Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Chromatin is folded into successive layers to organize linear DNA. Genes within the same topologically associating domains (TADs) demonstrate similar expression and histone-modification profiles, and boundaries separating different domains have important roles in reinforcing the stability of these features. Indeed, domain disruptions in human cancers can lead to misregulation of gene expression. However, the frequency of domain disruptions in human cancers remains unclear. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumor types, we analyzed 288,457 somatic structural variations (SVs) to understand the distributions and effects of SVs across TADs. Notably, SVs can lead to the fusion of discrete TADs, and complex rearrangements markedly change chromatin folding maps in the cancer genomes. Notably, only 14% of the boundary deletions resulted in a change in expression in nearby genes of more than twofold.


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published boundaries (Extended Data Fig. 1b). This showed that the current boundary regions were comparable with previously mapped boundaries even though they were identified at a different Hi-C resolution and using a different detection algorithm. Furthermore, we observed known TAD boundary signatures 4 around our boundary calls for each cell type (Extended Data Fig. 1c). Across all cell types, we identified a common set of 2,477 boundaries (Supplementary  Table 1, Extended Data Fig. 1d). There was a significant (P < 10 −6 ) overlap (a 50-kb distance was allowed) between TAD boundaries among all profiled cell types. The median distance between the common boundaries was approximately 750 kb, consistent with the reported median TAD size in human cells 4,19 (Extended Data Fig. 1e). The resulting 2,477 common regions were used for the rest of the analyses (referred to as boundaries hereafter).
Next, to test whether the overall chromatin architecture is similar in cancer and non-cancer cells, we intersected these boundaries with the TAD boundaries found in cancer cell lines. We observed a high overlap with boundaries from a leukemia cell line K562 (ref. 17 ) and a breast cancer cell line MCF7 (ref. 20 ) (85% and 83.4%, respectively; Extended Data Fig. 1f,g). These analyses revealed that a significant (P < 10 −7 ) percentage of boundaries was conserved between normal and malignant cells. We next examined the enrichment of CCCTC-binding factor (CTCF)-binding and DNase I hypersensitivity sites, as well as active transcription start sites and heterochromatic regions around boundaries from various cell types that have previously been profiled by the Encyclopedia of DNA Elements (ENCODE) consortium 19 and the Roadmap Epigenome project 21 . We observed that CTCF-binding sites and active promoter marks were enriched, whereas the heterochromatin state was depleted at the boundaries. In addition, TAD signal levels were the lowest at the boundaries compared with flanking sites (Fig. 1a), consistent with the role of TAD boundaries in the reduction of the contacts between adjacent domains. Overall, these common 2,477 boundaries exhibited the genomic features of TAD boundaries across different human cell types.
To understand the effects of SVs on TAD boundaries in human cancers, we used 288,457 high-confidence somatic SVs as part of the ICGC PCAWG project. The PCAWG Consortium aggregated whole-genome sequencing (WGS) data from 2,658 cancers across 38 tumor types generated by the ICGC and TCGA projects. These sequencing data were re-analyzed with standardized, high-accuracy pipelines to align to the human genome (reference build hs37d5) and identify germline variants and somatically acquired mutations, as described in the lead paper of the PCAWG Consortium 22 . We used SV breakpoint orientations as a measurement to classify deletions, inversions, duplications or complex rearrangements as described previously 23 . Complex rearrangements included chromothripsis 24 and other alterations, which covered SV break-ends with concomitant deletions, inversions or duplications. SVs were further categorized into two subgroups based on the length of the events-SVs that were longer than 2 Mb in genomic length (long-range SVs) and shorter than 2 Mb in genomic length (short-range SVs). The majority of deletions, inversions and duplications could be categorized as short-range; however, complex events tended to be longer in length (Extended Data Fig. 2a). In this study, we focused on short-range SVs because long-range SVs could affect multiple boundaries due to the genomic length of the event. We identified SVs that affected the TAD boundaries (boundary affecting (BA)) as the ones that spanned the whole length of a boundary (around 75 kb). As a result, 5.0%, 8.5%, 12.8% and 19.9% of all deletions, inversions, duplications and complex events were called BA events, respectively (Fig. 1b). Compared with the expected number of boundary disruptions based on randomly shuffled boundaries, these ratios are strongly enriched in BA-duplications (P < 10 −4 , 1.43-fold enrichment). In contrast, we observed a depletion (0.87-fold enrichment, P = 0.052) in BA-deletions, whereas BA-inversions and BA-complex events occurred at expected levels (P > 0.05) compared with the shuffled TAD boundaries (Fig. 1c). Overall, these results suggest that deletions tended to occur within the same TAD, whereas duplications tended to span regions across different TADs.
