Annual Report 2021

Division of Genome Analysis Platform Development

Yuichi Shiraishi, Naoko Iida, Ai Okada, Kenichi Chiba, Raúl Nicolás Mateos

Introduction

 We construct various analysis workflows for efficient analysis of cancer genome and transcriptome sequencing data. As an analysis platform that includes items necessary for primary analysis of sequencing data, we have constructed an analysis workflow that detects various mutations such as point mutations, deletions, insertions, and translocations from genome sequencing, and transcriptional abnormalities such as fusion genes, changes in expression levels, and splicing abnormalities from transcriptome sequencing. In addition, we conduct integrated analysis of genomic and transcriptomic data. In addition, we are conducting integrated analysis of genomic and transcriptomic data. With the development of high-throughput sequencing technology and the advancement of many methodologies and software around the world, we are developing the platform with various improvements such as speeding up and refinement.

Research activities

(1)  Development of mutation detection analysis for hereditary tumors and AYA (adolescent and young adult) generation cancers

 Although the development of high-throughput sequencing technology has enabled the comprehensive detection of mutations, it is still an important and challenging task to detect mutations with high sensitivity and accuracy by eliminating sequencing errors and artifacts. We have developed practical filtering tools to detect mutations in hereditary tumors and AYA generation cancers. 1. We constructed a database of genomic breakpoints due to structural abnormalities using WGS data from the 1000 Genome Project. Then, we developed a tool to detect the structural variants specific to the target samples by filtering the structural variants in the database. 2. We developed a tool to obtain mutation information (VCF file) to detect disease-related point mutations and deletion/insertion mutations efficiently. We performed GenomicsDBImport and GenotypeGVCF on the results of HaplotypeCaller in the GATK software, added multiple annotations, and filtered the results appropriately. We run this tool against WGS data of hereditary tumors and AYA generation cancers and detect candidate mutations associated with the disease. We have also created a post-process analysis flow, which performs filtering of results of GCATWorkflow analysis.

(2) Large-scale analysis of transcriptome data

 We have conducted analyses aimed at knowledge discovery using the large-scale transcriptome data stored in the public NCBI Sequence Read Archive (SRA). In addition to alignment and expression analysis using the software STAR, we are also conducting analysis using a tool we have developed to detect splicing abnormalities.

(3) Development of a long-read sequencing data analysis pipeline

 We developed an analysis flow for long-read sequences obtained by long-read sequencers, which have been attracting attention in recent years. We evaluated the performance of the mutation detection software “Medaka”, the haplotype caller “Whathap”, and the structural abnormality detection software “NanomonSV”. We used container technology to package the tools to ensure the reproducibility of the analysis.

(4) Spatial gene expression analysis using a cloud system

 We constructed an analysis environment for Space Ranger, a series of analysis pipelines that analyze gene expression from tissue sections while retaining cell location information. Space Ranger requires a high-spec machine, but we built an analysis system that uses the analysis environment with the necessary specifications when needed by using AWS virtual machines.

Education

 We supported the many researchers using our analysis pipeline by answering their bioinformatics questions. We hired postdocs and supported their research.

Future Prospects

 We have established the technological basis for cancer genome and transcriptome analysis. To develop applications of whole-genome analysis to genomic medicine, we will construct various genome analysis flows. In addition, we will apply the established analysis flows to large-scale data and conduct knowledge discovery from the obtained information.

List of papers published in 2021

Journal

1. Yasuda T, Sanada M, Kawazu M, Kojima S, Tsuzuki S, Ueno H, Iwamoto E, Iijima-Yamashita Y, Yamada T, Kanamori T, Nishimura R, Kuwatsuka Y, Takada S, Tanaka M, Ota S, Dobashi N, Yamazaki E, Hirose A, Murayama T, Sumi M, Sato S, Tange N, Nakamura Y, Katsuoka Y, Sakaida E, Kawamata T, Iida H, Shiraishi Y, Nannya Y, Ogawa S, Taniwaki M, Asou N, Hatta Y, Kiyoi H, Matsumura I, Horibe K, Mano H, Naoe T, Miyazaki Y, Hayakawa F. Two novel high-risk adult B-cell acute lymphoblastic leukemia subtypes with high expression of CDX2 and IDH1/2 mutations. Blood, 139:1850-1862, 2022

