Table 3 Comparison of methylation platforms for research and clinical practice.

From: Minimalist approaches to cancer tissue-of-origin classification by DNA methylation

Relative completeness of testing

Somatic mutation

DNA methylation

Best suited for

High

Whole exome and whole genome sequencing

Comprehensive genome wide profiling by methylation array or sequencing

Research; defining reference molecular landscapes of cancers

Intermediate

Examples: targeted NGS panels [34,35,36,37]

Examples: smaller arrays or targeted NGS panels (e.g., dozens to hundreds of CpG sites)

Clinical work and biomarker research; assays for pan-cancer or more limited settings (e.g., hematopoietic neoplasms)

Low

Examples: PCR-based tests (e.g., for BRAF p.V600E in melanoma)

Examples: PCR-based tests (e.g., 1–10 CpG sites for resolving limited differentials in surgical pathology) [11, 32]

Clinical work; day-to-day, inexpensive and rapid testing

  1. It is our intent to draw parallels between the current state of clinical somatic mutation testing and the potential future of clinical DNA methylation testing, as supported by the high accuracy of our minimalist models and other considerations (italics).
  2. NGS next-generation sequencing.
Back to article page