Annual Report 2017

Mamoru Kato, Asmaa Elzawahry, Eisaku Furukawa, Momoko Nagai, Iurii Nagornov, Daichi Narushima, Hanako Ono, Chieko Yoshida

Introduction

 Missions of the Department of Bioinformatics are 1) bioinformatics research and its application to clinical sequencing, 2) building new theories on cancer biology through big-data analysis such as OMICS-data and computational methods, and 3) providing bioinformatics support for experimental groups in the National Cancer Center (NCC) as well as other research institutions.

*We took charge of the bioinformatics part of the clinical sequencing project in the NCC. The bioinformatics part consists of 1) development of DNA-alteration calling programs, 2) development of medical information systems for clinical sequencing, and 3) management of the computer network for clinical sequencing.

1) We previously developed computer programs optimized for FFPE samples used in clinical sequencing. These programs detect SNV, indels, gene fusions, and copy number alterations from a large amount of data produced by the next generation sequencer (NGS). This year:

I. We improved these computer programs enough to be used as medical appliances in a clinic. We refactored source codes and improved functions. We also improved the fusion-calling algorithm. We enabled the application as a container using Docker.

II. We made cisCall open to the public. (https://www.ciscall.org/)

III. We tailored cisCall and performed required data analysis for IVD application.

2) We improved the doctor report and sequencing report to include QC information such as an insert size and a contamination rate. In order to help doctors understand, we improved the sequencing report to include COSMIC resisted frequency for detected mutations.

3) We set up the computer environment in the NCC Research Institute (NCCRI) building to call mutations. In addition, we constructed the closed network between the NCCRI building and the Department of Pathology and Clinical Laboratories in the NCC Hospital (NCCH), which makes it possible to directly transfer the detected mutation in the NCCRI building to the NCCH.

4) We renewed a cisVids (Clinical Sequencing Visual Data-summarization system), which enables users to view, extract, and analyze the NGS panel testing on a website.

5) We developed a cisMedi (Clinical Sequencing Medical Information system) as a web-based system, which enables users to edit, review, and approve sequence reports and expert panel reports from NGS panel testing.

6) We registered variant data of 133 cases from TOPICS-1 (Trial of Oncopanel for Introduction into Clinical Study-Phase 1) to the MGeND (Medical genomics Japan Variant Database).

*We identified biomarkers that can be usable in clinical sequencing. We used multi-omics big data to identify genomic biomarkers for immune checkpoint expression genes in bile duct cancer, and assessed the significance of the identified biomarkers that can be used to select patients who might get benefit from treatment using immune checkpoint therapy. We validated a few of the identified biomarkers using an external data set (TCGA cholangiocarcinoma data).

*We performed single-cell sequencing to reveal intra-tumor heterogeneity and cancer-cell evolution, collaborating with the Division of Caner Genomics of the NCCRI and the Chiba Cancer Center. Using a mouse model for cancer development, we performed single-cell exome and transcriptome sequencing and developed pipeline programs to analyze the dynamics of

 cancer-cell subpopulations along the time-course. We completed this analysis and submitted a paper.

*We gathered and rearranged data released from working groups in PCAWG (Pan Cancer Analysis of Whole Genomes). We processed this big-data to perform multi-omics survival analysis.

*We provided bioinformatics analysis supports for projects as follows:

1) Single-cell sequencing analysis for colon cancer in a mouse model in collaboration with the Division of Cancer Differentiation of the NCCRI

2) CNA analysis for 127 cases of esophageal cancer from JCOG (Japan Clinical Oncology Group) with cisCall

3) Whole genome sequencing of rats and DNA adductome analysis for the Division of Carcinogenesis and Cancer Prevention of the NCCRI

4) Automation of NextSeq data conversion and processing in clinical sequencing

5) Analysis of blood aldehyde for two cancer cohorts (colorectal and breast cancer cohorts)

6) Designing the statistical criteria for ependymoma (brain cancer) molecular diagnosis using pyrosequencing

7) Methylation analysis of Nanopore data to examine the DNA adductome

8) Genome-Wide Analysis and classification of methylation data in digestive refractory cancer

9) Survival analysis using the identified

 miRNAs as biomarkers for lung cancer for the Division of Genetic Diagnostics at the Chiba Cancer Center

10) Analysis of bacterial mutations and the mutational signatures for bacterial colonies exposed to different carcinogens

11) Comparison of our previous results of asbestos mutational signatures with published human mesothelioma signatures

Education

 Our department employed one researcher this year.

