Whole-Genome Bisulfite Sequencing

Overview

Whole-genome bisulfite sequencing (WGBS) is the gold-standard method for measuring DNA methylation at single-base resolution across the entire genome. Sodium bisulfite treatment converts unmethylated cytosines to uracil (read as thymine after PCR) while leaving 5-methylcytosine unchanged, enabling direct detection of methylated versus unmethylated CpG (and non-CpG) sites by sequencing. WGBS provides unbiased, genome-wide coverage but requires high sequencing depth (typically 20–30× per strand) and significant DNA input, making it expensive relative to array-based methylation profiling.

Used by

  • Run on 5 TCGA breast tumor samples as a validation experiment in the TCGA ILC/IDC multi-platform study (n=817) to confirm Illumina HumanMethylation450 BeadChip calls; validated the key finding that CDH1 promoter DNA hypermethylation is absent in ILC, contradicting older MSP-based reports. PMID:26451490
  • Bisulfite sequencing of the CDH1 promoter CpG island (with Sanger readout) detected hypermethylation in 4/5 CDH1 wild-type plasmacytoid bladder tumors and 0 CDH1-mutant or urothelial NOS tumors, explaining E-cadherin loss in mutation-negative cases. PMID:26901067
  • Applied to 40 MRT tumor/normal pairs plus 3 MRT cell lines, 3 hESC lines, and 4 NPCs; promoter CGI clustering identified two methylation sub-groups correlated with patient age (sub-group A enriched for patients >1 year; p=0.0013). Tumor-suppressor promoters (RASSF1, IRX1, TWIST2, DLEC1, TBX5) gained methylation vs hESC (Fisher p=0.02). PMID:26977886

Notes

  • WGBS requires bisulfite conversion followed by library preparation; strand-specific protocols (e.g., PBAT) minimize input DNA requirements.
  • Typical applications: CpG island methylation, differentially methylated regions (DMRs), allele-specific methylation, imprinting.
  • Distinguishes 5-methylcytosine (5mC) from 5-hydroxymethylcytosine (5hmC) requires oxidative bisulfite sequencing (oxBS) or TET-assisted bisulfite sequencing (TAB-seq).
  • Array-based methods (HM450, EPIC) cover ~450K–850K CpGs; WGBS covers ~28 million CpGs genome-wide.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:26901067

This page was processed by entity-page-writer on 2026-05-15. - PMID:26977886

This page was processed by entity-page-writer on 2026-05-15.