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Table 1 Overview of genome-wide 5hmC quantification methods

From: Towards precision medicine: advances in 5-hydroxymethylcytosine cancer biomarker discovery in liquid biopsy

Technique Advantages Disadvantages
Whole-genome TAB-Seq [70] (direct measurement of 5hmC) Whole-genome
Single nucleotide resolution
Absolute methylation value
High sequencing depth required
Input > 100 ng DNA
Whole-genome oxBS-Seq [71, 74] (inference of 5hmC)
RRBS TAB-Seq [91] (direct measurement of 5hmC) Single nucleotide resolution
Absolute methylation value
Targets CpG islands
Input > 500 ng DNA
RRBS oxBS-Seq [52] (inference of 5hmC) ~ 60 million PE reads/sample Input > 500 ng DNA
Nano-hmC-Seal [53] (direct measurement of 5hmC) Input 5 ng DNA
Excellent genomic coverage
High specificity for 5hmC
~ 30 million PE reads/sample
Lower resolution
  1. 5hmC, 5-hydroxymethlcytosine; TAB-Seq, Tet-assisted bisulfite sequencing; oxBS-Seq, oxidative bisulfite sequencing; PE, paired-end