Annual Report 2024
Department of Clinical Genomics
Kouya Shiraishi, Masahiro Gotoh, Masaru Katoh, Hanako Ono, Takashi Kubo, Mineko Ushiama
Introduction
The aim of the Department of Clinical Genomics is to contribute to the improvement of genomic medicine for cancer patients through the development and implementation of next-generation sequencing (NGS)-based genomic tests and the identification of novel pathogenic variants and biomarkers from NGS analyses of cancer patient genomes. We provide genomic analysis services as a part of the core facility functions of the Fundamental Innovative Oncology Core (FIOC) of the National Cancer Center Research Institute (NCCRI). In collaboration with the Department of Biobank, we perform genome, transcriptome, and methylation analyses using clinical specimens as a one-stop service to support clinicians and basic researchers in their research.
The Team and What We Do
The purpose of the team is to provide genomic analysis support at the request of clinicians and researchers.
Research Activities
1. Research support for researchers and clinicians
The Department of Clinical Genomics provides technical support for genome analysis using clinical samples to clinicians and researchers affiliated with hospitals and research institutes inside and outside the center. In FY2024, we published 9 papers related to research support in peer-reviewed international journals. As part of our support for writing papers, we provided technical guidance on bioinformatics using R and Python and assisted with the creation of figures on behalf of clinicians and researchers.
2. Core facility genomic analysis services
We provide next-generation sequencing analysis services as part of the core facility function of the NCCR FIOC. In FY2024, we received 57 requests for genome analysis support from clinicians and researchers and performed whole-exome/whole-genome sequencing or transcriptome analysis of 2,956 samples. We also returned a wide range of analysis results, including somatic mutation detection, copy number analysis, and gene expression analysis, to clinicians and researchers.
3. Support for genome analysis using publicly available genome information
We provided data analysis support using public databases (Project GENIE, cBioPortal, and C-CAT), which contributed to the acceptance of multiple research papers. We also advanced efforts to accumulate genomic data obtained from the NCC Biobank and established foundational information for the construction of the database.
Education
The Department of Clinical Genomics has accepted three graduate students as trainees.
Future Prospects
Having established a system to support genome analysis using clinical specimens, we plan to promote collaborative clinical research with companies in the future. We will continue to provide support for genome analysis in response to the needs of clinicians and researchers. Furthermore, we will focus on dry analysis and the training of personnel to perform it.
List of papers published in 2024
Journal
1. Sekita T, Asano N, Kubo T, Totsuka H, Mitani S, Hattori N, Yoshida A, Kobayashi E, Komiyama M, Ushijima T, Nakayama R, Nakamura M, Kawai A, Ichikawa H. Early separation and parallel clonal selection of dedifferentiated and well-differentiated components in dedifferentiated liposarcoma. Neoplasia (New York, N.Y.), 59:101074, 2025
2. Fujii E, Kato MK, Ono H, Yamaguchi M, Higuchi D, Koyama T, Komatsu M, Hamamoto R, Ishikawa M, Kato T, Kohno T, Shiraishi K, Yoshida H. TP53 Mutations and PD-L1 Amplification in Vulvar Adenocarcinoma of the Intestinal Type: Insights From Whole Exome Sequencing of 2 Cases. International journal of gynecological pathology, 44:358-363, 2025
3. Kitadai R, Yazaki S, Kuchiba A, Yamanaka T, Shiino S, Yamauchi C, Harano K, Saito M, Hirotsu Y, Aiba H, Yoshida T, Hamamoto R, Shimizu C, Shimomura A, Kojima Y, Shimoi T, Momozawa Y, Sudo K, Yoshida M, Sunami K, Hori M, Katanoda K, Shimada Y, Yamashita Y, Kogawa T, Murata T, Fujiwara S, Miyagi Y, Nakagomi H, Tachibana K, Omata M, Ohtake T, Suto A, Onishi T, Naito Y, Yamashita T, Yonemori K, Kohno T, Shiraishi K. Germline Pathogenic Variants and Clinical Outcomes in Asian Patients With Breast Cancer. Cancer science, 116:1048-1058, 2025
4. Kubo T, Sunami K, Koyama T, Kitami M, Fujiwara Y, Kondo S, Yonemori K, Noguchi E, Morizane C, Goto Y, Maejima A, Iwasa S, Hamaguchi T, Kawai A, Namikawa K, Arakawa A, Sugiyama M, Ohno M, Yoshida T, Hiraoka N, Yoshida A, Yoshida M, Nishino T, Furukawa E, Narushima D, Nagai M, Kato M, Ichikawa H, Fujiwara Y, Kohno T, Yamamoto N. The impact of rare cancer and early-line treatments on the benefit of comprehensive genome profiling-based precision oncology. ESMO open, 9:102981, 2024
5. Fujii E, Kato MK, Yamaguchi M, Higuchi D, Koyama T, Komatsu M, Hamamoto R, Ishikawa M, Kato T, Kohno T, Shiraishi K, Yoshida H. Genomic profiles of Japanese patients with vulvar squamous cell carcinoma. Scientific reports, 14:13058, 2024
6. Nakahara M, Ushiama M, Tanabe N, Gotoh M, Sakamoto H, Yoshida T, Hirata M. Multi-gene panel analysis in BRCA1/2-negative patients suspected of hereditary breast and ovarian cancer syndrome: Real-world data from a single institution. The journal of obstetrics and gynaecology research, 50:1591-1597, 2024
7. Fujiwara Y, Takahashi RU, Saito M, Umakoshi M, Shimada Y, Koyama K, Yatabe Y, Watanabe SI, Koyota S, Minamiya Y, Tahara H, Kono K, Shiraishi K, Kohno T, Goto A, Tsuchiya N. Oncofetal IGF2BP3-mediated control of microRNA structural diversity in the malignancy of early-stage lung adenocarcinoma. Proceedings of the National Academy of Sciences of the United States of America, 121:e2407016121, 2024
8. Nishino T, Yumura M, Sunami K, Kubo T, Ichikawa H, Yasuda T, Furukawa E, Nagai M, Yatabe Y, Kato M, Kohno T. Leveraging non-coding regions to guarantee the accuracy of small-sized panel-based tumor mutational burden estimates. Cancer science, 115:4045-4053, 2024
9. Suzuki Y, Iemura R, Sutani A, Mizuno Y, Adachi E, Ushiama M, Yoshida T, Hirata M, Hoshino A, Yamomoto K, Akashi T, Nakano Y, Isoda T, Takasawa K, Kato M, Takagi M, Okamoto K, Morio T, Kashimada K. Familial and early recurrent pheochromocytoma in a child with a novel in-frame duplication variant of VHL. Clinical pediatric endocrinology, 33:229-237, 2024