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Fixation and Sectioning

Fixation and Sectioning

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Related Experiment Video

Updated: Oct 10, 2025

Author Spotlight: FISH as a Tool for Precise Gene Amplification Assessment in Cancer Specimens

Author Spotlight: FISH as a Tool for Precise Gene Amplification Assessment in Cancer Specimens

Published on: July 12, 2024

MicroSEC filters sequence errors for formalin-fixed and paraffin-embedded samples.

Masachika Ikegami^1,2,3, Shinji Kohsaka⁴, Takeshi Hirose^5,6

¹Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan. ikegami-tky@umin.ac.jp.

Communications Biology

|December 16, 2021

Summary

This summary is machine-generated.

Sequencing errors in formalin-fixed, paraffin-embedded tumor samples are caused by DNA microhomology. A new pipeline, MicroSEC, effectively filters these errors, improving clinical sequencing reliability for cancer research.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Clinical tumor sequencing commonly uses formalin-fixed, paraffin-embedded (FFPE) samples.
FFPE samples are prone to significant sequencing errors, complicating accurate genomic analysis.
These errors often manifest as chimeric reads stemming from single-strand DNA with microhomology.

Purpose of the Study:

To identify the source of sequencing errors in FFPE samples.
To develop a computational pipeline for filtering these errors.
To enhance the reliability of clinical tumor sequencing and cancer research using FFPE specimens.

Main Methods:

Investigated chimeric reads caused by single-strand DNA with microhomology.
Identified mutations introduced during the end-repair step of library preparation due to mis-annealing of homologous sequences.
Developed and implemented the MicroSEC filtering pipeline, focusing on uneven mutation distribution within reads.

Main Results:

MicroSEC effectively removes sequencing errors in FFPE samples.
The pipeline avoids over-eliminating true mutations found in fresh frozen samples.
Validated MicroSEC with amplicon-based sequencing, achieving 97% sensitivity and 96% specificity for 97 mutations.

Conclusions:

MicroSEC accurately filters sequencing errors originating from DNA microhomology in FFPE samples.
The pipeline enhances the diagnostic accuracy of clinical sequencing.
Improved FFPE sample analysis will advance cancer research and personalized medicine.