Histopathological factors affecting the extraction of high quality genomic DNA from tissue sections for next‑generation sequencing

Fujii,Satoshi; Yoshino,Takayuki; Yamazaki,Kentaro; Muro,Kei; Yamaguchi,Kensei; Nishina,Tomohiro; Yuki,Satoshi; Shinozaki,Eiji; Shitara,Kohei; Bando,Hideaki; Mimaki,Sachiyo; Nakai,Chikako; Matsushima,Koutatsu; Suzuki,Yutaka; Akagi,Kiwamu; Yamanaka,Takeharu; Nomura,Shogo; Esumi,Hiroyasu; Sugiyama,Masaya; Nishida,Nao; Mizokami,Masashi; Koh,Yasuhiro; Abe ,Yukiko; Ohtsu,Atsushi; Tsuchihara,Katsuya

doi:10.3892/br.2019.1235

October-2019 Volume 11 Issue 4

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October-2019 Volume 11 Issue 4

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Article

Histopathological factors affecting the extraction of high quality genomic DNA from tissue sections for next‑generation sequencing

Authors:
- Satoshi Fujii
- Takayuki Yoshino
- Kentaro Yamazaki
- Kei Muro
- Kensei Yamaguchi
- Tomohiro Nishina
- Satoshi Yuki
- Eiji Shinozaki
- Kohei Shitara
- Hideaki Bando
- Sachiyo Mimaki
- Chikako Nakai
- Koutatsu Matsushima
- Yutaka Suzuki
- Kiwamu Akagi
- Takeharu Yamanaka
- Shogo Nomura
- Hiroyasu Esumi
- Masaya Sugiyama
- Nao Nishida
- Masashi Mizokami
- Yasuhiro Koh
- Yukiko Abe
- Atsushi Ohtsu
- Katsuya Tsuchihara
View Affiliations / Copyright

Affiliations: Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba 277‑8577, Japan, Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba 277‑8577, Japan, Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Nagaizumi, Shizuoka 411‑8777, Japan, Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Aichi 464‑8681, Japan, Department of Gastrointestinal Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo 135‑0063, Japan, Department of Gastrointestinal Medical Oncology, National Hospital Organization Shikoku Cancer Center, Matsuyama, Ehime 791‑0280, Japan, Department of Gastroenterology and Hepatology, Hokkaido University Hospital, Sapporo, Hokkaido 060‑8648, Japan, Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba 277‑8577, Japan, G&G Science Co. Ltd., Fukushima 960‑1242, Japan, Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277‑8562, Japan, Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362‑0806, Japan, Department of Biostatistics, Yokohama City University School of Medicine, Yokohama, Kanagawa 236‑0004, Japan, Biostatistics Division, Center for Research and Administration and Support, National Cancer Center, Kashiwa, Chiba 277‑8577, Japan, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278‑0022, Japan, Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba 277‑8516, Japan, Third Department of Internal Medicine, Wakayama Medical University, Wakayama 641‑8509, Japan, National Cancer Center Hospital East, Kashiwa, Chiba 277‑8577, Japan
Pages: 171-180
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Published online on: August 21, 2019

https://doi.org/10.3892/br.2019.1235
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Abstract

To enable the widespread application of genomic medicine, the extraction of genomic DNA from thin sections of archived formalin‑fixed and paraffin‑embedded (FFPE) tissue blocks for next‑generation sequencing (NGS) is often necessary. However, there are currently no guidelines available on which specific regions of the microtome sections to use for macrodissection with respect to the histopathological factors observed under microscopic examination. The aim of this study was to clarify the relationship between histopathological factors and DNA quality, and to standardize the macrodissection method for more efficient implementation of NGS. FFPE tissue specimens of 218 patients from the Biomarker Research for Anti‑EGFR Monoclonal Antibodies by Comprehensive Cancer Genomics study were used to investigate the relationship between 15 histopathological factors and the quantitative ratio of double‑stranded DNA (dsDNA) to total nucleic acids, as well as the ∆ crossing point value of each tissue specimen. Multivariate logistic regression analysis revealed that specimen storage of ≥3 years was negatively associated with dsDNA quality (P=0.0007, OR: 4.30, 95% CI: 1.85‑10.04). In contrast, the presence of a mucus pool was positively associated with dsDNA quality (P=0.0308, OR: 0.23, 95% CI: 0.06‑0.87). Metastatic tumors and longer specimen storage periods were significantly associated with lower ∆Cp values (P=0.0007, OR: 4.43, 95% CI: 1.87‑10.49; and P=0.0003, OR: 5.51, 95% CI: 2.18‑13.95, respectively). Therefore, macrodissection should not be performed on specimens exhibiting histopathological factors associated with poor DNA quality. In particular, the use of tissue blocks with a storage period of <3 years allows the extraction of genomic DNA suitable for NGS.

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Journals

International Journal of Molecular Medicine

International Journal of Oncology

Molecular Medicine Reports

Oncology Reports

Experimental and Therapeutic Medicine

Oncology Letters

Biomedical Reports

Molecular and Clinical Oncology

World Academy of Sciences Journal

International Journal of Functional Nutrition

International Journal of Epigenetics

Medicine International

Histopathological factors affecting the extraction of high quality genomic DNA from tissue sections for next‑generation sequencing

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Abstract

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