DNAとRNAシークエンシングデータを用いた統合変異解析ツールの開発

• Project/Area Number: 21K12117
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 62010:Life, health and medical informatics-related
• Research Institution: National Cancer Center Japan
• Principal Investigator: 上野 敏秀 国立研究開発法人国立がん研究センター, 研究所, 主任研究員 (40381446)
• Project Period (FY): 2021-04-01 – 2025-03-31
• Project Status: Granted (Fiscal Year 2023)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2024: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2023: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2022: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2021: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
• Keywords: バイオインフォマティクス / 変異解析 / 融合遺伝子検出 / ゲノム解析 / DNA・RNAシークエンシング

Outline of Research at the Start

DNA由来サンプルから変異解析やコピー数解析、RNA由来サンプルから発現量解析や融合遺伝子検出などのそれぞれの単体の解析を行うだけでなく、変異の有無の精度向上や疾患に起こっている現象を統合的に捉える工夫をDNAとRNAのデータから取得し、両方の結果を横断的・統合的に解析するパイプラインの開発を行う。

Outline of Annual Research Achievements

DNAとRNAサンプルからのゲノム異常検出を行う統合的解析パイプラインの開発のうち、本年度はDNAサンプルの変異解析部分のアップデートを行った。Telomere-to-Telomere (T2T) コンソーシアムからロングリードシークエンスによるヒトのリファレンス配列CHM13が公開されて以来CHM13を用いた解析要望が増えたためGRCh38に加えCHM13に設定一つで切り替えられるよう改訂している。研究開始当初は想定していなかった事案であるが、リファレンスの差し替えは今後も起こり得る事柄であるためこのタイミングで修正することとした。リファレンスの切り替えに伴い、アノテーションのためのデータベース入手や作成など統合的パイプライン作成を目指して準備した。また、ターゲットシークエンスや全エクソンシークエンス、全ゲノムシークエンスなどシークエンスタイプでも切り替えられる仕組みも組み込んでいる。シークエンスタイプが異なるとカバレッジに大きな差が出るため、探索したい範囲が異なる。カバレッジが高ければより低頻度の変異を求めたくなるため、サンプルごとに最適値を求める工夫も構築した。
また、変異コールの精度向上のためには正常部・腫瘍部のペアだけでなく、ある程度の正常サンプルから作成した正常データベースの活用が有効である。ブロード研究所が公開しているGATK（Genome Analysis Toolkit）の仕組みとは別に、独自の機構の開発に着手した。

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

異なるリファレンスやシークエンスタイプに対して切り替えられるような仕組みは当初考慮していなかったが、ある程度目処が立ったと考えている。WGS解析の高速化についてはもう少し検討が必要かもしれないが、概ね順調に進んでいると推測する。

Strategy for Future Research Activity

変異コールの精度を出すために幾つかのフィルターを設計し実装しているが、WGS解析の規模になると計算量の増大が懸念点である。フィルターの有無やプログラムの高速化を検討しパイプラインの刷新を目指す。

