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. 2022 Dec 30;4(1):128–147. doi: 10.1038/s43018-022-00491-x

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 7 — a. Waterfall plot of AURORA cases showing the difference between primary (n = 36 tumors) and metastasis (n = 60 tumors) (Difference: Metastasis – Primary gene expression value) ordered from the highest (left) to the lowest (right) signature score for HLA-A mRNA expression (upper panel). The bottom panel shows the difference between primary and metastases for GP2-Immune-Metagene values. Yellow stars highlight HLA-A Hypermethylated cases and green stars highlight the samples with DNA HLA-A focal deletions. b. Waterfall plot of RAP cases showing the difference between primary (n = 12 tumors) and metastasis (n = 40 tumors) (Difference: Metastasis – Primary gene expression value) ordered from the highest (left) to the lowest (right) signature score for HLA-A mRNA expression (upper panel). The bottom panel shows the difference of primary versus metastases for GP2-Immune-Metagene values. Pairs with a Normal-like primary tumor were removed from the analysis. LumA, Luminal A; LumB, Luminal B.