Table 1.
Advantages and disadvantages of cfDNA methylation detection methods for biomarker discovery.
| Method | |||||
|---|---|---|---|---|---|
| Features | MethDet-M3 | MSP | QMSP | Targeted Amplicon Sequencing | RRBS |
|
DNA methylation
discrimination |
Methylation-sensitive endonuclease |
Bisulfite Treatment |
Bisulfite Treatment |
Bisulfite Treatment |
Bisulfite Treatment |
| Coverage | Medium/Low | Targeted | Targeted | Targeted | Medium |
| Throughput | Medium | Low | Medium | Medium/High | High |
|
Analytical
Sensitivity |
Medium | Low | Medium | Low | Low |
|
Analytical
Specificity |
High | Low/Medium | Medium | Medium | Medium |
| Advantages | Scalable (e.g., microarray) | Fast results Cost-effective |
Quantitative | Scalable (e.g., NGS) Single CpG methylation status |
Scalable (e.g., NGS) Single CpG methylation status |
| Disadvantages | Risk of false positive/negative | Limited coverage | Limited coverage | May require extensive data analysis | Extensive data analysis |
| Popularity | Unpopular | Very Popular | Popular | Popular | Popular |