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

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, Lambros T. Koufariotis, Vanessa Lakis, Conrad Leonard, Scott Wood, Oliver Holmes, Qinying Xu, Karl Lewis, Theresa Medina, Rene Gonzalez, Robyn P. M. Saw, Andrew J. Spillane, Jonathan R. Stretch, Robert V. Rawson, Peter M. Ferguson, Tristan J. Dodds, John F. Thompson, Georgina V. Long, Mitchell P. Levesque, William A. Robinson, John V. Pearson, Graham J. Mann, Richard A. Scolyer, Nicola Waddell and Nicholas K. Hayward
Additional contact information
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
Pamela Mukhopadhyay: QIMR Berghofer Medical Research Institute
Natasa Broit: QIMR Berghofer Medical Research Institute
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
Andrew J. Spillane: The University of Sydney
Jonathan R. Stretch: The University of Sydney
Robert V. Rawson: The University of Sydney
Peter M. Ferguson: The University of Sydney
Tristan J. Dodds: The University of Sydney
John F. Thompson: The University of Sydney
Georgina V. Long: The University of Sydney
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
Richard A. Scolyer: The University of Sydney
Nicola Waddell: QIMR Berghofer Medical Research Institute
Nicholas K. Hayward: QIMR Berghofer Medical Research Institute

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-18988-3

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