Journal
JOURNAL OF SURGICAL RESEARCH
Volume 220, Issue -, Pages 125-132Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jss.2017.06.077
Keywords
Next generation sequencing; FFPE; DNA
Categories
Funding
- Denka Co., Ltd.
- Japan Society for the Promotion of Science (JSPS) [15H05676, 15K15471, 15H04927, 16K15610]
- Takeda Science Foundation
- NIH/NCI [R01CA160688]
- S.G. Komen Investigator Initiated Research grant [IIR12222224]
- Grants-in-Aid for Scientific Research [15H05676, 16K15610, 15K15471] Funding Source: KAKEN
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Introduction: Precision medicine is only possible in oncology practice if targetable genes in fragmented DNA, such as DNA from formalin-fixed paraffin-embedded (FFPE) samples, can be sequenced using next generation sequencing (NGS). The aim of this study was to examine the quality and quantity of DNA from FFPE cancerous tissue samples from surgically resected and biopsy specimens. Methods: DNA was extracted from unstained FFPE tissue sections prepared from surgically resected specimens of breast, colorectal and gastric cancer, and biopsy specimens of breast cancer. A total quantity of DNA >= 60 ng from a sample was considered adequate for NGS. The DNA quality was assessed by Q-ratios, with a Q-ratio >0.1 considered sufficient for NGS. Results: The Q-ratio for DNA from FFPE tissue processed with neutral-buffered formalin was significantly better than that processed with unbuffered formalin. All Q-ratios for DNA from breast, colorectal and gastric cancer samples indicated DNA levels sufficient for NGS. DNA extracted from gastric cancer FFPE samples prepared within the last 7 years is suitable for NGS analysis, whereas those older than 7 years may not be suitable. Our data suggested that adequate amounts of DNA can be extracted from FFPE samples, not only of surgically resected tissue but also of biopsy specimens. Conclusions: The type of formalin used for fixation and the time since FFPE sample preparation affect DNA quality. Sufficient amounts of DNA can be extracted from FFPE samples of both surgically resected and biopsy tissue, thus expanding the potential diagnostic uses of NGS in a clinical setting. (C) 2017 Elsevier Inc. All rights reserved.
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