In cancer cells, boundaries are affected to various degrees due to structural alterations, which suggests that some mechanistic differences could cause different SV types. Length distributions of the BA-SVs were uniformly distributed (Extended Data Fig. 2b). Most of the BA-SVs targeted a single boundary; 74% of BA-deletions, 65% of BA-inversions, 71% of BA-duplications and 64% of BA-complex events affected a single boundary per variant (Fig. 1d). The number of affected boundaries did not markedly change with the minimum length of the SVs (Fig. 1d, Extended Data Fig. 2c). The majority (98.4%) of the boundaries were affected in cancer genomes, although a few boundaries were located in the low-mappability regions of the genome. Interestingly, TAD boundaries are significantly less likely (P < 0.02) to be affected by known deletion and duplication polymorphisms derived from genomes of healthy human populations [25][26][27] (Extended Data Fig. 2d). Genomic length of the germline alterations tends to be shorter compared with somatic alterations observed in tumors due to negative selection against large SVs in the germline 28 . Therefore, we selected germline and somatic deletions with a genomic length between 75 kb and 250 kb that occurred in all cancer samples (Fig. 1e). This filtering ensured that the selected somatic (median, 137 kb) or germline (median, 113 kb) deletions had the length potential to disrupt TAD boundaries. We observed that germline deletions that affected TAD boundaries were rare (less than 0.1%; 6 affected out of total 924 deletions) compared with somatic deletions (4.1%), even in cases in which similar genomic ranges and less than 1% of the total boundaries were affected by germline events, suggesting that germline variations in TAD boundaries may not be as well tolerated as similar somatic alterations.
Chromatin folding disruptions are specific to histological subtypes. We next focused on the distributions of BA-SVs across 38 different histological cancer subtypes 22 . The number of BA-SVs generally followed the total number of SVs in a given cancer type. Our analysis revealed that, among all cancer types, leiomyosarcoma and uterus adenocarcinoma had higher numbers with-on average-25 and 22 BA-SVs per sample, respectively, compared with a median of around 7 BA-SVs per sample across all cancer samples (Fig. 2a, b). Ovarian, esophageal and breast adenocarcinomas also contained high numbers of BA-SVs with-on average-20, 19 and 18 BA-SVs per sample, respectively. On the other hand, hematopoietic cancers (myeloid-MDS or myeloid-AML) had the lowest BA-SV rates. Only glioblastoma samples (CNS-GBM) showed lower-than-expected BA-SVs (P < 10 −3 ) across all cancer types. The median SV length of a given cancer type was not strongly correlated with the observed distributions (r 2 = 0.03-0.45) (Extended Data Fig. 3a). The observed differences in BA-SV rates are likely driven by the differences in the burden and mechanisms of SVs across histological types. For instance, leiomyosarcoma and esophageal adenocarcinoma had a higher complex SV burden and, as a result, observed BA events were also mostly complex rearrangements (Fig. 2b), whereas ovary and stomach adenocarcinoma samples contained BA-duplications due to an overall higher duplication rate (Fig. 2b). Similarly, the total number of SVs in an individual tumor affects the observed BA-SVs in that sample (Fig. 2b, Extended Data Fig. 3b). Long-range BA-SVs had similar distributions across histological types. Again, leiomyosarcoma and breast adenocarcinoma contained a higher number of BA-SVs compared with other cancer types, whereas leukemia samples had no BA-SVs per sample (Extended Data Fig. 4a). Taken together, our findings show that the impact of BA-SVs is varied substantially across tumor types and these events were reflective of overall SV burden and type.

