Histopathological factors affecting the extraction of high quality genomic DNA from tissue sections for next-generation sequencing
| Autor: | Yukiko Abe, Takayuki Yoshino, Takeharu Yamanaka, Kentaro Yamazaki, Shogo Nomura, Yutaka Suzuki, Masaya Sugiyama, Hideaki Bando, Satoshi Yuki, Tomohiro Nishina, Katsuya Tsuchihara, Kohei Shitara, Eiji Shinozaki, Kiwamu Akagi, Nao Nishida, Sachiyo Mimaki, Yasuhiro Koh, Kensei Yamaguchi, Koutatsu Matsushima, Masashi Mizokami, Kei Muro, Hiroyasu Esumi, Atsushi Ohtsu, Satoshi Fujii, Chikako Nakai |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Pathology medicine.medical_specialty Genomics Biology General Biochemistry Genetics and Molecular Biology DNA sequencing law.invention 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine law Microtome medicine General Pharmacology Toxicology and Pharmaceutics General Neuroscience Cancer General Medicine Articles medicine.disease genomic DNA 030104 developmental biology chemistry 030220 oncology & carcinogenesis Biomarker (medicine) Macrodissection DNA |
| Popis: | 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 |
| Databáze: | OpenAIRE |
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