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Phasing analysis of lung cancer genomes using a long read sequencer

Author

Listed:
  • Yoshitaka Sakamoto

    (The University of Tokyo)

  • Shuhei Miyake

    (The University of Tokyo)

  • Miho Oka

    (The University of Tokyo
    Ono Pharmaceutical Co., Ltd)

  • Akinori Kanai

    (The University of Tokyo)

  • Yosuke Kawai

    (National Center for Global Health and Medicine)

  • Satoi Nagasawa

    (The University of Tokyo)

  • Yuichi Shiraishi

    (National Cancer Center Research Institute)

  • Katsushi Tokunaga

    (National Center for Global Health and Medicine)

  • Takashi Kohno

    (National Cancer Center Research Institute)

  • Masahide Seki

    (The University of Tokyo)

  • Yutaka Suzuki

    (The University of Tokyo)

  • Ayako Suzuki

    (The University of Tokyo)

Abstract

Chromosomal backgrounds of cancerous mutations still remain elusive. Here, we conduct the phasing analysis of non-small cell lung cancer specimens of 20 Japanese patients. By the combinatory use of short and long read sequencing data, we obtain long phased blocks of 834 kb in N50 length with >99% concordance rate. By analyzing the obtained phasing information, we reveal that several cancer genomes harbor regions in which mutations are unevenly distributed to either of two haplotypes. Large-scale chromosomal rearrangement events, which resemble chromothripsis events but have smaller scales, occur on only one chromosome, and these events account for the observed biased distributions. Interestingly, the events are characteristic of EGFR mutation-positive lung adenocarcinomas. Further integration of long read epigenomic and transcriptomic data reveal that haploid chromosomes are not always at equivalent transcriptomic/epigenomic conditions. Distinct chromosomal backgrounds are responsible for later cancerous aberrations in a haplotype-specific manner.

Suggested Citation

  • Yoshitaka Sakamoto & Shuhei Miyake & Miho Oka & Akinori Kanai & Yosuke Kawai & Satoi Nagasawa & Yuichi Shiraishi & Katsushi Tokunaga & Takashi Kohno & Masahide Seki & Yutaka Suzuki & Ayako Suzuki, 2022. "Phasing analysis of lung cancer genomes using a long read sequencer," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31133-6
    DOI: 10.1038/s41467-022-31133-6
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    1. Yilong Li & Nicola D. Roberts & Jeremiah A. Wala & Ofer Shapira & Steven E. Schumacher & Kiran Kumar & Ekta Khurana & Sebastian Waszak & Jan O. Korbel & James E. Haber & Marcin Imielinski & Joachim We, 2020. "Patterns of somatic structural variation in human cancer genomes," Nature, Nature, vol. 578(7793), pages 112-121, February.
    2. Natalia Voronina & John K. L. Wong & Daniel Hübschmann & Mario Hlevnjak & Sebastian Uhrig & Christoph E. Heilig & Peter Horak & Simon Kreutzfeldt & Andreas Mock & Albrecht Stenzinger & Barbara Hutter , 2020. "The landscape of chromothripsis across adult cancer types," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    3. Mircea Cretu Stancu & Markus J. Roosmalen & Ivo Renkens & Marleen M. Nieboer & Sjors Middelkamp & Joep Ligt & Giulia Pregno & Daniela Giachino & Giorgia Mandrile & Jose Espejo Valle-Inclan & Jerome Ko, 2017. "Mapping and phasing of structural variation in patient genomes using nanopore sequencing," Nature Communications, Nature, vol. 8(1), pages 1-13, December.
    4. Rahul Nahar & Weiwei Zhai & Tong Zhang & Angela Takano & Alexis J. Khng & Yin Yeng Lee & Xingliang Liu & Chong Hee Lim & Tina P. T. Koh & Zaw Win Aung & Tony Kiat Hon Lim & Lavanya Veeravalli & Ju Yua, 2018. "Elucidating the genomic architecture of Asian EGFR-mutant lung adenocarcinoma through multi-region exome sequencing," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    5. Yingyao Zhou & Bin Zhou & Lars Pache & Max Chang & Alireza Hadj Khodabakhshi & Olga Tanaseichuk & Christopher Benner & Sumit K. Chanda, 2019. "Metascape provides a biologist-oriented resource for the analysis of systems-level datasets," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    6. Daniel L. Cameron & Leon Stefano & Anthony T. Papenfuss, 2019. "Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    7. Ludmil B. Alexandrov & Jaegil Kim & Nicholas J. Haradhvala & Mi Ni Huang & Alvin Wei Tian Ng & Yang Wu & Arnoud Boot & Kyle R. Covington & Dmitry A. Gordenin & Erik N. Bergstrom & S. M. Ashiqul Islam , 2020. "The repertoire of mutational signatures in human cancer," Nature, Nature, vol. 578(7793), pages 94-101, February.
    8. Georgette Tanner & David R. Westhead & Alastair Droop & Lucy F. Stead, 2021. "Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
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    Cited by:

    1. Yasuhiko Haga & Yoshitaka Sakamoto & Keiko Kajiya & Hitomi Kawai & Miho Oka & Noriko Motoi & Masayuki Shirasawa & Masaya Yotsukura & Shun-Ichi Watanabe & Miyuki Arai & Junko Zenkoh & Kouya Shiraishi &, 2023. "Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma," Nature Communications, Nature, vol. 14(1), pages 1-19, December.

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