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Related Experiment Video

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Formalin-fixed paraffin-embedded sample conditions for deep next generation sequencing.

Masayuki Nagahashi1, Yoshifumi Shimada1, Hiroshi Ichikawa1

  • 1Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata City, Niigata, Japan.

The Journal of Surgical Research
|November 29, 2017
PubMed
Summary

High-quality DNA suitable for next-generation sequencing (NGS) can be extracted from formalin-fixed paraffin-embedded (FFPE) cancerous tissue. This study confirms FFPE samples, including biopsies, yield sufficient DNA for precision medicine applications in oncology.

Keywords:
BiopsyDNAFFPENext generation sequencingPrecision medicineSurgically resected specimen

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Area of Science:

  • Oncology
  • Molecular Biology
  • Genetics

Background:

  • Precision medicine in oncology relies on sequencing targetable genes from fragmented DNA.
  • Formalin-fixed paraffin-embedded (FFPE) samples are a common source of DNA but present challenges for sequencing.
  • Next-generation sequencing (NGS) requires high-quality and sufficient quantity DNA for accurate analysis.

Purpose of the Study:

  • To evaluate the quality and quantity of DNA extracted from FFPE cancerous tissue.
  • To determine the suitability of DNA from FFPE samples for NGS applications in clinical oncology.

Main Methods:

  • DNA was extracted from FFPE tissue sections of breast, colorectal, and gastric cancers (surgical and biopsy specimens).
  • DNA quantity was assessed, with ≥60 ng considered adequate for NGS.
  • DNA quality was determined using Q-ratios, with >0.1 deemed sufficient for NGS.

Main Results:

  • Neutral-buffered formalin resulted in significantly better DNA Q-ratios compared to unbuffered formalin.
  • All tested FFPE samples yielded sufficient DNA quantity and quality for NGS.
  • Gastric cancer FFPE samples prepared within 7 years were suitable for NGS; older samples may not be.

Conclusions:

  • Formalin type and sample age impact FFPE DNA quality for NGS.
  • Adequate DNA can be extracted from both surgical and biopsy FFPE specimens.
  • These findings support the expanded use of NGS in clinical oncology settings for FFPE samples.