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Annual Report 2018

Section of Genome Analysis Platform

Yuichi Shiraishi, Ai Okada, Kenichi Chiba, Daichi Narushima, Eisaku Furukawa, Hiromu Ochiai

Introduction

 The Section of Genome Analysis Platform in the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) focuses on developing and evaluating (1) Methodologies for detecting various types of somatic variants (SNV, indel, structural variations and so on) in cancer genomes, (2) Normalization of cancer genome data formats, (3) Workflows for cancer genome analysis and (4) Platform for analyzing and sharing cancer genome data using cloud computing. These products created by us will be best utilized in projects for collecting and managing cancer genome data. Also, we are preparing a platform for whole genome sequencing analysis in clinical settings.

Research activities

 We developed bioinformatics tools for genome sequencing and designed the Variant Call Format file (VCF) that contains meta-information lines, a header line, and then data lines each containing genomic variants information on samples for each position. Then, we developed a prototype pipeline for genomic sequence data analysis in C-CAT. We also reviewed the system design documents, generated the test data and evaluated the system flow. Furthermore, we implemented the GUI for inspection of the resultant reports. To extend our analysis for further pipelines, we tested the latest software such as DRAGEN (Illumina). We evaluated the pipeline for large data sets in Amazon Web Services (AWS) cloud by using ELT (Extract/ Load/Transform).

 To use cloud systems such as AWS securely, setting up the development environment has many difficulties and laborious issues. To circument these issues , the AWS CloudFormation system is a helpful service that enables us to create and provide AWS infrastructure deployments easily and repeatedly. We created template files that describe the resources that we want to provide in our AWS CloudFormation system and successfully implemented this system. Furthermore, we provided the system for automatically monitoring resources and reduced the cost of the system.

Education

 We supported many researchers who use our analysis pipelines by answering their questions about bioinformatics. We employed a postdoctoral fellow and supported his research.

Future prospects

 By utilizing current and novel sequencing technologies, this section will investigate and develop novel bioinformatics methods and a computer system for cancer genomics and clinical sequencing. We will also contribute to human resources for analyzing large-size cancer genomics data.

List of papers published in 2018

Journal

 1. Okuno Y, Murata T, Sato Y, Muramatsu H, Ito Y, Watanabe T, Okuno T, Murakami N, Yoshida K, Sawada A, Inoue M, Kawa K, Seto M, Ohshima K, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Narita Y, Yoshida M, Goshima F, Kawada JI, Nishida T, Kiyoi H, Kato S, Nakamura S, Morishima S, Yoshikawa T, Fujiwara S, Shimizu N, Isobe Y, Noguchi M, Kikuta A, Iwatsuki K, Takahashi Y, Kojima S, Ogawa S, Kimura H. Defective Epstein-Barr virus in chronic active infection and haematological malignancy. Nat Microbiol, 4:404-413, 2019

 2. Christen F, Hoyer K, Yoshida K, Hou HA, Waldhueter N, Heuser M, Hills RK, Chan W, Hablesreiter R, Blau O, Ochi Y, Klement P, Chou WC, Blau IW, Tang JL, Zemojtel T, Shiraishi Y, Shiozawa Y, Thol F, Ganser A, Lowenberg B, Linch DC, Bullinger L, Valk PJM, Tien HF, Gale RE, Ogawa S, Damm F. Genomic landscape and clonal evolution of acute myeloid leukemia with t(8;21): an international study on 331 patients. Blood, 133:1140-1151, 2019

 3. Kobayashi K, Mizuta S, Yamane N, Ueno H, Yoshida K, Kato I, Umeda K, Hiramatsu H, Suehiro M, Maihara T, Usami I, Shiraishi Y, Chiba K, Miyano S, Adachi S, Ogawa S, Kiyokawa N, Heike T. Paraneoplastic hypereosinophilic syndrome associated with IL3- IgH positive acute lymphoblastic leukemia. Pediatr Blood Cancer, 66:e27449, 2019

 4. Yamato G, Shiba N, Yoshida K, Hara Y, Shiraishi Y, Ohki K, Okubo J, Park MJ, Sotomatsu M, Arakawa H, Kiyokawa N, Tomizawa D, Adachi S, Taga T, Horibe K, Miyano S, Ogawa S, Hayashi Y. RUNX1 mutations in pediatric acute myeloid leukemia are associated with distinct genetic features and an inferior prognosis. Blood, 131:2266-2270, 2018

 5. Murakami N, Okuno Y, Yoshida K, Shiraishi Y, Nagae G, Suzuki K, Narita A, Sakaguchi H, Kawashima N, Wang X, Xu Y, Chiba K, Tanaka H, Hama A, Sanada M, Ito M, Hirayama M, Watanabe A, Ueno T, Kojima S, Aburatani H, Mano H, Miyano S, Ogawa S, Takahashi Y, Muramatsu H. Integrated molecular profiling of juvenile myelomonocytic leukemia. Blood, 131:1576-1586, 2018

 6. Matsuo H, Yoshida K, Fukumura K, Nakatani K, Noguchi Y, Takasaki S, Noura M, Shiozawa Y, Shiraishi Y, Chiba K, Tanaka H, Okada A, Nannya Y, Takeda J, Ueno H, Shiba N, Yamato G, Handa H, Ono Y, Hiramoto N, Ishikawa T, Usuki K, Ishiyama K, Miyawaki S, Itonaga H, Miyazaki Y, Kawamura M, Yamaguchi H, Kiyokawa N, Tomizawa D, Taga T, Tawa A, Hayashi Y, Mano H, Miyano S, Kamikubo Y, Ogawa S, Adachi S. Recurrent CCND3 mutations in MLL-rearranged acute myeloid leukemia. Blood Adv, 2:2879-2889, 2018

 7. Toki T, Yoshida K, Wang R, Nakamura S, Maekawa T, Goi K, Katoh MC, Mizuno S, Sugiyama F, Kanezaki R, Uechi T, Nakajima Y, Sato Y, Okuno Y, Sato-Otsubo A, Shiozawa Y, Kataoka K, Shiraishi Y, Sanada M, Chiba K, Tanaka H, Terui K, Sato T, Kamio T, Sakaguchi H, Ohga S, Kuramitsu M, Hamaguchi I, Ohara A, Kanno H, Miyano S, Kojima S, Ishiguro A, Sugita K, Kenmochi N, Takahashi S, Eto K, Ogawa S, Ito E. De Novo Mutations Activating Germline TP53 in an Inherited Bone-Marrow-Failure Syndrome. Am J Hum Genet, 103:440-447, 2018

 8. Shiraishi Y, Kataoka K, Chiba K, Okada A, Kogure Y, Tanaka H, Ogawa S, Miyano S. A comprehensive characterization of cis-acting splicing-associated variants in human cancer. Genome Res, 28:1111-1125, 2018

 9. Saito T, Niida A, Uchi R, Hirata H, Komatsu H, Sakimura S, Hayashi S, Nambara S, Kuroda Y, Ito S, Eguchi H, Masuda T, Sugimachi K, Tobo T, Nishida H, Daa T, Chiba K, Shiraishi Y, Yoshizato T, Kodama M, Okimoto T, Mizukami K, Ogawa R, Okamoto K, Shuto M, Fukuda K, Matsui Y, Shimamura T, Hasegawa T, Doki Y, Nagayama S, Yamada K, Kato M, Shibata T, Mori M, Aburatani H, Murakami K, Suzuki Y, Ogawa S, Miyano S, Mimori K. A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer. Nat Commun, 9:2884, 2018