The Japanese Society of Pathology Guidelines on the handling of pathological tissue samples for genomic research: Standard operating procedures based on empirical analyses

Abstract

Genome research using appropriately collected pathological tissue samples is expected to yield breakthroughs in the development of biomarkers and identification of therapeutic targets for diseases such as cancers. In this connection, the Japanese Society of Pathology (JSP) has developed “The JSP Guidelines on the Handling of Pathological Tissue Samples for Genomic Research” based on an abundance of data from empirical analyses of tissue samples collected and stored under various conditions. Tissue samples should be collected from appropriate sites within surgically resected specimens, without disturbing the features on which pathological diagnosis is based, while avoiding bleeding or necrotic foci. They should be collected as soon as possible after resection: at the latest within about 3 h of storage at 4°C. Preferably, snap‐frozen samples should be stored in liquid nitrogen (about −180°C) until use. When intending to use genomic DNA extracted from formalin‐fixed paraffin‐embedded tissue, 10% neutral buffered formalin should be used. Insufficient fixation and overfixation must both be avoided. We hope that pathologists, clinicians, clinical laboratory technicians and biobank operators will come to master the handling of pathological tissue samples based on the standard operating procedures in these Guidelines to yield results that will assist in the realization of genomic medicine.

Detection of Disease-specific Fusion Genes of Soft Tissue Tumors Using Formalin-fixed Paraffin-embedded Tissues; Its Diagnostic Usefulness and Factors Affecting the Detection Rates

“…The results obtained in this study, the storage periods or decalcification, were similar to the data reported by Kanai et al 24 However, these published data do not indicate how much they can respond to the routine work in general hospitals or data comparing the detection rates between primary and metastatic lesions, biopsy and resected material, or the presence or absence of treatment history. In our study, it was indicated that the fusion genes of tumors showing relatively simple chromosomal abnormalities can be detected by selecting FFPE blocks with short-storage periods and nondecalcification even at general hospitals.…”

Feasibility of methylome analysis using small amounts of genomic DNA from formalin‐fixed paraffin‐embedded tissue

“…Both of the patients provided written informed consent to the use of their materials. The tissue samples were immediately frozen and stored in liquid nitrogen in order to retain their quality, in accordance with the guidelines of the Japanese Society of Pathology . Then, also in accord with the same guidelines, surgical specimens were routinely fixed in 10% neutral buffered formalin for 1 to 3 days, cut and embedded in paraffin for routine pathological diagnosis.…”

“…The tissue samples were immediately frozen and stored in liquid nitrogen in order to retain their quality, in accordance with the guidelines of the Japanese Society of Pathology . Then, also in accord with the same guidelines, surgical specimens were routinely fixed in 10% neutral buffered formalin for 1 to 3 days, cut and embedded in paraffin for routine pathological diagnosis. After about 5 years of storage of the FFPE blocks at room temperature, the genomic DNA was extracted from 10 μm‐thick sections of the FFPE samples using a GeneRead DNA FFPE Kit (QIAGEN, Hilden, Germany).…”

Decalcification can cause the failure of BRAF molecular analyses and anti‐BRAFV600E VE1 immunohistochemistry

“…The guidelines of the Japanese Society of Pathology on the handling of pathological tissue samples recommends that the use of ethylenediaminetetraacetic acid must be favored for calcified samples that could required genomic analyses and also mentions that rapid decalcification must be avoided. 9 The rapid bone decalcifier solution used in our study may highly explain the failure of molecular analyses (i.e. NGS and Idylla) in our study.…”

“…Bone tumor samples having been decalcified during preanalytical processing also consist in “molecularly challenging“ samples because the decalcification process could result in poor DNA quality/extraction impairing mutation analysis (as for cases #1D, #2B, #3C, #4A in our study). The guidelines of the Japanese Society of Pathology on the handling of pathological tissue samples recommends that the use of ethylenediaminetetraacetic acid must be favored for calcified samples that could required genomic analyses and also mentions that rapid decalcification must be avoided . The rapid bone decalcifier solution used in our study may highly explain the failure of molecular analyses (i.e.…”