Assay | Target CpGs | Strengths | Weaknesses | References |
---|---|---|---|---|
MSP (qMSP) | DMR2 (CpG 71–86, 76–87) | Simple Low cost | Unable to analyze heterogeneous methylation | |
PSQ | DMR2 (CpG 74–78) | High accuracy | High cost Limitation of Amplicon length | |
MS-HRM | DMR2 (CpG 72–83, 72–89, 84–89) | Capable of analyzing heterogeneous methylation | Low accuracy Limitation of Amplicon length | |
HPLC | 500 bp upstream of TSS (CpG 1–20) DMR1 (CpG 22–59) DMR2 (CpG 72–98) | Simple Low cost Capable of analyzing long amplicons | Unstable measurement of paraffin-embedded specimen | Present study |