Effective Preparation of FFPE Tissue Samples for Preserving Appropriate Nucleic Acid Quality for Genomic Analysis in Thyroid Carcinoma

Yoichiro Okubo ¹, Nagisa Toyama ², Rika Kasajima ³

¹Department of Pathology, Kanagawa Cancer Center, 2-3-2, Nakao, Asahi-Ku, Yokohama, Kanagawa, 241-8515, Japan. yoichiro0207@hotmail.com.
²Department of Pathology, Kanagawa Cancer Center, 2-3-2, Nakao, Asahi-Ku, Yokohama, Kanagawa, 241-8515, Japan.
³Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, 2-3-2, Nakao, Asahi-Ku, Yokohama, Kanagawa, 241-8515, Japan.
⁴Department of Endocrine Surgery, Kanagawa Cancer Center, 2-3-2, Nakao, Asahi-Ku, Yokohama, Kanagawa, 241-8515, Japan.
⁵Department of Pathology, Yokohama Municipal Citizen's Hospital, 1-1 Mitsuzawanishimachi, Kanagawa-Ku, Yokohama, Kanagawa, 221-0855, Japan.
⁶Department of Cancer Genome Medicine, Kanagawa Cancer Center, 2-3-2, Nakao, Asahi-Ku, Yokohama, Kanagawa, 241-8515, Japan.
⁷Advanced Cancer Therapeutics Division, Kanagawa Cancer Center Research Institute, 2-3-2, Nakao, Asahi-Ku, Yokohama, Kanagawa, 241-8515, Japan.
⁸Department of Genetic Medicine, Cancer Prevention and Cancer Control Division, Kanagawa Cancer Center Research Institute, 2-3-2, Nakao, Asahi-Ku, Yokohama, Kanagawa, 241-8515, Japan.
⁹Cancer Prevention and Cancer Control Division, Kanagawa Cancer Center Research Institute, 2-3-2, Nakao, Asahi-Ku, Yokohama, Kanagawa, 241-8515, Japan.

⁰Department of Pathology, Kanagawa Cancer Center, 2-3-2, Nakao, Asahi-Ku, Yokohama, Kanagawa, 241-8515, Japan. yoichiro0207@hotmail.com.

Endocrine Pathology +

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November 19, 2024

View abstract on PubMed

Summary

This study presents an improved method for preparing formalin-fixed paraffin-embedded (FFPE) tissue samples, enhancing nucleic acid quality for thyroid carcinoma genomic analysis. Separately fixed samples and lymph node metastases show superior reliability for molecular profiling.

Area Of Science

Oncology
Genomics
Pathology

Background

Formalin-fixed paraffin-embedded (FFPE) tissues are crucial for genomic analysis in thyroid carcinomas, guiding targeted therapies.
Preserving nucleic acid quality in FFPE samples is essential for accurate genomic profiling.

Purpose Of The Study

To develop and validate a superior technique for preparing FFPE tissue samples to maximize nucleic acid quality.
To assess the impact of specimen type and preparation methods on DNA and RNA integrity.

Main Methods

Analysis of surgically resected thyroid tumors, lymph node metastases, and separately fixed samples.
Optimization of formalin fixation protocols.
Assessment of nucleic acid quality using indicators like DNA integrity number, cycle threshold ratio, RNA integrity number, and DV200.

Main Results

Separately fixed tumor samples demonstrated significantly higher DNA and RNA quality compared to conventionally processed samples.
Lymph node metastases exhibited nucleic acid quality comparable or superior to primary thyroid tumors.
Established quality indicators reliably reflect nucleic acid preservation.

Conclusions

Preparing separately fixed tumor samples is an effective strategy for preserving DNA and RNA quality for genomic analysis.
Lymph node metastases are a reliable source for comprehensive genetic profiling of thyroid carcinomas.
The developed method, utilizing biopsy punches, is adaptable for general medical practice, improving access to high-quality pathological samples.

Keywords:

Formalin-fixed paraffin-embedded Genomic analysis Nucleic acid quality Thyroid carcinoma