An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections

Utako Oba, Kenichi Kohashi, Yuhei Sangatsuda, Yoshinao Oda, Koh Hei Sonoda, Shouichi Ohga, Koji Yoshimoto, Yasuhito Arai, Shinichi Yachida, Tatsuhiro Shibata, Takashi Ito, Fumihito Miura

研究成果: ジャーナルへの寄稿学術誌査読

抄録

With the advent of new molecular diagnostic techniques, retrieving DNA from the formalin-fixed paraffin-embedded (FFPE) tissues has become an essential yet challenging step for efficient downstream processes. Owing to low quality and quantity of DNA retrieved from the FFPE sections, the process is often impractical and needs significant improvements. Here, we established an efficient method for the purification of DNA from FFPE specimens by optimizing incubation temperature, incubation time, and the concentration of a formalin scavenger tris(hydroxymethyl)aminomethane (Tris) for reverse-crosslinking. The optimized method, named "Highly concentrated Tris-mediated DNA extraction"(HiTE), yielded three times the DNA yield per tissue slice compared with a representative DNA extraction kit. Moreover, the use of HiTE-extracted DNA increased the yield of the sequencing library three times and accordingly yielded a log higher and more reproducible sequencing library compared with that obtained using the commonly used commercial kit. The sequencing library prepared from HiTE-extracted FFPE-DNA had longer inserts and produced reads that evenly covered the reference genome. Successful application of HiTE-extracted FFPE-DNA for whole-genome and targeted gene panel sequencing indicates its practical usability.

本文言語英語
論文番号bpac014
ジャーナルBiology Methods and Protocols
7
1
DOI
出版ステータス出版済み - 2022

!!!All Science Journal Classification (ASJC) codes

  • 生化学、遺伝学、分子生物学(全般)
  • 農業および生物科学(全般)

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