Table 2.
Comparison of different methylation assays.
| Methylation assay | Advantages | Disadvantages | Analytical tool used for NIPT |
|---|---|---|---|
| Sodium bisulfite | Not sensitive to sample impurities, methylation analysis at the base pair level | DNA degradation (>90%), 100% conversion is rarely achieved | * MSP, microarrays, Digital PCR, ** COBRA, *** NGS |
| Restriction enzyme digestion | Easy to perform and low cost | Sensitive to sample impurities, requires high amount of starting DNA, applicable to a limited number of DNA sequences | ** COBRA, digital PCR |
| **** MeDIP | Ideal for investigating low CG content regions, low cost assay, not sensitive to sample impurities, can be applied with low starting DNA amounts | Depends on antibody efficiency and ideal combination of affinity reagents | Real time-qPCR, microarrays |
* Methylation-specific PCR; ** combined bisulfite restriction analysis; *** next generation sequencing; **** methylated DNA immunoprecipitation.