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Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
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A sheet pocket to prevent cross-contamination of formalin-fixed paraffin-embedded block for application in next

Keiichi Iwaya1, Hisae Arai1, Nanao Takatou1

  • 1Department of Pathology, SASAKI Institute, Kyoundo Hospital, Chiyoda-ku, Tokyo, Japan.

Plos One
|May 4, 2022
PubMed

Insights

A novel sheet pocket effectively prevents cross-contamination during formalin-fixed paraffin-embedded (FFPE) block processing for next-generation sequencing. This innovation enhances the accuracy of translating histopathological data into genomic sequencing data.

Area of Science:

  • Biotechnology
  • Genomics
  • Pathology

Background:

  • Formalin-fixed paraffin-embedded (FFPE) blocks are crucial biomaterials for next-generation sequencing (NGS) in cancer research.
  • Cross-contamination in FFPE samples affects approximately 5% of DNA extractions, hindering the detection of genetic abnormalities.
  • Current methods for processing FFPE blocks lack effective solutions to prevent cellular mixing between specimens.

Purpose of the Study:

  • To evaluate novel sheet materials for their potential to prevent cell transmission during FFPE block processing.
  • To identify sheet materials that meet stringent International Organization for Standardization and Japanese Industrial Standards criteria.
  • To develop and test a sheet pocket designed to mitigate cross-contamination in FFPE samples for NGS.

Main Methods:

  • Screened 897 sheet materials based on six criteria: filter opening ≤5 μm, thickness ≤100 μm, chemical resistance, permeability ≥1.0 × 10-3 cm/s, water retention rate <200%, and cell transit test (≤2 cells/10 high-power fields).
  • Developed a sheet pocket using polyamide, polyethylene terephthalate, and polypropylene/polyethylene composite sheets that met all criteria.
  • Assessed the efficacy of the sheet pocket in preventing cell entry during FFPE block processing and its impact on hematoxylin and eosin staining.

Main Results:

  • Polyamide, polyethylene terephthalate, and polypropylene/polyethylene composite sheets satisfied all screening requirements.
  • The developed sheet pocket effectively blocked all cell types from entering during FFPE block processing.
  • No single cell from the cell pellet passed through the sheet pocket's outer layer.
  • Hematoxylin and eosin staining quality remained unaffected by the presence or absence of the sheet pocket.

Conclusions:

  • The novel sheet pocket is effective in preventing cross-contamination when processing FFPE blocks for next-generation sequencing.
  • This technology supports the precise translation of histopathological data into genome sequencing data in pathology laboratories.
  • The developed sheet pocket offers a practical solution to a significant challenge in FFPE sample preparation for molecular diagnostics.

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