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. 2021 Jun 7;12:3361. doi: 10.1038/s41467-021-23695-8

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© The Author(s) 2021

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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Fig. 2 — A Overview of structural variant identification by PLIER. B Schematic explanation of how butterfly plots of proximity-ligation products (green arches on top of chromosomes) between the target gene and the PLIER-identified rearrangement partner can help distinguish true target rearrangements (breakpoints 1–3, inside the probe targeted region) from non-target rearrangements (breakpoint 4, outside the probe targeted region). In a reciprocal rearrangement inside the target locus, the locus should reveal a 5’ part (section a) that preferentially forms proximity-ligation products with one side of the partner locus and that separates from a 3′ part (section b) that preferentially contacts and ligates the other part of the partner locus. If a breakpoint is present in cis outside the probe-targeted region (breakpoint 4), a 5′ (a) and 3′ (b) part of the target gene cannot be distinguished. C Three examples of reciprocal rearrangements uncovered by butterfly plots, involving MYC, BCL2, and BCL6, respectively. D Rearrangements can be non-reciprocal, such that only one part of a target locus fuses to a partner, as exemplified using butterfly plots of MYC, BCL2, and BCL6. E An example of identified amplification events. Such events are apparent from the elevated number of ligation products that are captured by all target genes (shown for MYC, BCL2, and BCL6 genes).