Digital PCR quantification of MGMT methylation refines prediction of clinical benefit from alkylating agents in glioblastoma and metastatic colorectal cancer

L. Barault, A. Amatu, F. E. Bleeker, C. Moutinho, C. Falcomatà, V. Fiano, A. Cassingena, G. Siravegna, M. Milione, P. Cassoni, F. de Braud, R. Rudà, R. Soffietti, T. Venesio, A. Bardelli, P. Wesseling, P. de Witt Hamer, F. Pietrantonio, S. Siena, M. EstellerA. Sartore-Bianchi, Federica di Nicolantonio

Research output: Contribution to journalArticle


Background: O6-methyl-guanine-methyl-transferase (MGMT) silencing by promoter methylation may identify cancer patients responding to the alkylating agents dacarbazine or temozolomide. Patients and methods: We evaluated the prognostic and predictive value of MGMT methylation testing both in tumor and cell-free circulating DNA (cfDNA) from plasma samples using an ultra-sensitive two-step digital PCR technique (methyl-BEAMing). Results were compared with two established techniques, methylation-specific PCR (MSP) and Bs-pyrosequencing. Results: Thresholds for MGMT methylated status for each technique were established in a training set of 98 glioblastoma (GBM) patients. The prognostic and the predictive value of MGMT methylated status was validated in a second cohort of 66 GBM patients treated with temozolomide in which methyl-BEAMing displayed a better specificity than the other techniques. Cutoff values of MGMT methylation specific for metastatic colorectal cancer (mCRC) tissue samples were established in a cohort of 60 patients treated with dacarbazine. In mCRC, both quantitative assays methyl-BEAMing and Bs-pyrosequencing outperformed MSP, providing better prediction of treatment response and improvement in progression-free survival (PFS) (P <0.001). Ability of methyl-BEAMing to identify responding patients was validated in a cohort of 23 mCRC patients treated with temozolomide and preselected for MGMT methylated status according to MSP. In mCRC patients treated with dacarbazine, exploratory analysis of cfDNA by methyl-BEAMing showed that MGMT methylation was associated with better response and improved median PFS (P = 0.008). Conclusions: Methyl-BEAMing showed high reproducibility, specificity and sensitivity and was applicable to formalin-fixed paraffin-embedded tissues and cfDNA. This study supports the quantitative assessment of MGMT methylation for clinical purposes since it could refine prediction of response to alkylating agents.

Original languageEnglish
Article numbermdv272
Pages (from-to)1994-1999
Number of pages6
JournalAnnals of Oncology
Issue number9
Publication statusPublished - Sep 1 2015



  • Alkylating agent
  • Cell free circulating DNA
  • Digital PCR
  • DNA methylation
  • Metastatic colorectal cancer
  • MGMT

ASJC Scopus subject areas

  • Oncology
  • Hematology

Cite this

Barault, L., Amatu, A., Bleeker, F. E., Moutinho, C., Falcomatà, C., Fiano, V., Cassingena, A., Siravegna, G., Milione, M., Cassoni, P., de Braud, F., Rudà, R., Soffietti, R., Venesio, T., Bardelli, A., Wesseling, P., de Witt Hamer, P., Pietrantonio, F., Siena, S., ... di Nicolantonio, F. (2015). Digital PCR quantification of MGMT methylation refines prediction of clinical benefit from alkylating agents in glioblastoma and metastatic colorectal cancer. Annals of Oncology, 26(9), 1994-1999. [mdv272].