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High-order chromatin architecture determines the landscape of

chromosomal alterations in cancer

Geoff Fudenberg1, Gad Getz2, Matthew Meyerson2,3,4,5, and Leonid Mirny2,6,7

1Harvard University, Program in Biophysics, Boston, Massachusetts

2The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

3Harvard Medical School, Boston, MA 02115, USA

4Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA

5Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02115, USA

6Harvard-MIT, Division of Health Sciences and Technology

7Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA

The rapid growth of cancer genome structural information provides an opportunity for a

better understanding of the mutational mechanisms of genomic alterations in cancer and the

forces of selection that act upon them. Here we test the evidence for two major forces,

spatial chromosome structure and purifying (or negative) selection, that shape the landscape

of somatic copy-number alterations (SCNAs) in cancer1. Using a maximum likelihood

framework we compare SCNA maps and three-dimensional genome architecture as

determined by genome-wide chromosome conformation capture (HiC) and described by the

proposed fractal-globule (FG) model2,3. This analysis provides evidence that the distribution

of chromosomal alterations in cancer is spatially related to three-dimensional genomic

architecture and additionally suggests that purifying selection as well as positive selection

shapes the landscape of SCNAs during somatic evolution of cancer cells.

Somatic copy-number alterations (SCNAs) are among the most common genomic

alterations observed in cancer, and recurrent alterations have been successfully used to

implicate cancer-causing genes1. Effectively finding cancer-causing genes using a genome-

wide approach relies on our understanding of how new genome alterations are generated

during the somatic evolution of cancer4–7. As such, we test the hypothesis that three-

dimensional chromatin organization and spatial co-localization influences the set of somatic

copy-number alterations observed in cancer (Fig. 1A, recently suggested by cancer genomic

data in a study of prostate cancer8. Spatial proximity and chromosomal rearrangements are

discussed more generally9–12). Unequivocally establishing a genome-wide connection

between SCNAs and three-dimensional chromatin organization in cancer has until now been

limited by our ability to characterize three-dimensional chromatin architecture, and the

resolution with which we are able to observe SCNAs in cancer. Here, we ask whether the

“landscape” of SCNAs across cancers1 can be understood with respect to spatial contacts in

a 3D chromatin architecture as determined by the recently developed HiC method for high-

throughput chromosome conformation capture2 or described theoretically via the fractal

globule (FG) model (theoretical concepts13, review3). Specifically, we investigate the model

presented in Figure 1A, and test whether distant genomic loci that are brought spatially close

Correspondence to: Leonid Mirny.

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Published in final edited form as:

Nat Biotechnol. ; 29(12): 1109–1113. doi:10.1038/nbt.2049.

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by 3D chromatin architecture during interphase are more likely to undergo structural

alterations and become end-points for amplifications or deletions observed in cancer.

Towards this end, we examine the statistical properties of SCNAs in light of spatial

chromatin contacts in the context of cancer as an evolutionary process. During the somatic

evolution of cancer14,15 as in other evolutionary processes, two forces determine the

accumulation of genomic changes (Fig. 1A): generation of new mutations and fixation of

these mutations in a population. The rate at which new SCNAs are generated may vary

depending upon the genetic, epigenetic, and cellular context. After an SCNA occurs, it

proceeds probabilistically towards fixation or loss according to its impact upon cellular

fitness. The fixation probability of an SCNA in cancer depends upon the competition

between positive selection if the SCNA provides the cancer cell with a fitness advantage,

and purifying (i.e. negative) selection if the SCNA has a deleterious effect on the cell. The

probability of observing a particular SCNA thus depends upon its rate of occurrence via

mutation, and the selective advantage or disadvantage conferred by the alteration (Fig. 1A).

Positive, neutral, and purifying selection are all evident in cancer genomes16.

