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Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis

Author

Listed:
  • Go Sato

    (Osaka University Graduate School of Medicine
    Osaka University)

  • Yuya Shirai

    (Osaka University Graduate School of Medicine
    Osaka University Graduate School of Medicine
    Osaka University)

  • Shinichi Namba

    (Osaka University Graduate School of Medicine)

  • Ryuya Edahiro

    (Osaka University Graduate School of Medicine
    Osaka University Graduate School of Medicine)

  • Kyuto Sonehara

    (Osaka University Graduate School of Medicine
    RIKEN Center for Integrative Medical Sciences
    the University of Tokyo)

  • Tsuyoshi Hata

    (Osaka University)

  • Mamoru Uemura

    (Osaka University)

  • Koichi Matsuda

    (the University of Tokyo)

  • Yuichiro Doki

    (Osaka University)

  • Hidetoshi Eguchi

    (Osaka University)

  • Yukinori Okada

    (Osaka University Graduate School of Medicine
    Osaka University
    RIKEN Center for Integrative Medical Sciences
    the University of Tokyo)

Abstract

Integrating genomic data of multiple cancers allows de novo cancer grouping and elucidating the shared genetic basis across cancers. Here, we conduct the pan-cancer and cross-population genome-wide association study (GWAS) meta-analysis and replication studies on 13 cancers including 250,015 East Asians (Biobank Japan) and 377,441 Europeans (UK Biobank). We identify ten cancer risk variants including five pleiotropic associations (e.g., rs2076295 at DSP on 6p24 associated with lung cancer and rs2525548 at TRIM4 on 7q22 nominally associated with six cancers). Quantifying shared heritability among the cancers detects positive genetic correlations between breast and prostate cancer across populations. Common genetic components increase the statistical power, and the large-scale meta-analysis of 277,896 breast/prostate cancer cases and 901,858 controls identifies 91 newly genome-wide significant loci. Enrichment analysis of pathways and cell types reveals shared genetic backgrounds across said cancers. Focusing on genetically correlated cancers can contribute to enhancing our insights into carcinogenesis.

Suggested Citation

  • Go Sato & Yuya Shirai & Shinichi Namba & Ryuya Edahiro & Kyuto Sonehara & Tsuyoshi Hata & Mamoru Uemura & Koichi Matsuda & Yuichiro Doki & Hidetoshi Eguchi & Yukinori Okada, 2023. "Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39136-7
    DOI: 10.1038/s41467-023-39136-7
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    as
    1. Corina Lesseur & Aida Ferreiro-Iglesias & James D McKay & Yohan Bossé & Mattias Johansson & Valerie Gaborieau & Maria Teresa Landi & David C Christiani & Neil C Caporaso & Stig E Bojesen & Christopher, 2021. "Genome-wide association meta-analysis identifies pleiotropic risk loci for aerodigestive squamous cell cancers," PLOS Genetics, Public Library of Science, vol. 17(3), pages 1-19, March.
    2. Kyriaki Michailidou & Sara Lindström & Joe Dennis & Jonathan Beesley & Shirley Hui & Siddhartha Kar & Audrey Lemaçon & Penny Soucy & Dylan Glubb & Asha Rostamianfar & Manjeet K. Bolla & Qin Wang & Jon, 2017. "Association analysis identifies 65 new breast cancer risk loci," Nature, Nature, vol. 551(7678), pages 92-94, November.
    3. David Lamparter & Daniel Marbach & Rico Rueedi & Zoltán Kutalik & Sven Bergmann, 2016. "Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics," PLOS Computational Biology, Public Library of Science, vol. 12(1), pages 1-20, January.
    4. Xia Jiang & Hilary K. Finucane & Fredrick R. Schumacher & Stephanie L. Schmit & Jonathan P. Tyrer & Younghun Han & Kyriaki Michailidou & Corina Lesseur & Karoline B. Kuchenbaecker & Joe Dennis & David, 2019. "Publisher Correction: Shared heritability and functional enrichment across six solid cancers," Nature Communications, Nature, vol. 10(1), pages 1-8, December.
    5. Xia Jiang & Hilary K. Finucane & Fredrick R. Schumacher & Stephanie L. Schmit & Jonathan P. Tyrer & Younghun Han & Kyriaki Michailidou & Corina Lesseur & Karoline B. Kuchenbaecker & Joe Dennis & David, 2019. "Shared heritability and functional enrichment across six solid cancers," Nature Communications, Nature, vol. 10(1), pages 1-23, December.
    6. Naim Panjwani & Fan Wang & Scott Mastromatteo & Allen Bao & Cheng Wang & Gengming He & Jiafen Gong & Johanna M Rommens & Lei Sun & Lisa J Strug, 2020. "LocusFocus: Web-based colocalization for the annotation and functional follow-up of GWAS," PLOS Computational Biology, Public Library of Science, vol. 16(10), pages 1-8, October.
    7. Sara R. Rashkin & Rebecca E. Graff & Linda Kachuri & Khanh K. Thai & Stacey E. Alexeeff & Maruta A. Blatchins & Taylor B. Cavazos & Douglas A. Corley & Nima C. Emami & Joshua D. Hoffman & Eric Jorgens, 2020. "Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    8. Masato Akiyama & Kazuyoshi Ishigaki & Saori Sakaue & Yukihide Momozawa & Momoko Horikoshi & Makoto Hirata & Koichi Matsuda & Shiro Ikegawa & Atsushi Takahashi & Masahiro Kanai & Sadao Suzuki & Daisuke, 2019. "Characterizing rare and low-frequency height-associated variants in the Japanese population," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    9. Clare Bycroft & Colin Freeman & Desislava Petkova & Gavin Band & Lloyd T. Elliott & Kevin Sharp & Allan Motyer & Damjan Vukcevic & Olivier Delaneau & Jared O’Connell & Adrian Cortes & Samantha Welsh &, 2018. "The UK Biobank resource with deep phenotyping and genomic data," Nature, Nature, vol. 562(7726), pages 203-209, October.
    10. Kyoko Watanabe & Erdogan Taskesen & Arjen Bochoven & Danielle Posthuma, 2017. "Functional mapping and annotation of genetic associations with FUMA," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    11. Yukinori Okada & Yukihide Momozawa & Saori Sakaue & Masahiro Kanai & Kazuyoshi Ishigaki & Masato Akiyama & Toshihiro Kishikawa & Yasumichi Arai & Takashi Sasaki & Kenjiro Kosaki & Makoto Suematsu & Ko, 2018. "Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
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