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Recurrently affected boundaries in specific cancer types. Next, we sought to identify the affected boundaries near known driver genes in the COSMIC cancer gene census 29 . We noted that many of the boundaries of cancer driver genes were altered in specific histological subtypes (Fig. 3a, Supplementary Table 2). Of those recurrently affected boundaries, two adjacent boundaries between KIAA1549 and BRAF were prone to BA-duplications specifically in samples of pilocytic astrocytoma (Fig. 3b). This region has previously been implicated in pilocytic astrocytoma, producing an oncogenic fusion between the aforementioned genes 30 . In addition, boundaries near the MDM2 locus were most affected in leiomyosarcoma (Fig. 3b), likely due to neochromosome formations that included the MDM2 and CDK4 genes 31 . We also observed a higher mutational load specifically on chromosome 12 in leiomyosarcoma samples (Fig. 3b). Another recurrent BA-SV event was the high number of BA-deletions around RBFOX1 in colorectal adenocarcinoma samples (Extended Data Fig. 4b). We surveyed the BA-SV distributions on individual chromosomes and observed a positive correlation with the number of boundaries (r 2 = 0.68-0.92) and gene density (r 2 = 0.7-0.85) on a given chromosome (Extended Data Fig. 4c,d). Notably, distributions of BA-SVs per chromosome were generally specific to the histology subtype; for example, chromosome 17 was affected predominantly by BA-complex events in breast and esophageal adenocarcinoma samples (Extended Data Fig. 5a,b). These findings emphasize the cancer specificity of BA-SVs, in which active mechanisms lead to the overall SV burden and type in different tumor types yield potential changes in TAD structures, especially around cancer driver genes. We next examined SVs that occurred within TADs, which potentially resulted in the disruption of CTCF-CTCF chromatin loops 32 . We identified a number of chromatin loops that were potentially disrupted in various cancer types (Supplementary Table 3). For instance, a CTCF site near FOXC1 overlaps with recurrent deletions in esophageal, gastric and colon adenocarcinomas (Fig. 3c). Other potentially altered loops include a CTCF site near BCL6 in hepatocellular carcinoma and breast adenocarcinoma, and CLCN4 in colorectal adenocarcinomas (Extended Data Fig. 6a,b). Therefore, chromatin folding perturbations can occur at various scales, include TADs and CTCF-CTCF chromatin loops in cancer genomes and recurrently altered boundaries are generally cancer-type specific.

Most domain disruptions do not result in marked gene-expression changes.
To ascribe potential functional effects of BA-SVs on chromatin domains, we annotated the TADs by profiling the context of aggregate chromatin states within each TAD. We used a probabilistic approach that calculated the occurrence of chromatin states in   Table 4). In addition, we used constitutive LADs 34 identified in three different human cell types to profile the outcomes of the SVs that occurred between LADs and inter-LADs. We evaluated the annotation results by profiling the distributions of domain sizes. Repressed domains were larger in size and covered the majority of the genome compared with active domains, in agreement with previous TAD annotations 19,35 (Extended Data Fig. 7a,b)

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BA-inversion, BA-duplication or BA-complex events. The majority of the BA-SVs affected the same flanking domain types, such as boundaries that separated low and low domains or low-active and low-active domains (Extended Data Fig. 8a). However, BA-SVs between different domain types occurred significantly more frequently than the expected rate, which suggests that BA-SVs have a potential role in gene-expression changes (Extended Data Fig. 8a). Therefore, we compared expression values of the genes that reside on each side of the SVs. We initially focused on BA-deletions between repressed and active domains, as previous studies showed that fused repressedactive domains could lead to an upregulation of nearby genes 38,39 . Indeed, genes located on the repressed side of deletions were significantly upregulated (P < 0.001, Supplementary Table 5) in samples with deletions compared with the rest of the samples in the same histological subtype (Fig. 4c), whereas the same effect was not observed for BA-deletions between repressed-repressed or active-active domains (Extended Data Fig. 8b). For example, a BA-deletion in a malignant lymphoma sample was associated with a 37-fold increase in the expression level of WNT4 compared with the rest of samples from patients with lymphoma (Fig. 4d). Similarly, a BA-deletion in the genome of a patient with breast adenocarcinoma correlated with 26-fold overexpression of SLC22A2 compared with the rest of the patients with breast cancer (Fig. 4e). However, this correlation of gene expression with BA-deletions between active and repressed domains was not universal. The fold change in expression of SLC2A10 was 1.10 in a uterus adenocarcinoma sample with a BA-deletion compared with the rest of uterus tumor samples (Fig. 4f). Therefore, not every BA-deletion correlated with a marked change in gene expression; in fact, only 25% of BA-deletions between repressed and active domains coincided with twofold changes in gene expression (Supplementary Table 5). To use a higher number of events, we next extended our analysis to all BA-deletions that occurred between different domain types. We classified domains as 'more' or 'less' transcriptionally active based on the annotations of domains (the ordering of domain types is described in Fig. 4a). This analysis resulted in a non-significant (P > 0.05) difference between genes that were located on more or less transcriptionally active domains after BA-deletions (Fig. 4g); and 14% of all BA-deletions coincided with a twofold change (Supplementary Table 5). We observed a similar non-significant difference for BA-duplications and BA-complex events (Extended Data Fig. 8c, Supplementary Tables 6,7).
