Table 3 Current methods available for single-cell DNA methylation sequencing
From: Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity
Technique | Technical characteristics | Designed by |
|---|---|---|
scBS-seq | scBS-seq is a technique for single-cell DNA methylation analysis with the advantages of single-cell resolution, high-precision detection and integrate multi-omics information; large and complex data; incomplete methylation reactions may lead to low coverage and bias | [83] |
BRIF-seq | BRIF-seq is a sequencing method with high read rate and genomic coverage by single strand ligation, MDA amplification and Tn5-based library building of small fragments generated by random amplification | [84] |
scWGBS | scWGBS is based on sulfite sequencing technology for single-cell whole-genome DNA methylation analysis with the advantages of single-cell resolution, whole-genome coverage and high resolution | [85] |
scRRBS | scRRBS narrows down the analysis of whole-genome DNA methylation sequencing to key CpG sites to achieve downscaling, high-precision detection, and sequencing cost savings; higher coverage in CpG islands and CpG-enriched regions, leading to potential bias | [82] |
RETrace | RETrace is a sequencing method that combines microsatellite capture with scRRBS; allowing simultaneous retrospective gene tracing and methylation analysis of single cells | [86] |
scAba-seq | scAba-seq is a technique for combinatorial analysis of single-cell antibodies with single-cell resolution, multi-parameter analysis, and high sensitivity; coverage of antibody probes, does not comprehensively reflect the expression of all antibodies; technological complexity | [87] |
CLEVER-seq | CLEVER-seq is a sequencing technology for the detection of long-range DNA sequence variation, featuring long-range sequencing, high sensitivity and high resolution; reliance on precise primer design; the need for high efficiency in DNA ligation reactions; and the detection of genomic structural variation and copy number variation | [88] |
scMAB-seq | scMAB-seq is a technique for single-cell multi-antibody combinatorial analysis of multiple antibody combinations in a single cell; characterized by multi-antibody analysis, high throughput, and single-cell resolution; limited by antibody probe coverage; technical complexity | [89] |
scTEM-seq | scTEM-seq combines transmission electron microscopy technology and sequencing technology for sequencing and analyzing individual cellular ultrastructures with high resolution and structural and transcriptome linkage; relatively low throughput; technical complexity; limited sample processing capacity; high cost | [90] |
scTAM-seq | scTAM-seq is a targeted bisulfite-free method that enables targeted high-confidence analysis of DNA methylation in single cells | [91] |
scAEBS | scAEBS is based on agarose-embedded bisulfite treatment to investigate DNA methylation at multiple loci by multiplex PCR (multiplex scAEBS) | [92] |
scCGI-seq | scCGI-seq is a technique for single-cell CpG island methylation status analysis with single-cell resolution, high resolution, and multi-omics correlation; technical complexity; and coverage is limited by the coverage of the selected CpG island probe | [93] |
snmC-seq | snmC-seq is a sequencing technology for DNA methylation profiling of individual cell nuclei with single-cell resolution and DNA methylation resolution; loss of cellular subcellular structural information; low signal-to-noise ratio; high cost per sample | [94] |
snmC-seq2 | snmC-seq2 is a technique for determining methylation in individual neuronal cells; resolves DNA methylation status at the single-cell level; genome-wide assessment of DNA methylation in single cells; technical complexity; high cost | [95] |
epi-gSCAR | epi-gSCAR is a single-tube, bisulfite-free method that allows simultaneous genome-wide analysis of DNA methylation and genetic variation in single cells | [96] |