Future prospects

 We will develop bioinformatics technologies for clinical sequencing, including cfDNA sequencing, and apply them to realize precision medicine. Collaborating with C-CAT, we will analyze medical big data to find novel tumor molecular markers and subtypes that are applicable to clinical sequencing. We will promote single-cell sequencing and theoretical studies to reveal

cancer-cell evolution. We will keep continue to provide bioinformatics support for other groups in the NCC and other institutions.

List of papers published in January 2017 - March 2018

Journal

1. Takahashi T, Elzawahry A, Mimaki S, Furukawa E, Nakatsuka R, Nakamura H, Nishigaki T, Serada S, Naka T, Hirota S, Shibata T, Tsuchihara K, Nishida T, Kato M. Genomic and transcriptomic analysis of imatinib resistance in gastrointestinal stromal tumors. Genes Chromosomes Cancer, 56:303-313, 2017

2. Fukushima S, Yamashita S, Kobayashi H, Takami H, Fukuoka K, Nakamura T, Yamasaki K, Matsushita Y, Nakamura H, Totoki Y, Kato M, Suzuki T, Mishima K, Yanagisawa T, Mukasa A, Saito N, Kanamori M, Kumabe T, Tominaga T, Nagane M, Iuchi T, Yoshimoto K, Mizoguchi M, Tamura K, Sakai K, Sugiyama K, Nakada M, Yokogami K, Takeshima H, Kanemura Y, Matsuda M, Matsumura A, Kurozumi K, Ueki K, Nonaka M, Asai A, Kawahara N, Hirose Y, Takayama T, Nakazato Y, Narita Y, Shibata T, Matsutani M, Ushijima T, Nishikawa R, Ichimura K. Genome-wide methylation profiles in primary intracranial germ cell tumors indicate a primordial germ cell origin for germinomas. Acta Neuropathol, 133:445-462, 2017

3. Hayashi H, Kohno T, Ueno H, Hiraoka N, Kondo S, Saito M, Shimada Y, Ichikawa H, Kato M, Shibata T, Morizane C, Sakamoto Y, Shimada K, Komatsu Y, Sakamoto N, Okusaka T. Utility of Assessing the Number of Mutated KRAS, CDKN2A, TP53, and SMAD4 Genes Using a Targeted Deep Sequencing Assay as a Prognostic Biomarker for Pancreatic Cancer. Pancreas, 46:335-340, 2017

4. Shiokawa D, Sato A, Ohata H, Mutoh M, Sekine S, Kato M, Shibata T, Nakagama H, Okamoto K. The Induction of Selected Wnt Target Genes by Tcf1 Mediates Generation of Tumorigenic Colon Stem Cells. Cell Rep, 19:981-994, 2017

5. Asano N, Yoshida A, Mitani S, Kobayashi E, Shiotani B, Komiyama M, Fujimoto H, Chuman H, Morioka H, Matsumoto M, Nakamura M, Kubo T, Kato M, Kohno T, Kawai A, Kondo T, Ichikawa H. Frequent amplification of receptor tyrosine kinase genes in welldifferentiated/ dedifferentiated liposarcoma. Oncotarget, 8:12941-12952, 2017

6. Sekine S, Mori T, Ogawa R, Tanaka M, Yoshida H, Taniguchi H, Nakajima T, Sugano K, Yoshida T, Kato M, Furukawa E, Ochiai A, Hiraoka N. Mismatch repair deficiency commonly precedes adenoma formation in Lynch Syndrome-Associated colorectal tumorigenesis. Mod Pathol, 30:1144-1151, 2017

7. Kato M, Vasco DA, Sugino R, Narushima D, Krasnitz A. Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer. Royal Society open science, 4:171060, 2017