Next, we compared the events between LADs and inter-LADs to profile whether alterations in the lamin organization could contribute to gene expression in tumor samples. We observed that deletions significantly occurred in LADs and duplications in inter-LADs, whereas SVs were less likely to occur between LADs and inter-LADs (Extended Data Fig. 8d). We noticed certain correlations between gene expression and events between LADs and inter-LADs-for example, a complex rearrangement in a melanoma sample coincided with a sevenfold upregulation of TRIM42 (which resides in a LAD) compared with the rest of the patients with melanoma (Fig. 4h). Overall, however, we did not observe a significant change for deletion, duplication and complex events between LADs and inter-LADs (Extended Data Fig. 8e, Supplementary Tables 8-10). These observations suggest that gene regulation in cancer genomes is multifactorial, although disruptions in chromatin folding domains may contribute to expression levels in certain cases, the effects of disruption do not always coincide with the expression changes.
Cell-type-specific alterations in chromatin folding patterns by different SV types. Next, to evaluate whether BA-SVs indeed altered chromatin folding patterns, we generated high-resolution Hi-C data for four cancer cell lines (SW480 and SNU-C1 for colorectal adenocarcinoma, HCC1954 for breast adenocarcinoma and OE33 for esophageal adenocarcinoma), which were previously profiled by WGS. For the majority of the BA-SVs detected by the WGS data (>90%), we were able to observe a change in the folding pattern in Hi-C contact maps of the respective cell line (Extended Data Fig. 9a). Break-ends of BA-SVs exhibited a strong contact frequency (14.6-fold) in cancer cells compared with non-cancerous cells (Extended Data Fig. 9b). The shortest BA-event with a detectable change in our Hi-C maps was a 460-kb long duplication in SW480 cells (Extended Data Fig. 9c). By contrast, we observed several discrepancies between SVs detected in WGS data and Hi-C maps. These SV break-ends tended to be located in repetitive regions of the genome or overlapped with inter-chromosomal translocations (Extended Data Fig. 9a,c). Our results demonstrate that BA-SVs detected using WGS data generally result in altered chromatin folding patterns in cancer cells.
