Mining cancer methylomes: prospects and challenges.
Level 5 - mechanism / opinion, no new human data
Narrative review of technological platforms and published cancer methylomes
PubMed 24368016 · doi:10.1016/j.tig.2013.11.004
What was done
This review evaluated technologies used for genome-wide DNA methylation profiling in cancer research, comparing array-based and high-throughput sequencing methods across coverage of promoters, gene bodies, intergenic regions, and their ability to quantify individual CpG methylation states across the >28 million CpG sites in the human genome.
What was found
The human genome contains over 28 million CpG sites. Except for whole-genome bisulfite sequencing (WGBS), most commonly used genome-wide profiling technologies assess less than 5% of all human CpG sites. No additional quantitative performance comparisons or dataset counts were reported in the abstract.
Why it matters
It highlights a major limitation in cancer epigenomics: most widely used genome-wide methylation assays leave over 95% of genomic CpG sites uncharacterized, underscoring critical trade-offs between coverage, resolution, and platform feasibility.
Limits
This is a narrative technological review with no original empirical data, clinical trial outcomes, or systematic review search methodology. Specific comparative performance metrics, sequencing depths, and cost-effectiveness data are absent from the abstract.
Cited by
- context The human genome contains approximately 28 million cytosine locations, roughly a quarter of which change methylation status with age.