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Hidaka M, Iwaizumi M, Taniguchi T, Baba S, Osawa S, Sugimoto K, Maekawa M. Pure somatic pathogenic variation profiles for patients with serrated polyposis syndrome: a case series. BMC Res Notes 2022; 15:350. [PMID: 36419139 PMCID: PMC9682711 DOI: 10.1186/s13104-022-06245-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE The serrated pathway is a distinct genetic/epigenetic mechanism of the adenoma-carcinoma sequence in colorectal carcinogenesis. Although many groups have reported the genetic-phenotypic correlation of serrated lesions (SLs), previous studies regarding the serrated pathway were conducted on patients with SLs that have different germline and environmental genetic backgrounds. We aimed to compare pure somatic genetic profiles among SLs within identical patient with SPS. RESULTS We analyzed SLs from one patient with SPS (Case #1) and compared DNA variant profiles using targeted DNA multigene panels via NGS among the patient's hyperplastic polyp (HP), three sessile serrated lesions (SSLs), and one traditional serrated adenoma (TSA), and separately analyzed three SSLs and one tubular adenoma (TA) within another patient with SPS (Case #2). In two patients, known pathogenic variant of BRAF (c.1799 T > A, p.Val600Glu) was observed in one TSA and one SSL in Case #1, and in three SSLs within Case #2. The pure somatic pathogenic variant BRAF (c.1799 T > A, p.Val600Glu) among SLs with identical germline genetic background supports its importance as a strong contributor for SLs.
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Affiliation(s)
- Misaki Hidaka
- grid.505613.40000 0000 8937 6696Department of Laboratory Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu, 431-3192 Japan
| | - Moriya Iwaizumi
- grid.505613.40000 0000 8937 6696Department of Laboratory Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu, 431-3192 Japan
| | - Terumi Taniguchi
- grid.505613.40000 0000 8937 6696Department of Laboratory Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu, 431-3192 Japan
| | - Satoshi Baba
- grid.471533.70000 0004 1773 3964Department of Diagnostic Pathology, Hamamatsu University Hospital, Hamamatsu, Japan
| | - Satoshi Osawa
- grid.505613.40000 0000 8937 6696Department of Endoscopic and Photodynamic Medicine, Hamamatsu University of School of Medicine, Hamamatsu, Japan
| | - Ken Sugimoto
- grid.505613.40000 0000 8937 6696First Department of Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masato Maekawa
- grid.505613.40000 0000 8937 6696Department of Laboratory Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu, 431-3192 Japan
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Maekawa M, Taniguchi T, Nishio K, Sakai K, Matsushita K, Nakatani K, Ishige T, Ikejiri M, Nishihara H, Sunami K, Yatabe Y, Hatanaka KC, Hatanaka Y, Yamamoto Y, Fukuyama K, Oda S, Saito K, Yokomura M, Kubo Y, Sato H, Tanaka Y, Fuchioka M, Yamasaki T, Matsuda K, Kurachi K, Funai K, Baba S, Iwaizumi M. Precision cancer genome testing needs proficiency testing involving all stakeholders. Sci Rep 2022; 12:1494. [PMID: 35087199 PMCID: PMC8795413 DOI: 10.1038/s41598-022-05589-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 01/13/2022] [Indexed: 01/17/2023] Open
Abstract
To implement precision oncology, analytical validity as well as clinical validity and utility are important. However, proficiency testing (PT) to assess validity has not yet been systematically performed in Japan. To investigate the quality of next-generation sequencing (NGS) platforms and cancer genome testing prevalent in laboratories, we performed pilot PT using patient samples. We prepared genomic DNA from the cancer tissue and peripheral blood of 5 cancer patients and distributed these to 15 laboratories. Most participating laboratories successfully identified the pathogenic variants, except for two closely located KRAS variants and 25 bp delins in EGFR. Conversely, the EGFR L858R variant was successfully identified, and the allele frequency was similar for all the laboratories. A high DNA integrity number led to excellent depth and reliable NGS results. By conducting this pilot study using patient samples, we were able to obtain a glimpse of the current status of cancer genome testing at participating laboratories. To enhance domestic cancer genome testing, it is important to conduct local PT and to involve the parties concerned as organizers and participants.
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Affiliation(s)
- Masato Maekawa
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan.
| | - Terumi Taniguchi
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Sayama, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Sayama, Japan
| | | | - Kaname Nakatani
- Department of Clinical Laboratory, Mie University Hospital, Tsu, Japan
- Iga City General Hospital, Iga, Japan
| | - Takayuki Ishige
- Department of Laboratory Medicine, Chiba University Hospital, Chiba, Japan
| | - Makoto Ikejiri
- Department of Clinical Laboratory, Mie University Hospital, Tsu, Japan
| | - Hiroshi Nishihara
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Kuniko Sunami
- Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Kanako C Hatanaka
- Center for Development of Advanced Diagnostics, Hokkaido University Hospital, Sapporo, Japan
| | - Yutaka Hatanaka
- Center for Development of Advanced Diagnostics, Hokkaido University Hospital, Sapporo, Japan
- Research Division of Genome Companion Diagnostics, Hokkaido University Hospital, Sapporo, Japan
| | - Yoshihiro Yamamoto
- Department of Clinical Oncology, Kyoto University Hospital, Kyoto, Japan
| | - Keita Fukuyama
- Department of Clinical Oncology, Kyoto University Hospital, Kyoto, Japan
| | - Shinya Oda
- Cancer Genetics Laboratory, Clinical Research Institute, National Hospital Organization, Kyushu Cancer Center, Fukuoka, Japan
| | - Kayoko Saito
- Institute of Medical Genetics, Tokyo Women's Medical Genetics, Tokyo, Japan
| | - Mamoru Yokomura
- Institute of Medical Genetics, Tokyo Women's Medical Genetics, Tokyo, Japan
| | - Yuji Kubo
- Genetic Analysis Department, Tsukiji Registered Clinical Laboratory, Riken Genesis Co., Ltd., National Cancer Center, Tokyo, Japan
| | - Hiroko Sato
- Genetic Analysis Department, Kawasaki Registered Clinical Laboratory, RIKEN Genesis Co., Ltd., Life Innovation Center, Kawasaki, Japan
| | - Yoshinori Tanaka
- Genetic Analysis Department, Kawasaki Registered Clinical Laboratory, RIKEN Genesis Co., Ltd., Life Innovation Center, Kawasaki, Japan
| | - Misa Fuchioka
- Genetic & Pathology Department, SRL, Inc., Hachioji, Japan
| | | | - Koichiro Matsuda
- Molecular Genetic Analysis Department, Advanced Technology Center, LSI Medience Corporation, Tokyo, Japan
| | - Kiyotaka Kurachi
- Second Department of Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuhiro Funai
- First Department of Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Satoshi Baba
- Department of Diagnostic Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Moriya Iwaizumi
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
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