We subsequently studied how BA-deletions, BA-inversions, BA-duplications and BA-complex rearrangements change the contact maps and noticed distinct interaction patterns in chromatin contact maps for different BA-SVs (Fig. 5a, Extended Data Fig. 9d-f). This observation of specific changes in Hi-C maps due to different SV types is consistent with findings from a recent study 40 . Furthermore, it has also been suggested that SVs could lead to TAD fusions 40 (also referred to as neo-TADs 3,4 ); we therefore analyzed whether the BA-SVs observed in our cancer cell lines exhibited similar neo-TAD formation. We grouped bins on the basis of their location compared with the SV breakpoints and the nearest TAD boundary. If bins were between the SV breakpoints and the nearest TAD boundary, we classified these interactions as intra-TAD/ SV and if bins were not constrained by the nearest boundary, we classified these interactions as inter-TAD/SV (Fig. 5b). Our analysis revealed that intra-TAD/SV interactions were stronger than the inter-TAD/SV interactions, when controlling for genomic distance effects, which suggests that the SVs can lead to cross-boundary interactions and potentially the formation of new chromatin folding domains based on the location of existing nearby TAD boundaries (Fig. 5b). For instance, an inversion in OE33 cells that encompassed ERBB2 formed a neo-TAD on chromosome 17 (Fig. 5c), a duplication in HCC1954 cells on chromosome 4 (Fig. 5c) and a duplication near KRAS in SW480 cells (Extended Data Fig. 9g) resulted in a TAD-like configuration between previously disparate two TADs (Fig. 5c). These new TAD-like patterns could only be observed in cell lines that had the SV, suggesting that these folding patterns were the result of a specific alteration (Extended Data Fig. 10a). In all of these events, we observed that new interactions spanned the nearest boundary and formed 'triangular shapes' that were consistent with the TAD patterns observed in non-rearranged genomes. Therefore, BA-SVs have the potential to form new TAD structures in cancer cells that could reconfigure cis-regulatory interactions.

Complex rearrangements markedly change chromatin folding maps in the cancer genomes.
We noticed that complex rearrangements in which deletion, inversion or duplication break-ends overlapped resulted in marked changes in Hi-C maps. SNU-C1 cells contain a complex rearrangement (chromothripsis) across the entire chromosome 15, which was reported by WGS and spectral karyotyping 41 . This chromosome has 239 rearrangements in the SNU-C1 cells and we observed marked changes only in SNU-C1 Hi-C maps in which the differences in folding patterns overlapped with the identified SV break-ends (Fig. 6a, Extended Data Fig. 10b). Similarly, we noticed a chromothripsis-like event that covered chromosome 21 of HCC1954 cells in WGS data and, similarly, the Hi-C map of chromosome 21 in HCC1954 cells showed considerable changes (Fig. 6b). In addition to the complex rearrangements that covered whole chromosomes, we noticed regional complex rearrangements that had abnormal chromatin folding patterns. For example, the MYC locus in SW480 cells contains 135 rearrangements in a 4-Mb genomic window (Fig. 6c), whereas a larger Articles NATurE GENETICS complex event was observed in HCC1954 cells around the similar locus, which also involved two other cancer driver genes, TERT and APC, on chromosome 5 (Fig. 6d). We could detect the changes in biological Hi-C replicates, suggesting that these BA-SV effects are reproducible (Extended Data Fig. 10c). Given that complex rearrangements are the most frequent genomic alterations observed in the cancer genomes (Fig. 1b), studying the causes and consequences of these events using the chromatin conformation-based datasets would be critical for our understanding of the contribution of these events to the formation of cancer.

Discussion
We explored the distributions of somatic SVs in a variety of tumor types and their potential roles in the disruption of chromatin folding and gene regulation. We found that certain boundaries are affected in a cancer-specific manner, which was likely due to the distribution of cancer-specific driver genes. Additionally, we observed a difference between the disruptions between different SV types; deletions tended to occur within TADs and LADs, whereas duplications tended to span TADs and generally occurred within inter-LAD regions. These results suggest that mechanistic differences may underlie the generation of different types of SV. For example, genome organization may influence partner selection during genomic rearrangements, as suggested by the distribution of different SV types in the genome to varying degrees. Disruption of folding domains could result in aberrant interactions between flanking domains and potentially contribute to the re-shaping of gene expression around the affected regions. Notably, we did not observe a strong association between global changes in gene expression after the disruption of each TAD, and only 14% of overall cases resulted in upregulation of more than twofold, which is consistent with the findings of recent studies 42,43 . These low expression changes may be reminiscent of mutations, in which there is a subset of chromatin-scale events that may be more likely to have functional effects (drivers) among a backdrop of considerable passenger events. Although we compared expression patterns of tumors in this study, cancer genomes may have other alterations that could affect the observed gene expression patterns, including copy-number alterations, dysregulation of transcription factors, chromatin regulators or cis-regulatory elements 44 . Therefore, the availability of histology-specific matched control samples coupled with WGS and chromatin organization datasets will augment our understanding of the functions of SV in genome folding and transcriptional dysregulation in cancers and contribute to our ability to discern signal from noise in appropriate contexts.

