) or Cell-free DNA BCT® tubes (Streck) cfDNA stable up to 14 days and CTC up to 7 days [18] Can be stored at room temperature [21] |
Disadvantages | Must be processed within 1–2 h to prevent contamination with DNA from white blood cells | Expensive Limited availability and experience Strict adherence to product guidelines necessary Transportation to external laboratory required |
2.1.3. Methods for DNA Analysis
2.1.4. Real-Time (quantitative) PCR (qPCR) Assay
2.1.5. Digital Droplet PCR (ddPCR) Assay
2.1.6. Next Generation Sequencing (NGS) Assay
Hybrid Capture-Based NGS
Amplicon-Based NGS (PCR Capture)
2.1.7. Comparison of PCR-Based and NGS-Based Methods
2.2. Circulating Tumor Cells (CTCs)
2.2.1. Antigen-Based CTC Isolation
2.2.2. CTC Isolation Based on Biological and Physical Characteristics
2.2.3. Interpretation of CTCs
2.3. miRNA
2.4. Extracellular Vesicles (EVs)
3. Clinical Applications
3.1. ctDNA
3.1.1. Mutational Assessment
3.1.2. EGFR Mutations
3.1.3. ALK Rearrangement
3.1.4. ROS1 Gene Fusions
3.1.5. MET Rearrangements
3.1.6. RET Rearrangements
3.1.7. BRAF Mutations
3.1.8. ERBB-2/Her-2 Alterations:
3.1.9. KRAS Mutations
3.1.10. NTRK Fusions
3.1.11. Immunotherapy and Tumor Mutational Burden (TMB)
3.1.12. Prognostic Value of DNA Methylation in cfDNA and CTCs
3.2. CTCs
3.2.1. Mutational Assessment
3.2.2. Immunotherapy and PD-L1 Expression
3.3. miRNA
3.4. EVs
3.4.1. sEVs
3.4.2. lEVs
4. State-of-the-Art Approaches and Future Perspectives
4.1. Screening Programs
4.2. Monitoring MRD after Curative Intended Therapy and Surgery
4.3. Treatment Monitoring in Advanced Stage (Metastatic) NSCLC
4.4. Limitations
4.4.1. Sensitivity and Specificity
4.4.2. Early Stages
4.4.3. Financial Aspects/Accessibility
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Method | Limit of Detection | Advantages | Disadvantages | Clinical Use | |
---|---|---|---|---|---|
Targeted PCR-Based Assays | |||||
Digital PCR (ddPCR, BEAMing) | DNA fractionation into different reactions sites for parallel qPCR | 0.04–0.1% | Highly sensitive and specific Quantitative Low turnaround time | Not suitable for unknown alterations | Resistance genotyping |
qPCR (e.g., Cobas®, Therascreen®) | Amplification of predefined DNA sequences | 0.1–1% | Highly sensitive and specific Low turnaround time | Limited multiplexing Semi-quantitative | Initial and resistance genotyping of known mutations |
Next generation sequencing (NGS) methods | |||||
WGS | NGS of the full genome | 10% | Detection of unknown alterations and new mechanisms of resistance (MOR) | Low specificity (false positives) Risk of detecting germline mutations Low sensitivity extensive bioinformatics High costs | Not in clinical routine, more experimental use |
WES | NGS of the full exome (i.e., coding regions) | 5% | |||
Hybrid-capture based NGS (e.g., Guardant360® CDx, FoundationOne® Liquid CDx) | Sequencing of target regions, that are captured by hybridization | 0.001–0.5% | High sensitivity detection of SNPs, CNVs and gene fusions Simultaneous detection of predefined genes of interest as well as unknown mutations | Lower specificity (65%) than amplicon-based NGS unable to detect fusions without prior knowledge of partners | Initial and resistance genotyping |
Amplicon-based (PCR-capture) NGS | Sequencing of target regions, that are amplified by PCR | 0.01–2% | High sensitivity detection of SNPs, CNVs and gene fusions Simultaneous detection of predefined genes of interest as well as unknown mutations Higher specificity than hybrid-capture NGS (>99%) | Bias of CNVs and AFs (due to amplification) Unable to detect fusions without prior knowledge of partners |
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Kemper, M.; Krekeler, C.; Menck, K.; Lenz, G.; Evers, G.; Schulze, A.B.; Bleckmann, A. Liquid Biopsies in Lung Cancer. Cancers 2023, 15, 1430. https://doi.org/10.3390/cancers15051430
Kemper M, Krekeler C, Menck K, Lenz G, Evers G, Schulze AB, Bleckmann A. Liquid Biopsies in Lung Cancer. Cancers. 2023; 15(5):1430. https://doi.org/10.3390/cancers15051430
Chicago/Turabian StyleKemper, Marcel, Carolin Krekeler, Kerstin Menck, Georg Lenz, Georg Evers, Arik Bernard Schulze, and Annalen Bleckmann. 2023. "Liquid Biopsies in Lung Cancer" Cancers 15, no. 5: 1430. https://doi.org/10.3390/cancers15051430
APA StyleKemper, M., Krekeler, C., Menck, K., Lenz, G., Evers, G., Schulze, A. B., & Bleckmann, A. (2023). Liquid Biopsies in Lung Cancer. Cancers, 15(5), 1430. https://doi.org/10.3390/cancers15051430