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. 2023 Jun 7;619(7968):184–192. doi: 10.1038/s41586-023-06157-7

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© The Author(s) 2023

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 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/.

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Extended Data Fig. 11 — Top: Haplotype-specific Chr.4 DNA copy number (250 kb bins) determined from newly generated DNA-Seq data (~5X mean sequencing depth) of the bridge clones. Black arcs represent intra-chromosomal rearrangements determined from previous whole-genome sequencing of the same bridge clones and subclones (10-60X mean depth)¹¹. Rearrangements are phased to each homologue based on haplotype-specific copy-number changes at rearrangement breakpoints. The shaded box denotes the region of 27-37 Mb on Chr.4p with reduced ATAC-Seq signal as shown in Fig. 5c. We detected no clonal or subclonal breakpoints in this region (based on both DNA copy-number changepoints and rearrangement junctions) in bridge clones I, II, IV, VI, VII, IX, X. Bridge clone VIII and XI contain the most breakpoints within this region but display no significant change of ATAC density after normalization for copy-number variation. In bridge clone III, ATAC reduction is most prominent between 27 and 30.5 Mb and this region is far away from rearrangements that affect two segments between 32.19-32.23 Mb. Bridge clones V and XII both contain multiple copy-number and rearrangement breakpoints in this region and display modest but significant ATAC reduction (based on the permutation test). Bottom: Haplotype-specific gene transcription (TPM) ratio on Chr.4. Each dot represents the average TPM ratio of a single gene calculated from all 12 bridge clones, excluding samples with complete DNA deletion. Arrows point to the PCDH7 gene residing in the region with reduced ATAC signal.