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author contributions and competing interests; and statements of data and code availability are available at https://doi.org/10.1038/ s41588-019-0564-y.

M et ho ds
Hi-C data analysis. Chromatin conformation assay (Hi-C) data for cell lines of GM12878, HUVEC, IMR90, HMEC, NHEK and K562 were downloaded from GEO (GSE63525). Intra-chromosomal 25-kb-resolution raw observed, MAPQGE30-filtered values were normalized by dividing by the multiplication of Knight and Ruiz normalization scores for two contacting loci. We calculated the TAD signal by moving a window across the Hi-C matrix diagonal, the sum of the interaction for a given bin of up to 2-Mb flanking regions and log 2 of the observed bin to the mean of interaction values within the given 2-Mb window. To identify TAD boundaries, we used an approach that is based on insulation score calculation 18 , and called TAD boundaries for each chromosome of each cell line with the following parameters: '-is 1000000 -ids 200000 -im mean -bmoe 1 -nt 0.1 --v' .
To calculate the significance of overlap between different TAD boundary calls, we converted the boundary regions into binary bins per genome to compare the overlap between previously published IMR90 TAD boundaries 4 with our IMR90 boundary calls. We performed logical AND operation, in which the region is counted as overlapping boundaries between two datasets if only two bins for the same genomic location of each condition are 1. We used bootstrapping to determine the distribution of the random overlap numbers between two calls, and calculated P values based on the observed number and distribution of the shuffled boundaries. Shuffled boundaries are generated by randomly assigning boundaries while keeping the number of boundaries per chromosome constant. Obtained shuffled boundaries were also converted to binary string and the same logical AND operation was applied. Shuffling was performed 10,000 times for a given boundary set. This procedure is applied in the rest of our study to generate shuffled boundaries. Next, we computed cumulative distribution of expected overlaps, z-scores were calculated based on the observed number and obtained distribution from bootstrapping. A two-tailed unpaired Student's t-test was used to calculate P values.
Common TAD boundaries were identified for boundaries of all five cell-types (GM12878, HUVEC, IMR90, HMEC and NHEK) that occurred within two Hi-C bins or 50 kb in genomic range. The same bootstrapping method (described above) was applied to calculate the significance of the overlap between common boundaries with TAD boundaries from the cancer cell lines K562 and MCF7.
To cluster individual TADs (defined as genomic regions between two adjacent common boundaries) based on epigenetic modifications, we used a comprehensive epigenome-profiling dataset from various human cell types. To this end, we used an entropy-based approach (epilogos) to calculate the occurrence of each chromatin state enrichment for a given genomic region across all cell types profiled by Roadmap Epigenome Consortia (http://compbio.mit.edu/epilogos/). We calculated the ratio of a TAD genomic space covered by each chromatin state, divided by the length of the TAD, and generated a normalized matrix in which columns are TADs and rows are each chromatin state, which have been extensively studied by the Roadmap Epigenome Consortia 21 . We applied hierarchical clustering to rows to identify similar chromatin states and k-means clustering to columns to group TADs that contain similar epigenetic modifications. We performed k-means clustering with k = 2-8 clusters and decided on k = 5 clusters as previous chromatin studies 17,19 have used 5 distinct epigenetically modified chromosomal domains and k = 5 corresponded to better visually discernible domains. To determine how our TAD clustering correlate with gene expression in cancer-free and cancerous tissues, we downloaded normalized gene expression values for 2,663 different cancer-free samples from the GTEx Portal 36 (v.1.6) and used normalized gene-expression values for ICGC cancer samples. We plotted the median expression of the genes in GTEx and ICGC samples, located in each domain type. Expression differences between heterochromatin and repressed domain expression with active domain expression were tested with one-tailed Mann-Whitney U-test. We also calculated the total number of genomic regions covered by each domain type. Finally, identified open and closed chromatin compartments (at a 100-kb resolution) in cancer samples using DNA methylation levels were identified as described previously 37 . We determined the percentage of our domain calls covered with open and closed chromatin calls from available cancer types.
