Best practices for the extraction of genomic DNA from formalin-fixed paraffin-embedded tumor tissue for cancer genomic profiling tests

Pathol Int. 2021 May;71(5):360-364. doi: 10.1111/pin.13086. Epub 2021 Mar 3.

Abstract

Recently, two cancer genomic profiling tests have been approved in Japan and implemented in routine clinical practice: the FDA-approved FoundationOne CDx test, and the OncoGuide NCC Oncopanel test. The quality and quantity of DNA significantly affects the sequencing results; therefore, preparing a sufficient amount of high-quality DNA for clinical cancer genomic profiling tests is important. We examined the best practices for the extraction of cancer genomic DNA from formalin-fixed paraffin-embedded (FFPE) tumor tissues of pancreatic, lung and colon cancer specimens. We found that the quality of cancer genomic DNA extracted from 10-μm-thick FFPE samples improved significantly, compared with that from 4-μm-thick FFPE samples, suggesting that 10-μm-thick FFPE samples are preferable for clinical cancer genomic profiling tests. For convenience, we created a quick reference table for calculating the required number of FFPE slides.

Keywords: cancer genomic profiling tests; formalin-fixed paraffin-embedded (FFPE) tumor tissue; genomic DNA extraction.

MeSH terms

  • DNA* / analysis
  • DNA* / chemistry
  • Genomics / methods
  • Humans
  • Japan
  • Neoplasms / genetics
  • Paraffin Embedding* / methods
  • Tissue Fixation* / methods

Substances

  • DNA