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Melanoma is a cancer of melanocytes, with multiple subtypes based on body site location. Cutaneous melanoma is associated with skin exposed to ultraviolet radiation; uveal melanoma occurs in the eyes; mucosal melanoma occurs in internal mucous membranes; and acral melanoma occurs on the palms, soles, and nail beds. Here, we present the largest whole-genome sequencing study of melanoma to date, with 570 tumors profiled, as well as methylation and RNA sequencing for subsets of tumors. Uveal melanoma is genomically distinct from other melanoma subtypes, harboring the lowest tumor mutation burden and with significantly mutated genes in the G-protein signaling pathway. Most cutaneous, acral, and mucosal melanomas share alterations in components of the MAPK, PI3K, p53, p16, and telomere pathways. However, the mechanism by which these pathways are activated or inactivated varies between melanoma subtypes. Additionally, we identify potential novel germline predisposition genes for some of the less common melanoma subtypes., Significance: This is the largest whole-genome analysis of melanoma to date, comprehensively comparing the genomics of the four major melanoma subtypes. This study highlights both similarities and differences between the subtypes, providing insights into the etiology and biology of melanoma. This article is highlighted in the In This Issue feature, p. 2711., (©2022 The Authors; Published by the American Association for Cancer Research.)

We concurrently examine the whole genome, transcriptome, methylome, and immune cell infiltrates in baseline tumors from 77 patients with advanced cutaneous melanoma treated with anti-PD-1 with or without anti-CTLA-4. We show that high tumor mutation burden (TMB), neoantigen load, expression of IFNγ-related genes, programmed death ligand expression, low PSMB8 methylation (therefore high expression), and T cells in the tumor microenvironment are associated with response to immunotherapy. No specific mutation correlates with therapy response. A multivariable model combining the TMB and IFNγ-related gene expression robustly predicts response (89% sensitivity, 53% specificity, area under the curve [AUC], 0.84); tumors with high TMB and a high IFNγ signature show the best response to immunotherapy. This model validates in an independent cohort (80% sensitivity, 59% specificity, AUC, 0.79). Except for a JAK3 loss-of-function mutation, for patients who did not respond as predicted there is no obvious biological mechanism that clearly explained their outlier status, consistent with intratumor and intertumor heterogeneity in response to immunotherapy., Competing Interests: Declaration of interests I.P.S. has received travel support by BMS and MSD, and speaker fee by Roche, BMS, MSD, and Novartis. J.F.T. has received honoraria for advisory board participation from Merck Sharpe Dohme Australia and Bristol Myers Squibb Australia and received honoraria and travel expenses from GSK and Provectus Inc. R.A.S. has received fees for professional services from Evaxion, Provectus Biopharmaceuticals Australia, Qbiotics Group Limited, Novartis Pharma AG, MSD Sharp & Dohme (Australia), NeraCare, AMGEN Inc., Bristol-Myers Squibb, Novartis Pharmaceuticals Australia Pty Limited, Myriad Genetics GmbH, and GlaxoSmithKline Australia. G.V.L. is consultant advisor for Aduro Biotech Inc, Agenus Inc, Amgen Inc, Array Biopharma inc, Boehringer Ingelheim International GmbH, Bristol-Myers Squibb, Evaxion Biotech A/S, Hexel AG, Highlight Therapeutics S.L., Merck Sharpe & Dohme, Novartis Pharma AG, OncoSec, Pierre Fabre, QBiotics Group Limited, Regeneron Pharmaceuticals Inc, SkylineDX B.V., Specialised Therapeutics Australia Pty Ltd. R.P.M.S has participated in advisory boards for MSD, Novartis, and Qbiotics and received speaking honoraria from BMS. J.V.P. and N.W. are founders and shareholders of genomiQa Pty Ltd, and members of its Board. M.S.C. is a consultant advisor to MSD, BMS, Novartis, Roche, Pierre Fabre, Sanofi, Merck Serono, Nektar, Eisia, and Ideaya and received honoraria from MSD, BMS, and Novartis. A.M.M. has participated in advisory boards for BMS, MSD, Novartis, Roche, and Pierre-Fabre. C.U.B. has served on advisory boards for BMS, MSD, Roche, Novartis, GSK, AZ, Pfizer, Lilly, GenMab, Pierre Fabre, and Third Rock Ventures; received research funding from BMS, MSD, 4SC, Novartis, and NanoString; has stock ownership in Uniti Cars; and is a cofounder of Immagene BV. The remaining authors declare no competing interests., (Copyright © 2021 Elsevier Inc. All rights reserved.)

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.