We used HiCPlotter 45 to plot Hi-C data with different features, TAD boundaries or gene-expression fold changes after deletion between repressed and active domains.
ENCODE and Roadmap data. ENCODE replication timing data were downloaded from the UCSC Genome Browser ENCODE portal for the following cell types: BJ, GM06990, GM12801, GM12812, GM12813, GM12878, HeLa-S3, HepG2, HUVEC, IMR-90, K-562, MCF-7, NHEK and SK-N-SH. Replication timing values for smoothed wavelength transformed data were binned into 25-kb windows across the genome to discretize the data. Averages of the values in each bin across all cell types were calculated and used as average replication timing throughout the study.
We downloaded CTCF binding sites and DNase I hypersensitivity for five cell types (GM12878, HUVEC, IMR90, HMEC, NHEK) from the UCSC Genome Browser ENCODE portal. In addition, H3K9me3 and input DNA ChIP-seq alignment files (.bam) for each cell type were also downloaded. We randomly selected the same number of alignment reads for H3K9me3 and input DNA from .bam files and calculated log 2 -transformed enrichment levels of H3K9me3 over input DNA.
We downloaded all available CTCF peak-calling results and DNase I hypersensitivity regions from the UCSC Genome Browser ENCODE portal from 80 and 115 different cell lines, respectively (Supplementary Table 11). Occurrences of CTCF-binding and DNase I hypersensitivity sites per 25-kb window across the genome were calculated for all downloaded cell types and used to calculate TAD boundary and shuffled boundary enrichments.
Structural alterations. Somatic and germline variant calls, mutational signatures, subclonal reconstructions, transcript abundance, splice calls and other core data generated by the ICGC/TCGA PCAWG Consortium are described by the lead paper 22 of the PCAWG Consortium and available for download at https:// dcc.icgc.org/releases/PCAWG. Additional information on accessing the data, including raw read files, can be found at https://docs.icgc.org/pcawg/data/. In accordance with the data access policies of the ICGC and TCGA projects, most molecular, clinical and specimen data are in an open tier that does not require access approval. To access potentially identifying information, such as germline alleles and underlying sequencing data, researchers will need to apply to the TCGA Data Access Committee (DAC) via dbGaP (https://dbgap.ncbi.nlm.nih. gov/aa/wga.cgi?page=login) for access to the TCGA portion of the dataset, and to the ICGC Data Access Compliance Office (DACO; http://icgc.org/daco) for the ICGC portion. In addition, to access somatic SNVs derived from TCGA donors, researchers will need to obtain dbGaP authorization.
We obtained the consensus SV calls and annotations of each variation (deletions, inversions, duplications and complex rearrangements), which can be found at Synapse (https://www.synapse.org/) with accession number syn7596712. The SV classification algorithm is comprehensively defined in another study 23 . The code for the classification algorithm is available on GitHub (https://github.com/ cancerit/ClusterSV/). In brief, this algorithm clusters individual SV junctions into SV events that may involve multiple junctions. The single junction events were interpreted, as the 'basic' SV types (deletion, tandem duplication, translocation and inversions). However, in many cases events involving multiple SV junctions were detected. The SV events that involved many SV junctions could not be classified into any simple SV types. Therefore, these SV events were classified as complex. We specifically focused on the events that occurred within a chromosome in this study; we therefore did not use the translocation event calls between different chromosomes. To understand the effects of SVs, we first grouped the deletions, inversions or duplications on the basis of the length of the SVs.
Short-range SVs were identified as events with a length of less than 2 Mb and we mainly focused on these events in this study. BA-SVs were identified as SVs that spanned the whole length of a TAD boundary, the rest of the SVs were classified as 'within TAD' in Fig. 1b. To determine the distribution of random BA-SV events, we used the same bootstrapping method mentioned above, mainly generated random boundary events 10,000 times and calculated random BA-SV event distributions. The z-scores and P values were calculated on the basis of the observed number and distribution obtained from bootstrapping. In this study, we analyzed each event separately for deletion, duplication and inversion calls, albeit in a given sample these events might occur concurrently.
