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Review
. 2019 Nov 6;11(11):1741.
doi: 10.3390/cancers11111741.

Cell-Free DNA Methylation Profiling Analysis-Technologies and Bioinformatics

Jinyong Huang  1 , Liang Wang  1
Affiliations
Review

Cell-Free DNA Methylation Profiling Analysis-Technologies and Bioinformatics

Jinyong Huang et al. Cancers (Basel). .

Abstract

Analysis of circulating nucleic acids in bodily fluids, referred to as "liquid biopsies", is rapidly gaining prominence. Studies have shown that cell-free DNA (cfDNA) has great potential in characterizing tumor status and heterogeneity, as well as the response to therapy and tumor recurrence. DNA methylation is an epigenetic modification that plays an important role in a broad range of biological processes and diseases. It is well known that aberrant DNA methylation is generalizable across various samples and occurs early during the pathogenesis of cancer. Methylation patterns of cfDNA are also consistent with their originated cells or tissues. Systemic analysis of cfDNA methylation profiles has emerged as a promising approach for cancer detection and origin determination. In this review, we will summarize the technologies for DNA methylation analysis and discuss their feasibility for liquid biopsy applications. We will also provide a brief overview of the bioinformatic approaches for analysis of DNA methylation sequencing data. Overall, this review provides informative guidance for the selection of experimental and computational methods in cfDNA methylation-based studies.

Keywords: DNA methylation; bioinformatic; cell-free DNA; liquid biopsies; next-generation sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Cytosine variants and their products by bisulfite conversion. DNA methyltransferases (DNMTs) convert unmodified cytosine (C) to 5-methylcytosine (5mC) by adding a methyl group. Ten-eleven translocation (TET) enzymes oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Thymine DNA glycosylase (TDG) and the base excision repair (BER) pathway allow for regeneration of C from 5fC and 5caC. Upon bisulfite treatment, unmethylated cytosine (C) is deaminated to uracil (U) and eventually converted to thymine (T) via DNA amplification, while methylated C remains unaffected. 5hmC also protects C from deamination, while 5fC and 5caC do not.
Figure 2
Figure 2
Schematic diagram of bisulfite-based cfDNA methylation profiling technologies, including whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS), methylated CpG tandems amplification and sequencing (MCTA-seq), and targeted bisulfite sequencing.
Figure 3
Figure 3
Schematic diagram of enrichment-based cfDNA methylation profiling technologies, including cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq), 5hmC-Seal, and hmC-CATCH.
Figure 4
Figure 4
Computational pipeline for DNA methylation sequencing data analysis.
See this image and copyright information in PMC

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