Research Products

• [Journal Article] Multiomic molecular characterization of the response to combination immunotherapy in MSS/pMMR metastatic colorectal cancer (2024)
  • Author(s): Takei S、Tanaka Y、Lin Yi-Tzu、Koyama S、Fukuoka S、Hara H、Nakamura Y、Kuboki Y、Kotani D、Kojima T、Bando H、Mishima S、Ueno T、Kojima S、Wakabayashi M、Sakamoto N、Kojima M、Kuwata T、Yoshino T、Nishikawa H、Mano H、Endo I、Shitara K、Kawazoe A
  • Journal Title: Journal for ImmunoTherapy of Cancer Volume: 12 Issue: 2 Pages: 8210-8210
  • DOI: 10.1136/jitc-2023-008210
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Promoter swapping of truncated PDGFRB drives Ph-like acute lymphoblastic leukemia (2023)
  • Author(s): Miyazaki Bunpei、Ueno Toshihide、Sugiyama Masanaka、Kojima Shinya、Arakawa Ayumu、Tao Kayoko、Tanimura Kazuki、Shiraishi Kouya、Yagishita Shigehiro、Kohsaka Shinji、Kato Mamoru、Kiyokawa Nobutaka、Goto Yasushi、Yatabe Yasushi、Hamada Akinobu、Mano Hiroyuki、Ogawa Chitose、Tanaka Yosuke
  • Journal Title: npj Precision Oncology Volume: 7 Issue: 1 Pages: 132-132
  • DOI: 10.1038/s41698-023-00485-7
  • Peer Reviewed / Open Access
• [Journal Article] Subclonal accumulation of immune escape mechanisms in microsatellite instability-high colorectal cancers (2023)
  • Author(s): Kobayashi Y, Niida A, Nagayama S, Saeki K, （中略）, Mizuno S, Kawazu M, Kohsaka S, Ueno T, Mano H, Ishihara S, Uemura M, Mori M, Doki Y, Eguchi H, Oshima M, Suzuki Y, Shibata T, Mimori K.
  • Journal Title: Br J Cancer Volume: 129 Issue: 7 Pages: 1105-1118
  • DOI: 10.1038/s41416-023-02395-8
  • Peer Reviewed / Open Access
• [Journal Article] Genome Doubling Shapes High-Grade Transformation and Novel EWSR1::LARP4 Fusion Shows SOX10 Immunostaining in Hyalinizing Clear Cell Carcinoma of Salivary Gland (2023)
  • Author(s): Kobayashi Kenya、Kawazu Masahito、Yoshimoto Seiichi、Ueno Toshihide、Omura Go、Saito Yuki、Ando Mizuo、Ryo Eigitsu、Sakyo Airi、Yoshida Akihiko、Yatabe Yasushi、Mano Hiroyuki、Mori Taisuke
  • Journal Title: Laboratory Investigation Volume: 103 Issue: 10 Pages: 100213-100213
  • DOI: 10.1016/j.labinv.2023.100213
  • Peer Reviewed
• [Journal Article] Strategic Approach to Heterogeneity Analysis of Cutaneous Adnexal Carcinomas Using Computational Pathology and Genomics (2023)
  • Author(s): Nishimura Yuuki、Ryo Eijitsu、Inoue Satoshi、Kawazu Masahito、Ueno Toshihide、Namikawa Kenjiro、Takahashi Akira、Ogata Dai、Yoshida Akihiko、Yamazaki Naoya、Mano Hiroyuki、Yatabe Yasushi、Mori Taisuke
  • Journal Title: JID Innovations Volume: 3 Issue: 6 Pages: 100229-100229
  • DOI: 10.1016/j.xjidi.2023.100229
  • Peer Reviewed / Open Access
• [Journal Article] Somatic mutations can induce a noninflamed tumour microenvironment via their original gene functions, despite deriving neoantigens (2023)
  • Author(s): Ishino Takamasa、Kawashima Shusuke、Tanji Etsuko、Ueno Toshihide、Ueda Youki、Ogasawara Sadahisa、Sato Kazuhito、Mano Hiroyuki、Ishihara Soichiro、Kato Naoya、Kawazu Masahito、Togashi Yosuke
  • Journal Title: British Journal of Cancer Volume: 128 Issue: 6 Pages: 1166-1175