Long-range SVs were identified as events with a length of more than 2 Mb and we mentioned the results obtained with long-range SVs in the main text, as appropriate.
To understand the germline BA-SV occurrences, we downloaded structural alteration calls from three different studies: deletion events (total of 8,941) from WGS data of the 1000 Genomes project 26 ; deletions (total of 7,511) and duplications (total of 7,501) from WGS data from 236 individuals representing 125 human populations 27 ; and from a comprehensive review of deletions (total of 11,530) and duplications (total of 1,170) events from 23 different studies including 2,647 different individuals 25 . We noticed that the number of BA-SVs present in germline deletions and duplications was low and these events happened less than expected by chance, which was estimated using a bootstrapping method.
We next profiled short-range SVs and BA-SVs for each of the cancer studies in our ICGC dataset. To calculate the average number of SVs or BA-SVs per sample for each of the cancer studies, we divided the sum of all observed short-range SVs or BA-SVs in a given cancer type by the total number of samples in that cancer study. Observed SVs and BA-SVs across cancer studies were plotted as stacked bar charts representing deletions, inversions and duplications.
To identify the recurrently affected boundaries in each cancer study, we generated a matrix in which each column represented a sample in the cancer study and rows represented the TAD boundaries. A binary score was assigned to each row (a TAD boundary) that indicated whether that boundary was affected by BA-SV(s) in a given sample. Boundaries that were affected in more than 10% of the samples in a cancer study, are reported as recurrently affected boundaries in Supplementary Corresponding author(s): Andrew Futreal Last updated by author(s): Nov 29, 2019 Reporting Summary Nature Research wishes to improve the reproducibility of the work that we publish. This form provides structure for consistency and transparency in reporting. For further information on Nature Research policies, see Authors & Referees and the Editorial Policy Checklist.

Statistics
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A description of all covariates tested A description of any assumptions or corrections, such as tests of normality and adjustment for multiple comparisons A full description of the statistical parameters including central tendency (e.g. means) or other basic estimates (e.g. regression coefficient) AND variation (e.g. standard deviation) or associated estimates of uncertainty (e.g. confidence intervals) For null hypothesis testing, the test statistic (e.g. F, t, r) with confidence intervals, effect sizes, degrees of freedom and P value noted Give P values as exact values whenever suitable.

For Bayesian analysis, information on the choice of priors and Markov chain Monte Carlo settings
For hierarchical and complex designs, identification of the appropriate level for tests and full reporting of outcomes Estimates of effect sizes (e.g. Cohen's d, Pearson's r), indicating how they were calculated Our web collection on statistics for biologists contains articles on many of the points above.

Software and code
Policy information about availability of computer code Data collection Data and metadata were collected from International Cancer Genome Consortium (ICGC) consortium members using custom software packages designed by the ICGC Data Coordinating Centre. The general-purpose core libraries and utilities underlying this software have been released under the GPLv3 open source license as the "Overture" package and are available at https://www.overture.bio. Other data collection software used in this effort, such as ICGC-specific portal user interfaces, are available upon request to contact@overture.bio.

Data analysis
The workflows executing core WGS alignment, QC and variant-calling software are packaged as executable Dockstore images and available at: https://dockstore.org/search?labels.value.keyword=pcawg&searchMode=files. Individual software components are as follows: BWA-MEM v0.78.8-r455; DELLY v0. For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors/reviewers. We strongly encourage code deposition in a community repository (e.g. GitHub). See the Nature Research guidelines for submitting code & software for further information.

Data
Policy information about availability of data All manuscripts must include a data availability statement. This statement should provide the following information, where applicable: -Accession codes, unique identifiers, or web links for publicly available datasets -A list of figures that have associated raw data -A description of any restrictions on data availability WGS somatic and germline variant calls, mutational signatures, subclonal reconstructions, transcript abundance, splice calls and other core data generated by the ICGC/TCGA Pan-cancer Analysis of Whole Genomes Consortium are available for download at https://dcc.icgc.org/releases/PCAWG. Additional information on