Illumina 450k methylation array

Overview

Bead-based array measuring DNA methylation at ~450,000 CpG sites across the human genome, used in cBioPortal corpus papers for epitype/epigenomic characterization PMID:35927489.

Used by

  • PMID:35927489 — DNA methylation profiling of 490 CLL samples (part of n=999 methylation cohort, complemented by RRBS n=509) supporting the n-CLL/i-CLL/m-CLL epitype framework and the epiCMIT mitotic clock PMID:35927489.
  • PMID:38117484 — Illumina 450K BeadChip used alongside the EPIC array for DNA methylation profiling of 354 samples (132 initial + 132 recurrent + 90 other time points) from the GLASS International consortium; identified genome-wide methylation loss at recurrence in IDH-mutant gliomas, especially with treatment PMID:38117484.
  • Illumina 450k methylation arrays profiled 510 breast tumors; DNA methylation patterns differentiated basal-like from luminal subtypes and identified BRCA1-silenced cases PMID:23000897
  • Used Illumina HumanMethylation450 arrays for DNA methylation profiling of 40 oral squamous cell carcinomas in an integrated multi-platform study PMID:23619168
  • Applied Illumina Infinium HumanMethylation450 BeadChip to 192 of 200 AML samples in TCGA AML integrated analysis; IDH1/IDH2-mutant samples showed extensive methylation gains and triple NPM1+DNMT3A+FLT3 samples showed extensive methylation loss PMID:23634996
  • Applied Illumina Infinium 450K to all 373 endometrial carcinoma samples; identified MSI hypermutated tumours via MLH1 promoter hypermethylation and defined the POLE-ultramutated, MSI, copy-number-low, and copy-number-high subtypes PMID:23636398
  • Used in TCGA clear cell renal cell carcinoma study (n=224 samples) to profile DNA methylation, revealing SETD2 mutation-associated regional hypomethylation at non-promoter CpGs and VHL promoter silencing in ~7% of tumors PMID:23792563
  • Used in TCGA PTC multiplatform profiling; methylation clusters aligned with BVL/RL meta-cluster split, and a CpG-island RL-PTC sub-cluster was associated with higher tumor purity and reduced lymphocyte infiltration PMID:25417114
  • Illumina 450K methylation BeadChip applied to 138 CCA cases to reveal two distinct hypermethylation subgroups: CpG-island (Cluster 1/Fluke-Pos) and CpG-shore (Cluster 4/Fluke-Neg) patterns PMID:28667006
  • Illumina 450K methylation arrays profiled 1,256 medulloblastoma cases; t-SNE on 12,454 most-variable probes resolved eight molecular subtypes within Group 3/4, the largest methylation-based MB classification to date PMID:28726821

Notes

  • DNA methylome variation in CLL was dominated by cell-of-origin and proliferative history rather than driver mutation status PMID:35927489.

Sources

This page was processed by crosslinker on 2026-05-09. - PMID:23000897

This page was processed by crosslinker on 2026-05-09. - PMID:23619168

This page was processed by crosslinker on 2026-05-09. - PMID:23634996

This page was processed by crosslinker on 2026-05-09. - PMID:23636398

This page was processed by crosslinker on 2026-05-09. - PMID:23792563

This page was processed by crosslinker on 2026-05-09. - PMID:25417114

This page was processed by wiki-cli on 2026-05-14. - PMID:28667006

This page was processed by wiki-cli on 2026-05-15. - PMID:28726821

This page was processed by wiki-cli on 2026-05-15.