  • DOI: 10.1038/s41416-023-02165-6
  • Peer Reviewed / Open Access
• [Journal Article] Transcriptomic Profiling of MSI-H/dMMR Gastrointestinal Tumors to Identify Determinants of Responsiveness to Anti?PD-1 Therapy (2022)
  • Author(s): Chida K、Kawazoe A、Suzuki T、Kawazu M、Ueno T、Takenouchi K、Nakamura Y、Kuboki Y、Kotani D、Kojima T、Bando H、Mishima S、Kuwata T、Sakamoto N、Watanabe J、Mano H、Ikeda M、Shitara K、Endo I、Nakatsura T、Yoshino T
  • Journal Title: Clinical Cancer Research Volume: 28 Issue: 10 Pages: 2110-2117
  • DOI: 10.1158/1078-0432.ccr-22-0041
  • Peer Reviewed
• [Journal Article] Tumor mutational burden measurement using comprehensive genomic profiling assay (2022)
  • Author(s): Kage Hidenori、Kohsaka Shinji、Tatsuno Kenji、Ueno Toshihide、Ikegami Masachika、Zokumasu Koichi、Shinozaki-Ushiku Aya、Nagai Sumimasa、Aburatani Hiroyuki、Mano Hiroyuki、Oda Katsutoshi
  • Journal Title: Japanese Journal of Clinical Oncology Volume: 52 Issue: 8 Pages: 925-929
  • DOI: 10.1093/jjco/hyac063
  • Peer Reviewed
• [Journal Article] Exploration of predictive biomarkers for postoperative recurrence of stage II/III colorectal cancer using genomic sequencing (2022)
  • Author(s): Kishigami Fumishi、Tanaka Yosuke、Yamamoto Yoko、Ueno Toshihide、Kojima Shinya、Sato Kazuhito、Inoue Satoshi、Sugaya Saori、Ishihara Soichiro、Mano Hiroyuki、Kawazu Masahito
  • Journal Title: Cancer Medicine Volume: 11 Issue: 18 Pages: 3457-3470
  • DOI: 10.1002/cam4.4710
  • Peer Reviewed / Open Access
• [Journal Article] High-Throughput Functional Evaluation of MAP2K1 Variants in Cancer (2022)
  • Author(s): Mizuno Sho、Ikegami Masachika、Koyama Takafumi、Sunami Kuniko、Ogata Dai、Kage Hidenori、Yanagaki Mitsuru、Ikeuchi Hiroshi、Ueno Toshihide、Tanikawa Michihiro、Oda Katsutoshi、Osuga Yutaka、Mano Hiroyuki、Kohsaka Shinji
  • Journal Title: Molecular Cancer Therapeutics Volume: 22 Issue: 2 Pages: 227-239
  • DOI: 10.1158/1535-7163.mct-22-0302
  • Peer Reviewed / Open Access
• [Journal Article] Mixed Response to Cancer Immunotherapy is Driven by Intratumor Heterogeneity and Differential Interlesion Immune Infiltration (2022)
  • Author(s): T. Morinaga, T. Inozume, Y. Togashi et al.
  • Journal Title: Cancer Research Communications Volume: 2 Issue: 7 Pages: 739-753
  • DOI: 10.1158/2767-9764.crc-22-0050
  • Peer Reviewed / Open Access
• [Journal Article] PD-1 blockade therapy promotes infiltration of tumor-attacking exhausted T cell clonotypes (2022)
  • Author(s): Nagasaki Joji、Inozume Takashi、Yosuke Togashi et al.
  • Journal Title: Cell Reports Volume: 38 Issue: 5 Pages: 110331-110331
  • DOI: 10.1016/j.celrep.2022.110331
  • NAID: 120007192058
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Lactic acid promotes PD-1 expression in regulatory T cells in highly glycolytic tumor microenvironments (2022)
  • Author(s): Kumagai S, Koyama S, Itahashi K, Tanegashima T, Lin YT, Togashi Y, Kamada T, Irie T, Okumura G, Kono H, Ito D, Fujii R, Watanabe S, Sai A, Aokage K, Suzuki J, Ishii G, Kuwata T, Sakamoto N, Kawazu M, Ueno T, Mori T, Yamazaki N, Tsuboi M, Yatabe Y, Kinoshita T, Doi T, Shitara K, Mano H, Nishikawa H
