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Review
. 2022 May 8;10(1):71.
doi: 10.1186/s40478-022-01371-2.

DNA methylation as a diagnostic tool

Kristyn Galbraith  1 , Matija Snuderl  2   3
Affiliations
Review

DNA methylation as a diagnostic tool

Kristyn Galbraith et al. Acta Neuropathol Commun. .

Abstract

DNA methylation of cytosines in CpG sites throughout the genome is an epigenetic mark contributing to gene expression regulation. DNA methylation patterns are specific to tissue type, conserved throughout life and reflect changes during tumorigenesis. DNA methylation recently emerged as a diagnostic tool to classify tumors based on a combination of preserved developmental and mutation induced signatures. In addition to the tumor classification, DNA methylation data can also be used to evaluate copy number variation, assess promoter methylation status of specific genes, such as MGMT or MLH1, and deconvolute the tumor microenvironment, assessing the tumor immune infiltrate as a potential biomarker for immunotherapy. Here we review the role for DNA methylation in tumor diagnosis.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Diagnostically and clinically useful DNA methylation report with an indeterminate score. A hematoxylin and eosin stained section of a glioblastoma with about 50% cellularity (a). Classified by DNA methylation as a glioblastoma subclass mesenchymal with an indeterminate score of 0.569. T-SNE shows this case clustering closely with glioblastoma, subclass mesenchymal in green (b). The copy number plot generated from the DNA methylation data shows an EGFR amplification, consistent with the diagnosis of glioblastoma, as well as MDM4, MDM2, and CDK4 amplifications (c)
See this image and copyright information in PMC

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