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Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity

Author

Listed:
  • Felicity Newell

    (QIMR Berghofer Medical Research Institute)

  • James S. Wilmott

    (The University of Sydney)

  • Peter A. Johansson

    (QIMR Berghofer Medical Research Institute)

  • Katia Nones

    (QIMR Berghofer Medical Research Institute)

  • Venkateswar Addala

    (QIMR Berghofer Medical Research Institute
    The University of Queensland)

  • Pamela Mukhopadhyay

    (QIMR Berghofer Medical Research Institute)

  • Natasa Broit

    (QIMR Berghofer Medical Research Institute
    The University of Queensland)

  • Carol M. Amato

    (Center for Rare Melanomas, University of Colorado Cancer Center, Aurora)

  • Robert Gulick

    (Center for Rare Melanomas, University of Colorado Cancer Center, Aurora)

  • Stephen H. Kazakoff

    (QIMR Berghofer Medical Research Institute)

  • Ann-Marie Patch

    (QIMR Berghofer Medical Research Institute)

  • Lambros T. Koufariotis

    (QIMR Berghofer Medical Research Institute)

  • Vanessa Lakis

    (QIMR Berghofer Medical Research Institute)

  • Conrad Leonard

    (QIMR Berghofer Medical Research Institute)

  • Scott Wood

    (QIMR Berghofer Medical Research Institute)

  • Oliver Holmes

    (QIMR Berghofer Medical Research Institute)

  • Qinying Xu

    (QIMR Berghofer Medical Research Institute)

  • Karl Lewis

    (Center for Rare Melanomas, University of Colorado Cancer Center, Aurora)

  • Theresa Medina

    (Center for Rare Melanomas, University of Colorado Cancer Center, Aurora)

  • Rene Gonzalez

    (Center for Rare Melanomas, University of Colorado Cancer Center, Aurora)

  • Robyn P. M. Saw

    (The University of Sydney
    The University of Sydney
    Royal Prince Alfred Hospital)

  • Andrew J. Spillane

    (The University of Sydney
    The University of Sydney
    Royal North Shore Hospital)

  • Jonathan R. Stretch

    (The University of Sydney
    The University of Sydney
    Royal Prince Alfred Hospital)

  • Robert V. Rawson

    (The University of Sydney
    The University of Sydney
    Royal Prince Alfred Hospital
    New South Wales Health Pathology)

  • Peter M. Ferguson

    (The University of Sydney
    The University of Sydney
    Royal Prince Alfred Hospital
    New South Wales Health Pathology)

  • Tristan J. Dodds

    (The University of Sydney)

  • John F. Thompson

    (The University of Sydney
    The University of Sydney
    Royal Prince Alfred Hospital)

  • Georgina V. Long

    (The University of Sydney
    The University of Sydney
    Royal North Shore Hospital)

  • Mitchell P. Levesque

    (Dermatology Clinic, University Hospital Zürich, University of Zurich)

  • William A. Robinson

    (Center for Rare Melanomas, University of Colorado Cancer Center, Aurora)

  • John V. Pearson

    (QIMR Berghofer Medical Research Institute)

  • Graham J. Mann

    (The University of Sydney
    John Curtin School of Medical Research, Australian National University
    Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead)

  • Richard A. Scolyer

    (The University of Sydney
    The University of Sydney
    Royal Prince Alfred Hospital
    New South Wales Health Pathology)

  • Nicola Waddell

    (QIMR Berghofer Medical Research Institute
    The University of Queensland)

  • Nicholas K. Hayward

    (QIMR Berghofer Medical Research Institute)

Abstract

To increase understanding of the genomic landscape of acral melanoma, a rare form of melanoma occurring on palms, soles or nail beds, whole genome sequencing of 87 tumors with matching transcriptome sequencing for 63 tumors was performed. Here we report that mutational signature analysis reveals a subset of tumors, mostly subungual, with an ultraviolet radiation signature. Significantly mutated genes are BRAF, NRAS, NF1, NOTCH2, PTEN and TYRP1. Mutations and amplification of KIT are also common. Structural rearrangement and copy number signatures show that whole genome duplication, aneuploidy and complex rearrangements are common. Complex rearrangements occur recurrently and are associated with amplification of TERT, CDK4, MDM2, CCND1, PAK1 and GAB2, indicating potential therapeutic options.

Suggested Citation

  • Felicity Newell & James S. Wilmott & Peter A. Johansson & Katia Nones & Venkateswar Addala & Pamela Mukhopadhyay & Natasa Broit & Carol M. Amato & Robert Gulick & Stephen H. Kazakoff & Ann-Marie Patch, 2020. "Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18988-3
    DOI: 10.1038/s41467-020-18988-3
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    Cited by:

    1. Farshad Farshidfar & Kahn Rhrissorrakrai & Chaya Levovitz & Cong Peng & James Knight & Antonella Bacchiocchi & Juan Su & Mingzhu Yin & Mario Sznol & Stephan Ariyan & James Clune & Kelly Olino & Laxmi , 2022. "Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Chuanyuan Wei & Wei Sun & Kangjie Shen & Jingqin Zhong & Wanlin Liu & Zixu Gao & Yu Xu & Lu Wang & Tu Hu & Ming Ren & Yinlam Li & Yu Zhu & Shaoluan Zheng & Ming Zhu & Rongkui Luo & Yanwen Yang & Yingy, 2023. "Delineating the early dissemination mechanisms of acral melanoma by integrating single-cell and spatial transcriptomic analyses," Nature Communications, Nature, vol. 14(1), pages 1-20, December.

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