Robustness of a Cancer Profiling Test Using Formalin-fixed Paraffin Embedded Tumor Specimens

Anticancer Res. 2021 Mar;41(3):1341-1348. doi: 10.21873/anticanres.14891.


Background/aim: Cancer profiling tests using formalin-fixed paraffin-embedded (FFPE) specimens with various conditions have become an essential tool for cancer treatment. The robustness of these tests needs to be addressed.

Materials and methods: A cancer profiling test, NCC oncopanel, was tested with FFPE specimens from various tissues with different storage conditions and fixation lengths. Next generation sequencing was performed with Miseq and the data were assembled using the human reference genome hg19.

Results: Duration of storage and fixation affected the mapping statistics. Prolonged storage increased outward read paring and longer fixation rates caused increased singletons and unmapped reads.

Conclusion: Our results indicate that a cancer profiling test with target capturing method, NCC oncopanel, shows robustness for FFPE cancer specimens with various storage conditions.

Keywords: Cancer profiling test; formalin-fixed paraffin-embedded samples; next generation sequencing.

MeSH terms

  • Fixatives / chemistry
  • Formaldehyde / chemistry
  • Gene Expression Profiling / methods*
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Mutation
  • Neoplasms / genetics*
  • Neoplasms / pathology
  • Paraffin Embedding / methods*
  • Specimen Handling / methods*
  • Tissue Fixation / methods*


  • Fixatives
  • Formaldehyde