Prediction of DNA methylation state of MGMT promoter based on HM-450K and HM-27K infinium platforms (from Illumina Company)

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Warning! The R package mgmtstp27 is still in development and the documentation need some corrections (e.g. language, etc ...).

Installation

To install this package, load the archive containing the package mgmtstp27 (see below), start R and enter:

Documentation

• Introduction to R package mgmtstp27 (version 0.1, in preparation): intromgmtstp27.pdf
  
• Effect of normalization on the prediction of DNA methylation status of MGMT promoter: example with HM-450K Infinium data from TCGA and the R package mgmtstp27 (version 0.1, in preparation): docmgmtstp27.pdf
• Prediction of the DNA methylation of MGMT with raw data (format IDAT) from HM-27k (version 0.1, in preparation): MgmtPredTCGA.pdf

Archives

• Follow Installation instructions to use this package in your R session.
• Package Source: mgmtstp27_0.2.tar.gz (OLD version, see section "depository" for new version)
• Windows Binary: mgmtstp27_0.2.zip (32- & 64-bit, OLD version, see section "depository" for new version)
• Browse/checkout source: log
• Manual: mgmtstp27.pdf
• Archive: here
  

Depository

• Github: here
  
• Gitlab SIB: here
  

References

• Bady, P., D. Sciuscio, A.-C. Diserens, J. Bloch, M. J. van den Bent, C. Marosi, P.-Y. Dietrich, M. Weller, L. Mariani, F. L. Heppner, D. R. McDonald, D. Lacombe, R. Stupp, M. Delorenzi, and M. E. Hegi. (2012). MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status. Acta Neuropathologica 124:547-560. PubMed
• Bady P., Delorenzi M., Hegi M. (accepted) Sensitivity analysis of the MGMT-STP27 model and impact of genetic/epigenetic context to predict the MGMT methylation status in gliomas and other tumors, Journal of Molecular Diagnostics, 18 (3), 350-361. PubMed