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Nagahashi M, Shimada Y, Ichikawa H, Kameyama H, Takabe K, Okuda S, Wakai T. Next generation sequencing-based gene panel tests for the management of solid tumors. Cancer Sci 2019; 110:6-15. [PMID: 30338623 PMCID: PMC6317963 DOI: 10.1111/cas.13837] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 12/16/2022] Open
Abstract
Next generation sequencing (NGS) has been an invaluable tool to put genomic sequencing into clinical practice. The incorporation of clinically relevant target sequences into NGS-based gene panel tests has generated practical diagnostic tools that enable individualized cancer-patient care. The clinical utility of gene panel testing includes investigation of the genetic basis for an individual's response to therapy, such as signaling pathways associated with a response to specific therapies, microsatellite instability and a hypermutated phenotype, and deficiency in the DNA double-strand break repair pathway. In this review, we describe the concept of precision cancer medicine using target sequences in gene panel tests as well as the importance of the control of sample quality in routine NGS-based genomic testing. We describe geographic and ethnic differences in cancer genomes, and discuss issues that need to be addressed in the future based on our experiences in Japan.
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Affiliation(s)
- Masayuki Nagahashi
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Yoshifumi Shimada
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Hiroshi Ichikawa
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Hitoshi Kameyama
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Kazuaki Takabe
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
- Breast SurgeryRoswell Park Cancer InstituteBuffaloNew York
- Department of SurgeryThe State University of New York Jacobs School of Medicine and Biomedical SciencesUniversity at BuffaloBuffaloNew York
| | - Shujiro Okuda
- Division of BioinformaticsGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
| | - Toshifumi Wakai
- Division of Digestive and General SurgeryGraduate School of Medical and Dental SciencesNiigata UniversityNiigataJapan
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Nagahashi M, Shimada Y, Ichikawa H, Nakagawa S, Sato N, Kaneko K, Homma K, Kawasaki T, Kodama K, Lyle S, Takabe K, Wakai T. Formalin-fixed paraffin-embedded sample conditions for deep next generation sequencing. J Surg Res 2017; 220:125-132. [PMID: 29180174 PMCID: PMC5726294 DOI: 10.1016/j.jss.2017.06.077] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/26/2017] [Accepted: 06/28/2017] [Indexed: 12/16/2022]
Abstract
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.
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Affiliation(s)
- Masayuki Nagahashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata City, Niigata, Japan.
| | - Yoshifumi Shimada
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata City, Niigata, Japan
| | - Hiroshi Ichikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata City, Niigata, Japan
| | - Satoru Nakagawa
- Department of Surgery, Niigata Cancer Center Hospital, Niigata City, Niigata, Japan
| | - Nobuaki Sato
- Department of Breast Oncology, Niigata Cancer Center Hospital, Niigata City, Niigata, Japan
| | - Koji Kaneko
- Department of Breast Oncology, Niigata Cancer Center Hospital, Niigata City, Niigata, Japan
| | - Keiichi Homma
- Department of Pathology, Niigata Cancer Center Hospital, Niigata City, Niigata, Japan
| | - Takashi Kawasaki
- Department of Pathology, Niigata Cancer Center Hospital, Niigata City, Niigata, Japan
| | - Keisuke Kodama
- Diagnostics Research Department, Life innovation Research Institute, Denka innovation Center, Denka Co., Ltd, Machida City, Tokyo, Japan
| | - Stephen Lyle
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Boston, Massachusetts; KEW, Inc, Boston, Massachusetts
| | - Kazuaki Takabe
- Breast Surgery, Department of Surgical Oncology, Roswell Park Cancer Institute, Buffalo, New York; Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, New York
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata City, Niigata, Japan
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