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Table 3 Comparison of established protocols with the present study protocols in MGMT methylation analysis

From: Assessment of MGMT methylation status using high-performance liquid chromatography in newly diagnosed glioblastoma

Assay Target CpGs Strengths Weaknesses References
MSP
(qMSP)
DMR2 (CpG 71–86, 76–87) Simple
Low cost
Unable to analyze heterogeneous methylation [12, 17]
PSQ DMR2 (CpG 74–78) High accuracy High cost
Limitation of Amplicon length
[12, 23]
MS-HRM DMR2 (CpG 72–83, 72–89, 84–89) Capable of analyzing heterogeneous methylation Low accuracy
Limitation of Amplicon length
[10, 12, 22]
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
  1. CpG numbers on MGMT CpG islands were defined by Harris et al. [16]
  2. DMR differentially methylated region, MSP methylation-specific polymerase chain reaction, PSQ pyrosequencing,
  3. qMSP quantitative MSP, MS-HRM methylation-sensitive high-resolution melting analysis, TSS transcription start site