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Annual Report 2021

Division of Bioinformatics

Mamoru Kato, Jo Nishino, Daichi Narushima, Eisaku Furukawa, Iurii Nagornov, Momoko Nagai, Ritsuko Onuki, Yoko Iwahara, Hanako Ono

Introduction

 The activities of the Division of Bioinformatics are as follows: (1) development of new bioinformatics methods and data analysis for cancer research and medicine, (2) building new mathematical theories in biology through data analysis and computational approaches, and (3) bioinformatics analysis for experimental groups at this Center as well as other research institutions.

Research activities

1.  Development of bioinformatics technologies for cancer genome medicine

 We previously developed a clinical sequencing caller, cisCall, which has been used in the NCC Oncopanel. This fiscal year, developing and testing new methods, we improved cisCall as follows:

  • For the NCC Oncopanel, improvement of mutation detection and copy number analysis methods, and implementation of structural variant (SV) detection. These improvements were approved by the government as Partial Changes in the Medical Device Manufacturing Approval.
  • Update of the public version of cisCall
  • Performance evaluation of the mutation detection method based on deep learning. Some verifications, such as the number of mutations to reach an F-value of over 0.9
  • Performance evaluation of the mutation detection method with molecular barcode sequencing
  • Performance enhancement of the mutation detection with pseudo-molecular barcodes generated computationally
  • Development of software to detect structural variants in the germline
  • Development of a pipeline for the whole genome analysis
  • Development of a cloud infrastructure for accelerating the calling calculations

2.  Development of numerical simulation-based personalized medicine

 We have developed tugHall, which is a simulator to simulate cancer cell evolution in the context of personalized medicine. This fiscal year, we developed a new tugHall version which includes calculation of copy number alterations (duplications and deletions) at the gene level.

3.  Bioinformatics analysis support

  • Biomarker analysis using clinical trial data for glioblastoma
  • Exome sequencing analysis of chemical-induced lung cancer using a mouse model
  • SNV/indel and CNA analyses of esophageal cancer patients from the Japan Clinical Oncology Group (JCOG), as well as pathway and GO analyses with the tumor mutations.
  • Multi-omics analysis of data released from working groups in Pan Cancer Analysis of Whole Genomes (PCAWG) and comparative analysis of PCAWG data and the data released from The Cancer Genome Atlas (TCGA).
  • ICGC clinico-genomic data analysis in stomach cancer
  • Mutational signature analysis of rats, mice and bacteria that were exposed to carcinogens.
  • Whole genome sequencing analysis of germinoma
  • Gene expression analysis of mouse colitis-derived models
  • Searching for potentially translated sequences in RNA for various species
  • Building a collaborative system and developing analysis methods with the Biostatistics Division of the Center for Research Administration and Support toward clinical research involving omics data
  • Monitoring the early stage of tumors using DNA barcodes
  • Building a new system for detecting DNA adducts using deep learning
  • Establishing a VUS functional estimation method utilizing the existing software

Education

 We have provided bioinformatics education and support for research groups in the NCC and other institutions.

Future Prospects

 We will continue to develop core bioinformatics technologies for cancer genome medicine and proceed toward the realization of precision medicine by transferring the technologies. We will also carry out basic research. To achieve these purposes, we will utilize machine-learning and AI technologies and perform large-scale computational analysis using cloud computing platforms.

List of papers published in 2021

Journal

1. Oshima K, Kato K, Ito Y, Daiko H, Nozaki I, Nakagawa S, Shibuya Y, Kojima T, Toh Y, Okada M, Hironaka S, Akiyama Y, Komatsu Y, Maejima K, Nakagawa H, Onuki R, Nagai M, Kato M, Kanato K, Kuchiba A, Nakamura K, Kitagawa Y. Prognostic biomarker study in patients with clinical stage I esophageal squamous cell carcinoma: JCOG0502-A1. Cancer science, 113:1018-1027, 2022

2. Yachida S, Totoki Y, Noë M, Nakatani Y, Horie M, Kawasaki K, Nakamura H, Saito-Adachi M, Suzuki M, Takai E, Hama N, Higuchi R, Hirono S, Shiba S, Kato M, Furukawa E, Arai Y, Rokutan H, Hashimoto T, Mitsunaga S, Kanda M, Tanaka H, Takata S, Shimomura A, Oshima M, Hackeng WM, Okumura T, Okano K, Yamamoto M, Yamaue H, Morizane C, Arihiro K, Furukawa T, Sato T, Kiyono T, Brosens LAA, Wood LD, Hruban RH, Shibata T . Comprehensive Genomic Profiling of Neuroendocrine Carcinomas of the Gastrointestinal System. Cancer discovery, 12:692-711, 2022

3. Ono H, Arai Y, Furukawa E, Narushima D, Matsuura T, Nakamura H, Shiokawa D, Nagai M, Imai T, Mimori K, Okamoto K, Hippo Y, Shibata T, Kato M. Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model. BMC biology, 19:207, 2021

4. Mizuno S, Yamaguchi R, Hasegawa T, Hayashi S, Fujita M, Zhang F, Koh Y, Lee SY, Yoon SS, Shimizu E, Komura M, Fujimoto A, Nagai M, Kato M, Liang H, Miyano S, Zhang Z, Nakagawa H, Imoto S. Immunogenomic pan-cancer landscape reveals immune escape mechanisms and immunoediting histories. Scientific reports, 11:15713, 2021