The Japanese Society of Pathology Practical Guidelines on the handling of pathological tissue samples for cancer genomic medicine

Pathol Int. 2021 Nov;71(11):725-740. doi: 10.1111/pin.13170. Epub 2021 Oct 6.


Clinical cancer genomic testing based on next-generation sequencing can help select genotype-matched therapy and provide diagnostic and prognostic information. Pathological tissue from malignant tumors obtained during routine practice are frequently used for genomic testing. This article is aimed to standardize the proper handling of pathological specimens in practice for genomic medicine based on the findings established in "Guidelines on the handling of pathological tissue samples for genomic medicine (in Japanese)" published by The Japanese Society of Pathology (JSP) in 2018. The two-part practical guidelines are based on empirical data analyses; Part 1 describes the standard preanalytic operating procedures for tissue collection, processing, and storage of formalin-fixed paraffin-embedded (FFPE) samples, while Part 2 describes the assessment and selection of FFPE samples appropriate for genomic testing, typically conducted by a pathologist. The guidelines recommend that FFPE sample blocks be used within 3 years from preparation, and the tumor content should be ≥30% (minimum 20%). The empirical data were obtained from clinical studies performed by the JSP in collaboration with leading Japanese cancer genome research projects. The Japanese Ministry of Health, Labour, and Welfare (MHLW) recommended to comply with the JSP practical guidelines in implementing cancer genomic testing under the national health insurance system in over 200 MHLW-designated core and cooperative cancer genome medicine hospitals in Japan.

Keywords: cancer genomic medicine; gene panel testing; next-generation sequencing; sample processing.

Publication types

  • Practice Guideline

MeSH terms

  • Genetic Testing / methods
  • Genetic Testing / standards*
  • Genomics / methods
  • Genomics / standards*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Japan
  • Neoplasms / genetics*
  • Neoplasms / pathology*
  • Specimen Handling / methods
  • Specimen Handling / standards*
  • Tissue Preservation / methods
  • Tissue Preservation / standards