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2020 Fiscal Year Research-status Report

Next generation sequencing of circulating tumor DNA to monitor treatment response to nivolumab in advanced gastric cancer

Research Project

Project/Area Number 20K07709
Research InstitutionJapanese Foundation for Cancer Research

Principal Investigator

LOW SIEWKEE  公益財団法人がん研究会, がんプレシジョン医療研究センター 免疫ゲノム医療開発プロジェクト, 研究員 (40634720)

Project Period (FY) 2020-04-01 – 2023-03-31
Keywordsliquid biopsy / ctDNA
Outline of Annual Research Achievements

The proposal aims to establish a customized circulating tumor DNA (ctDNA) cancer panel to evaluate the mutation profiles of cancer patients who receive immune checkpoint inhibitor (ICI).
Firstly, actionable mutations of cancer genes and genes related to ICI response were retrieved from literature review. The frequency of the hotspot mutations on these genes were assessed and incorporated into Ion AmpliSeq Designer.
The customized ctDNA panel was designed with the amplicon range 75-125bp with high specificity. The number of primer pools, amplicons inclusion and coverage of the panel were evaluated. The protocol of ultradeep targeted next sequencing (NGS) was designed to yield overall coverage of 50,000x using Ion S5 Prime system.

Current Status of Research Progress
Current Status of Research Progress

3: Progress in research has been slightly delayed.

Reason

The customized ctDNA amplicon-based panel is designed. However, optimization is needed to increase the coverage and the specificity of the designed panel. Other parameters such as linearity of individual amplicon depth and molecular barcode tagging efficiency of the customized panel will also have to be evaluated as measurements of quality control by using NGS standard control samples before using the panel on cancer patient's samples.

Strategy for Future Research Activity

After the establishment and optimization of the customized ctDNA panel, ctDNA from serial sampling of cancer patients who receive ICI will be assessed. The efficacy and limit of detection of the customized panel will be evaluated.
Subsequently, mutations that are associated with the mechanism of resistance/non-responsive will be evaluated when patients encounter progression disease after receiving ICI treatment.

  • Research Products

    (10 results)

All 2020

All Journal Article (6 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 6 results,  Open Access: 4 results) Presentation (4 results) (of which Int'l Joint Research: 3 results,  Invited: 1 results)

  • [Journal Article] Ultradeep targeted sequencing of circulating tumor DNA in plasma of early and advanced breast cancer2020

    • Author(s)
      Chin Yoon Ming、Takahashi Yoko、Chan Hiu Ting、Otaki Masumi、Fujishima Makoto、Shibayama Tomoko、Miki Yoshio、Ueno Takayuki、Nakamura Yusuke、Low Siew‐Kee
    • Journal Title

      Cancer Science

      Volume: 112 Pages: 454~464

    • DOI

      10.1111/cas.14697

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Clonal Hematopoiesis in Liquid Biopsy: From Biological Noise to Valuable Clinical Implications2020

    • Author(s)
      Chan Hiu Ting、Chin Yoon Ming、Nakamura Yusuke、Low Siew-Kee
    • Journal Title

      Cancers

      Volume: 12 Pages: 2277~2277

    • DOI

      10.3390/cancers12082277

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Plasma or Serum: Which Is Preferable for Mutation Detection in Liquid Biopsy?2020

    • Author(s)
      Pittella-Silva Fabio、Chin Yoon Ming、Chan Hiu Ting、Nagayama Satoshi、Miyauchi Eisaku、Low Siew-Kee、Nakamura Yusuke
    • Journal Title

      Clinical Chemistry

      Volume: 66 Pages: 946~957

    • DOI

      10.1093/clinchem/hvaa103

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases2020

    • Author(s)
      Ishigaki Kazuyoshi、Akiyama Masato、Kanai Masahiro、Takahashi Atsushi、Kawakami Eiryo、Sugishita Hiroki、Sakaue Saori、Matoba Nana、Low Siew-Kee、et al., Nakamura Yusuke、Raychaudhuri Soumya、Inazawa Johji、Yamauchi Toshimasa、Kadowaki Takashi、Kubo Michiaki、Kamatani Yoichiro
    • Journal Title

      Nature Genetics

      Volume: 52 Pages: 669~679

    • DOI

      10.1038/s41588-020-0640-3

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Clinical significance of clonal hematopoiesis in the interpretation of blood liquid biopsy2020

    • Author(s)
      Chan Hiu Ting、Nagayama Satoshi、Chin Yoon Ming、Otaki Masumi、Hayashi Rie、Kiyotani Kazuma、Fukunaga Yosuke、Ueno Masashi、Nakamura Yusuke、Low Siew‐Kee
    • Journal Title

      Molecular Oncology

      Volume: 14 Pages: 1719~1730

    • DOI

      10.1002/1878-0261.12727

    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Clinical significance of gene mutation in ctDNA analysis for hormone receptor-positive metastatic breast cancer2020

    • Author(s)
      Shibayama Tomoko、Low Siew-Kee、Ono Makiko、Kobayashi Takayuki、Kobayashi Kokoro、Fukada Ippei、Ito Yoshinori、Ueno Takayuki、Ohno Shinji、Nakamura Yusuke、Takahashi Shunji
    • Journal Title

      Breast Cancer Research and Treatment

      Volume: 180 Pages: 331~341

    • DOI

      10.1007/s10549-019-05512-5

    • Peer Reviewed / Int'l Joint Research
  • [Presentation] Evaluation of Genexus system that automates specimen-to-report for cancer genomic profiling using liquid biopsy2020

    • Author(s)
      SK Low, K Uchibori, R Hayashi, HT Chan, R Ariyasu, S Kitazono, N Yanagitani, M Nishio and Y Nakamura.
    • Organizer
      The 79th Annual Meeting of the Japanese Cancer Association
  • [Presentation] Evaluation of Genexus system that automates specimen-to-report for cancer genomic profiling within a day using liquid biopsy2020

    • Author(s)
      SK Low, K Uchibori, R Hayashi, HT Chan, R Ariyasu, S Kitazono, N Yanagitani, M Nishio and Y Nakamura
    • Organizer
      American Society of Clinical Oncology (ASCO) Annual Meeting, 2020
    • Int'l Joint Research
  • [Presentation] NGS of circulating tumor DNA in clinical cancer research.2020

    • Author(s)
      SK Low, YM Chin, HT Chan, K Uchibori, S Nagayama, E Miyauchi, T Ueno, S Takahashi, M Nishio and Y Nakamura
    • Organizer
      7th US-Japan Workshop on Biomarkers for Cancer Early Detection
    • Int'l Joint Research / Invited
  • [Presentation] Next generation sequencing of circulating tumor DNA to monitor treatment response to CDK4/6 inhibitors in breast cancer.2020

    • Author(s)
      YM Chin, T Shibayama, M Otaki, HT Chan, M Ono, Y Ito, S Takahashi, S Ohno, T Ueno, Y Nakamura, SK Low
    • Organizer
      Advances in liquid biopsy, American Association for Cancer Research (AACR)
    • Int'l Joint Research

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Published: 2021-12-27  

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