  • Journal Title: Cancer Cell Volume: 40 Issue: 2 Pages: 201-218
  • DOI: 10.1016/j.ccell.2022.01.001
  • Peer Reviewed / Open Access
• [Journal Article] HLA Class I Analysis Provides Insight Into the Genetic and Epigenetic Background of Immune Evasion in Colorectal Cancer With High Microsatellite Instability (2022)
  • Author(s): Kawazu M, Ueno T, Saeki K, Sax N, Togashi Y, Kanaseki T, Chida K, Kishigami F, Sato K, Kojima S, Tanegashima T, Matsubara D, Tane K, Tanaka Y, Iinuma H, Hashiguchi Y, Hazama S, Khor SS, Tokunaga K, Tsuboi M, Niki T, Eto M, Shitara K, Torigoe T, Ishihara S, Aburatani H, Haeno H, Nishikawa H, Mano H
  • Journal Title: Gastroenterology Volume: 162 Issue: 3 Pages: 799-812
  • DOI: 10.1053/j.gastro.2021.10.010
  • Peer Reviewed / Open Access
• [Journal Article] Multi-omic profiling of peritoneal metastases in gastric cancer identifies molecular subtypes and therapeutic vulnerabilities (2021)
  • Author(s): Tanaka Yosuke、Chiwaki Fumiko、Kojima Shinya、Kawazu Masahito、Komatsu Masayuki、Ueno Toshihide、Inoue Satoshi、Sekine Shigeki、Matsusaki Keisuke、Matsushita Hiromichi、Boku Narikazu、Kanai Yae、Yatabe Yasushi、Sasaki Hiroki、Mano Hiroyuki
  • Journal Title: Nature Cancer Volume: 2 Issue: 9 Pages: 962-977
  • DOI: 10.1038/s43018-021-00240-6
  • Peer Reviewed / Open Access
• [Journal Article] MicroSEC; Sequence error filtering pipeline for formalin-fixed and paraffin-embedded samples. (2021)
  • Author(s): Ikegami M, Kohsaka S, Hirose T, Ueno T, Inoue S, Konomata N, Yamauchi H, Mori T, Sekine S, Inamoto Y, Yatabe Y, Kobayashi H, Tanaka S, Mano H.
  • Journal Title: Commun Biol Volume: 4 Issue: 1 Pages: 1396-1396
  • DOI: 10.1038/s42003-021-02930-4
  • Peer Reviewed / Open Access
• [Journal Article] Comparative Study on the Efficacy and Exposure of Molecular Target Agents in Non?small Cell Lung Cancer PDX Models with Driver Genetic Alterations (2021)
  • Author(s): Jo Hitomi、Yagishita Shigehiro、Hayashi Yoshiharu、Ryu Shoraku、Suzuki Mikiko、Kohsaka Shinji、Ueno Toshihide、Matsumoto Yuji、Horinouchi Hidehito、Ohe Yuichiro、Watanabe Shun-ichi、Motoi Noriko、Yatabe Yasushi、Mano Hiroyuki、Takahashi Kazuhisa、Hamada Akinobu
  • Journal Title: Molecular Cancer Therapeutics Volume: 21 Issue: 2 Pages: 359-370
  • DOI: 10.1158/1535-7163.mct-21-0371
  • Peer Reviewed / Open Access
• [Journal Article] Transcript-targeted analysis reveals isoform alterations and double-hop fusions in breast cancer (2021)
  • Author(s): Namba Shinichi、Ueno Toshihide、Kojima Shinya、Kobayashi Kenya、Kawase Katsushige、Tanaka Yosuke、Inoue Satoshi、Kishigami Fumishi、Kawashima Shusuke、Maeda Noriko、Ogawa Tomoko、Hazama Shoichi、Togashi Yosuke、Ando Mizuo、Shiraishi Yuichi、Mano Hiroyuki、Kawazu Masahito
  • Journal Title: Communications Biology Volume: 4 Issue: 1 Pages: 1320-1320
  • DOI: 10.1038/s42003-021-02833-4
  • Peer Reviewed / Open Access
