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. 2020 Jul 6;21:166. doi: 10.1186/s13059-020-02076-2

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© The Author(s) 2020

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 3 — Recurrent gene^UIB fusions that massively upregulate target mRNA. a–j Differential gene expression between the target gene^UIB fusion-positive and fusion-negative groups. The ratio between the group means is noted. The BRCA genes are ordered by their expression ratio. Those samples in which the over-expression was less than fourfold compared to the median of the control samples are noted by an asterisk and are excluded from k since they are less likely to be functional. Upstream intergenic breakpoint (UIB) distances were described using gradation color in the fusion-positive group. The UIB distance is defined as the base pair distance from the target gene to the upstream intergenic breakpoint. k A distribution of UIB distances in 10 genes. Notably, 28% of breakpoints (21/75) were more than 2 Mb away from the putative target gene. l The landscape of gene^UIB fusion in 40 breast cancer samples. Basal type in PAM50 classification (classifier based on differential expression of 50 genes) is known to assimilate to triple-negative (TN) breast cancer type