DNA Methylation Testing Guidelines

Academic and Clinical Testing Centers

The National Comprehensive Cancer Network recommends DNA methylation testing to be performed at academic tertiary centers with specialized expertise, particularly for specific conditions like medulloblastoma, where genome-wide DNA methylation with brain tumor classifier application is considered the gold standard for diagnosis and subgroup classification 1
The National Cancer Institute and similar institutions perform integrated analysis incorporating histology, next-generation sequencing, and DNA methylation for CNS tumors 1
Specialized testing should be referred to academic tertiary centers with expertise in this area for medulloblastoma and other central nervous system tumors 2

Several analysis packages are available for studying DNA methylation differences, including methylkit and DSS (Dispersion Shrinkage for Sequencing) 3, 4

DNA methylation testing is routinely performed in European countries (France, Germany, UK) as part of clinical protocols, according to the European Organisation for Research and Treatment of Cancer (EORTC) 1
The EORTC incorporates DNA methylation testing as part of central neuropathology review in clinical trials 1

DNA methylation testing has diagnostic utility in cancer diagnosis and subtyping (particularly brain tumors) 1
DNA methylation testing has diagnostic utility in epigenetic aging clock measurements 5

Centers should implement proper quality control measures, including filtering based on coverage levels and DNA methylation percentage, and correction for SNP genotypes when calling methylation 4, 6, 7
Centers should have expertise in both the technical aspects of methylation testing and clinical interpretation of results, as recommended by the National Comprehensive Cancer Network 1
Appropriate statistical analysis methods for differential methylation should be used, such as those that account for overdispersion in statistical models 8

DNA methylation testing results can be affected by PCR bias, low read coverage, SNPs at CpG sites, and overdispersion in statistical models 3, 4, 7, 8
Different algorithms for detecting differentially methylated regions (DMRs) can lead to different DNA methylation values even when using the same whole-genome bisulfite sequencing data 9
Interpretation of results requires specialized expertise, particularly for clinical applications, as emphasized by the National Comprehensive Cancer Network 1