• [Journal Article] TIGIT/CD155 axis mediates resistance to immunotherapy in patients with melanoma with the inflamed tumor microenvironment (2021)
  • Author(s): Kawashima S, Inozume T, Kawazu M, Ueno T, Nagasaki J, Tanji E, Honobe A, Ohnuma T, Kawamura T, Umeda Y, Nakamura Y, Kawasaki T, Kiniwa Y, Yamasaki O, Fukushima S, Ikehara Y, Mano H, Suzuki Y, Nishikawa H, Matsue H, Togashi Y.
  • Journal Title: Journal for ImmunoTherapy of Cancer Volume: 9 Issue: 11 Pages: e003134-e003134
  • DOI: 10.1136/jitc-2021-003134
  • NAID: 120007175403
  • Peer Reviewed / Open Access
• [Journal Article] Highly sensitive fusion detection using plasma cell-free RNA in non-small-cell lung cancers. (2021)
  • Author(s): Hasegawa N, Kohsaka S, Kurokawa K, Shinno Y, Takeda Nakamura I, Ueno T, Kojima S, Kawazu M, Suehara Y, Ishijima M, Goto Y, Kojima Y, Yonemori K, Hayashi T, Saito T, Shukuya T, Takahashi F, Takahashi K, Mano H.
  • Journal Title: Cancer Sci Volume: 112 Issue: 10 Pages: 4393-4403
  • DOI: 10.1111/cas.15084
  • Peer Reviewed / Open Access
• [Journal Article] Comprehensive functional evaluation of variants of fibroblast growth factor receptor genes in cancer. (2021)
  • Author(s): Takeda Nakamura I, Kohsaka S, Ikegami M, Ueno T, Li K, Beyett T, Koyama T, Shimizu T, Yamamoto N, Takahashi F, Takahashi K, Eck M, Mano H.
  • Journal Title: NPJ Precision Oncology Volume: 16 Issue: 1 Pages: 66-66
  • DOI: 10.1038/s41698-021-00204-0
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A Low Tumor Mutational Burden and <i>PTEN</i> Mutations Are Predictors of a Negative Response to PD-1 Blockade in MSI-H/dMMR Gastrointestinal Tumors (2021)
  • Author(s): Chida Keigo, Kawazoe Akihito, Kawazu Masahito et al.
  • Journal Title: Clinical Cancer Research Volume: 27 Issue: 13 Pages: 3714-3724
  • DOI: 10.1158/1078-0432.ccr-21-0401
  • NAID: 130008144997
  • Peer Reviewed / Open Access
• [Journal Article] Rapid reprogramming of tumour cells into cancer stem cells on double-network hydrogels (2021)
  • Author(s): Suzuka J, Tsuda M, Wang L, Kohsaka S, Kishida K, Semba S, Sugino H, Aburatani S, Frauenlob M, Kurokawa T, Kojima S, Ueno T, Ohmiya Y, Mano H, Yasuda K, Gong JP, Tanaka S
  • Journal Title: Nat Biomed Eng Volume: － Issue: 8 Pages: 914-925
  • DOI: 10.1038/s41551-021-00692-2
  • Peer Reviewed / Open Access
• [Journal Article] Development of an optimal protocol for molecular profiling of tumor cells in pleural effusions at single-cell level (2021)
  • Author(s): Takeda Nakamura I, Ikegami M, Hasegawa N, Hayashi T, Ueno T, Kawazu M, Yagishita S, Goto Y, Shinno Y, Kojima Y, Takamochi K, Takahashi F, Takahashi K, Mano H, Kohsaka S
  • Journal Title: Cancer Sci Volume: － Issue: 5 Pages: 2006-2019
  • DOI: 10.1111/cas.14821
  • Peer Reviewed / Open Access
• [Presentation] 君にもできるゲノミクス：体細胞変異解析入門１ (2023)
  • Author(s): 上野 敏秀
  • Organizer: 第82回日本癌学会学術総会
  • Invited
• [Presentation] 2.君にもできるゲノミクス：体細胞変異解析入門２ (2023)
  • Author(s): 上野 敏秀
  • Organizer: 第82回日本癌学会学術総会
  • Invited