Estimation of age-related DNA degradation from formalin-fixed and paraffin-embedded tissue according to the extraction methods

Mototsugu Watanabe, Shinsuke Hashida, Hiromasa Yamamoto, Takehiro Matsubara, Tomoaki Ohtsuka, Ken Suzawa, Yuho Maki, Junichi Sou, Hiroaki Asano, Kazunori Tsukuda, Shinichi Toyooka, Shinichiro Miyoshi

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Techniques for the extraction and use of nucleic acids from formalin-fixed and paraffin-embedded (FFPE) tissues, preserved over long time periods in libraries, have been developed. However, DNA extracted from FFPE tissues is generally damaged, and long-term storage may affect DNA quality. Therefore, it is important to elucidate the effect of long-term storage on FFPE tissues and evaluate the techniques used to extract DNA from them. In the present study, the yield, purity, and integrity of DNA in FFPE tissue samples was evaluated. Two DNA extraction techniques were used: A silica-binding DNA collection method using QIAamp DNA FFPE Tissue kit (QIA) and a total tissue DNA collection method using a WaxFree DNA extraction kit (WAX). A total of 25 FFPE tissues from lung adenocarcinomas were studied, which had been surgically resected and fixed at Okayama University Hospital prior to examination and subsequent storage at room temperature for 0.5, 3, 6, 9 and 12 years. Extracted DNA was quantified using ultraviolet absorbance, fluorescent dye, and quantitative polymerase chain reaction (qPCR). The quality of the DNA was defined by the absorbance ratio of 260 to 280 nm (A260/280) and Q-score, which is the quantitative value of qPCR product size ratio. The results demonstrated that the yield of total DNA extracted using WAX was significantly greater than when QIA was used (P<0.01); however, DNA extracted using WAX included more contaminants and was significantly more fragmented compared with DNA extracted using QIA (P<0.01). Aging had no significant effect on absolute DNA yield or DNA purity, although it did significantly contribute to increased DNA degradation for both QIA and WAX extraction (QIA P=0.02, WAX P=0.03; 0.5 years vs. 3 years, QIA P<0.01, WAX P=0.03; 9 years vs. 12 years). Both extraction methods are viable depending on whether high yield or high quality of extracted DNA is required. However, due to the increased degradation with age, storage time limits the available DNA in FFPE tissues regardless of the extraction method.

Original languageEnglish
Pages (from-to)2683-2688
Number of pages6
JournalExperimental and Therapeutic Medicine
Volume14
Issue number3
DOIs
Publication statusPublished - 2017

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Paraffin
Formaldehyde
DNA
Polymerase Chain Reaction
Fluorescent Dyes
Silicon Dioxide
Nucleic Acids
Libraries

Keywords

  • DNA extraction
  • Formalin-fixed and paraffin-embedded
  • QIAamp kit
  • Quality check
  • WaxFree DNA extraction kit

ASJC Scopus subject areas

  • Medicine(all)
  • Immunology and Microbiology (miscellaneous)
  • Cancer Research

Cite this

Estimation of age-related DNA degradation from formalin-fixed and paraffin-embedded tissue according to the extraction methods. / Watanabe, Mototsugu; Hashida, Shinsuke; Yamamoto, Hiromasa; Matsubara, Takehiro; Ohtsuka, Tomoaki; Suzawa, Ken; Maki, Yuho; Sou, Junichi; Asano, Hiroaki; Tsukuda, Kazunori; Toyooka, Shinichi; Miyoshi, Shinichiro.

In: Experimental and Therapeutic Medicine, Vol. 14, No. 3, 2017, p. 2683-2688.

Research output: Contribution to journalArticle

Watanabe, Mototsugu ; Hashida, Shinsuke ; Yamamoto, Hiromasa ; Matsubara, Takehiro ; Ohtsuka, Tomoaki ; Suzawa, Ken ; Maki, Yuho ; Sou, Junichi ; Asano, Hiroaki ; Tsukuda, Kazunori ; Toyooka, Shinichi ; Miyoshi, Shinichiro. / Estimation of age-related DNA degradation from formalin-fixed and paraffin-embedded tissue according to the extraction methods. In: Experimental and Therapeutic Medicine. 2017 ; Vol. 14, No. 3. pp. 2683-2688.
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