Annual Report 2024
Division of Bioinformatics
Mamoru Kato, Jo Nishino, Eisaku Furukawa, Momoko Nagai, Iurii Nagornov, Munmee Dutta, Satsuki Kase, Ritsuko Onuki, Daichi Narushima, Shotatsu Takeshige, Yota Noboru, Towa Fujii
Introduction
The research activities of this division include (1) Development of new bioinformatics technologies and data analysis for cancer research and medicine; (2) Construction of new mathematical biology theories through data analysis and computational methods; and (3) Bioinformatics and data analysis through collaborative research with other laboratories and institutions.
Research Activities
1. Development of information systems for cancer genome medicine projects
We have worked on improving the functions and performance of cisCall, the gene mutation detection program used in the NCC Oncopanel, while also exploring new methods and developing programs. Achievements this year include:
- Added further filtering for SNV detection in the developing version of cisCall
- Accuracy validation of mutation detection using deep learning
- Development of an analysis pipeline for whole-genome sequencing, including:
a) Development of a simulation program for read depth and variant allele frequency, and evaluation of detection performance
b) Added HRD detection
c) Added custom filters for somatic SV and somatic SNV
d) Enhanced support for large-scale data and systems
e) Explored improvements for somatic SV detection
f) Investigated a new MSI detection tool
g) Validated reconstruction target regions
h) Improved duplicate read removal
- Built cloud infrastructure for speed optimization
- Developed a program for high-precision removal of PCR duplicate reads
- Verified a germline copy number alteration detection program
- Validated the effectiveness of a Panel of Normal (PON)
2. Development of numerical simulation–based personalized medicine theory
We have been developing tugHall, a simulator that models cancer cell evolution based on mathematical models and connects it to personalized medicine. This year, we made the following changes:
- Reinforced the speed-up algorithms
- Reinforced conversion functionality to real-time units
- Conceived a drug resistance model
- Reorganized computation workflows, including refactoring input/output data and interface updates
- Designed an ABC analysis pipeline and input data file generator
- Expanded output data (statistics, TMB, etc.)
- Examined code coverage analysis and refactoring
- Examined an automated testing environment
- Prepared full documentation for the package
- Applied to real data
3. Application of quantum computing to bioinformatics
We explored the possibilities of applying quantum computing to bioinformatics.
4. Collaborative research and bioinformatics support
- Biomarker analysis using clinical trial data on glioblastoma
- Exome analysis of chemically induced lung cancer in mouse models
- Multi-omics analysis of PCAWG data and comparative analysis with TCGA data
- Mutational signature analysis of rats/mice/bacteria exposed to various carcinogens
- Establishment of a collaboration framework with the Biostatistics Department at the Research Support Center for clinical research involving omics data, and development of analysis methods
- Functional inference of VUS using existing software
- Exploration of synthetic lethal gene pairs
- Support for evaluation of gene roles in melanoma using TCGA data
Education
We provide bioinformatics analysis support and technical training to other departments and institutions, as well as research guidance to affiliated graduate students.
Future Prospects
We aim to develop core information technologies for cancer genome medicine and promote technology transfer for the realization of personalized medicine. At the same time, we will continue basic research, actively utilizing machine learning, artificial intelligence technologies, and cloud infrastructure.
List of papers published in 2024
Journal
1. Nishino J, Miya F, Kato M. Gene-based Hardy-Weinberg equilibrium test using genotype count data: application to six types of cancers. BMC genomics, 26:124, 2025
2. 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
3. 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
4. Hasegawa S, Shoji Y, Kato M, Elzawahry A, Nagai M, Gi M, Suzuki S, Wanibuchi H, Mimaki S, Tsuchihara K, Totsuka Y. Whole Genome Sequencing Analysis of Model Organisms Elucidates the Association Between Environmental Factors and Human Cancer Development. International journal of molecular sciences, 25:11191, 2024