2. Kogure Y, Kameda T, Koya J, Yoshimitsu M, Nosaka K, Yasunaga JI, Imaizumi Y, Watanabe M, Saito Y, Ito Y, McClure MB, Tabata M, Shingaki S, Yoshifuji K, Chiba K, Okada A, Kakiuchi N, Nannya Y, Kamiunten A, Tahira Y, Akizuki K, Sekine M, Shide K, Hidaka T, Kubuki Y, Kitanaka A, Hidaka M, Nakano N, Utsunomiya A, Sica RA, Acuna-Villaorduna A, Janakiram M, Shah U, Ramos JC, Shibata T, Takeuchi K, Takaori-Kondo A, Miyazaki Y, Matsuoka M, Ishitsuka K, Shiraishi Y, Miyano S, Ogawa S, Ye BH, Shimoda K, Kataoka K. Whole-genome landscape of adult T-cell leukemia/lymphoma. Blood, 139:967-982, 2022

3. Sagawa R, Sakata S, Gong B, Seto Y, Takemoto A, Takagi S, Ninomiya H, Yanagitani N, Nakao M, Mun M, Uchibori K, Nishio M, Miyazaki Y, Shiraishi Y, Ogawa S, Kataoka K, Fujita N, Takeuchi K, Katayama R. Soluble PD-L1 works as a decoy in lung cancer immunotherapy via alternative polyadenylation. JCI insight, 7:2022

4. Mikami T, Kato I, Wing JB, Ueno H, Tasaka K, Tanaka K, Kubota H, Saida S, Umeda K, Hiramatsu H, Isobe T, Hiwatari M, Okada A, Chiba K, Shiraishi Y, Tanaka H, Miyano S, Arakawa Y, Oshima K, Koh K, Adachi S, Iwaisako K, Ogawa S, Sakaguchi S, Takita J. Alteration of the immune environment in bone marrow from children with recurrent B cell precursor acute lymphoblastic leukemia. Cancer science, 113:41-52, 2022

5. Hirata H, Niida A, Kakiuchi N, Uchi R, Sugimachi K, Masuda T, Saito T, Kageyama SI, Motomura Y, Ito S, Yoshitake T, Tsurumaru D, Nishimuta Y, Yokoyama A, Hasegawa T, Chiba K, Shiraishi Y, Du J, Miura F, Morita M, Toh Y, Hirakawa M, Shioyama Y, Ito T, Akimoto T, Miyano S, Shibata T, Mori M, Suzuki Y, Ogawa S, Ishigami K, Mimori K. The Evolving Genomic Landscape of Esophageal Squamous Cell Carcinoma Under Chemoradiotherapy. Cancer research, 81:4926-4938, 2021

6. Namba S, Ueno T, Kojima S, Kobayashi K, Kawase K, Tanaka Y, Inoue S, Kishigami F, Kawashima S, Maeda N, Ogawa T, Hazama S, Togashi Y, Ando M, Shiraishi Y, Mano H, Kawazu M. Transcript-targeted analysis reveals isoform alterations and double-hop fusions in breast cancer. Communications biology, 4:1320, 2021

7. Fujii Y, Sato Y, Suzuki H, Kakiuchi N, Yoshizato T, Lenis AT, Maekawa S, Yokoyama A, Takeuchi Y, Inoue Y, Ochi Y, Shiozawa Y, Aoki K, Yoshida K, Kataoka K, Nakagawa MM, Nannya Y, Makishima H, Miyakawa J, Kawai T, Morikawa T, Shiraishi Y, Chiba K, Tanaka H, Nagae G, Sanada M, Sugihara E, Sato TA, Nakagawa T, Fukayama M, Ushiku T, Aburatani H, Miyano S, Coleman JA, Homma Y, Solit DB, Kume H, Ogawa S. Molecular classification and diagnostics of upper urinary tract urothelial carcinoma. Cancer cell, 39:793-809.e8, 2021

8. Ochi Y, Yoshida K, Huang YJ, Kuo MC, Nannya Y, Sasaki K, Mitani K, Hosoya N, Hiramoto N, Ishikawa T, Branford S, Shanmuganathan N, Ohyashiki K, Takahashi N, Takaku T, Tsuchiya S, Kanemura N, Nakamura N, Ueda Y, Yoshihara S, Bera R, Shiozawa Y, Zhao L, Takeda J, Watatani Y, Okuda R, Makishima H, Shiraishi Y, Chiba K, Tanaka H, Sanada M, Takaori-Kondo A, Miyano S, Ogawa S, Shih LY. Clonal evolution and clinical implications of genetic abnormalities in blastic transformation of chronic myeloid leukaemia. Nature communications, 12:2833, 2021

9. Saiki R, Momozawa Y, Nannya Y, Nakagawa MM, Ochi Y, Yoshizato T, Terao C, Kuroda Y, Shiraishi Y, Chiba K, Tanaka H, Niida A, Imoto S, Matsuda K, Morisaki T, Murakami Y, Kamatani Y, Matsuda S, Kubo M, Miyano S, Makishima H, Ogawa S. Combined landscape of single-nucleotide variants and copy number alterations in clonal hematopoiesis. Nature medicine, 27:1239-1249, 2021