Our statistical analysis of SCNAs argues that both contact probability due to chromosomal

organization at interphase and purifying selection contribute to the observed spectrum of

SCNAs in cancer. From the full set of reported SCNAs across 3,131 cancer specimens in1,

we selected 39,568 intra-arm SCNAs (26,022 amplifications and 13,546 deletions) longer

than a megabase for statistical analysis, excluding SCNAs which start or end in centromeres

or telomeres. To establish that our results were robust to positive selection acting on cancer-

associated genes, we analyzed a collection of 24,301 SCNAs that do not span highly-

recurrent SCNA regions (16,521 amplifications and 7,789 deletions, respectively 63% and

58% of the full set1, see Methods). We present results for the less-recurrent SCNAs, and

note that our findings are robust to the subset of chosen SCNAs. We performed our analysis

by considering various models of chromosomal organization and purifying selection, which

were used to calculate the likelihood of the observed SCNA given the model. The likelihood

framework was then used to discriminate between competing models. Statistical significance

was further evaluated using permutation tests. The strong association we find between

SCNAs and high-order chromosomal structure is not only consistent with the current

understanding of the mechanisms of SCNA initiation17, but provides insight into how spatial

proximity may be arrived at via chromosomal architecture and the significance of

chromosomal architecture for patterns of SCNAs observed at a genomic scale.

Results

Patterns of three-dimensional chromatin architecture are evident in the landscape of

SCNAs

The initial motivation for our study was an observation that the length of focal SCNAs and

the length of chromosomal loops (i.e. intra-chromosomal contacts) have similar distributions

(Figs. 1B and 1C), both exhibiting ~ 1/L scaling. Analysis of HiC data for human cells

showed that the mean contact probability over all pairs of loci a distance L apart on a

chromosome goes as PHiC (L) ~ 1/L for a range of distances L= 0.5 to 7Mb2. This scaling

for mean contact probability was shown to be consistent with a fractal globule (FG) model

of chromatin architecture. Similarly, the mean probability to observe a focal SCNA of length

L goes approximately as PSCNA (L) ~ 1/L for the same range of distances L= 0.5 to 10 Mb

as noted in 1. Mathematically, the observation that the mean probability to observe an SCNA

decays with its length is quite significant. If two SCNA ends were chosen randomly within a

chromosome arm, the mean probability to observe an SCNA of length L would remain

constant. Positive selection, which tends to amplify oncogenes or delete tumor suppressors,

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again does not give rise to a distribution whose mean decreases with length. Either purifying

selection or a length-dependent mutational mechanism is required to observe this result.

The connection between three-dimensional genomic architecture and SCNA structure goes

beyond the similarity of their length distributions: loci that have higher probability of

chromosomal contacts are also more likely to serve as SCNA end points (Fig. 2). To

quantitatively determine the relationship between three-dimensional genomic architecture

and SCNA, both data sets were converted into the same form. For each chromosome, we

represent HiC data as a matrix of counts of spatial contacts between genomic locations i and

j as determined in the GM06990 cell line using a fixed bin size of 1 Mb2. Similarly, we

construct SCNA matrices by counting the number of amplifications or deletions that start at

genomic location i and end at location j of the same chromosomes across the 3,131 tumors.

Figure 2 presents HiC and SCNA matrices (heatmaps) for chromosome 17. Away from

centromeric and telomeric regions, which are not considered in this analysis, the SCNA

heatmap appears similar to the HiC heatmap (Pearson’s r = .55, p < 0.001, see

Supplementary Table S1 for other chromosomes). In particular, regions enriched for 3D

interactions also appear to experience frequent SCNA. Since the Pearson correlation

coefficient is not suited for describing rare probabilistic events like SCNAs, for further

analysis we employ the Poisson likelihood, a widely-used method to statistically analyze

rare events18.

Likelihood analysis demonstrates that observed SCNAs are fit best by fractal globular

chromatin architecture, and all fits are improved when purifying selection is considered

To further test the role of chromosome organization for the generation of SCNA, we

developed a series of statistical models of possible SCNA-generating processes, computed

the Poisson likelihoods of the SCNA data given these models (see Eq. 6), and performed

model selection using their Bayesian Information Criterion (BIC) values, which is the log-

likelihood of a given model penalized by its number of fitting parameters (see Eq. 7).

Considered models take into account different mechanisms of the generation of SCNA, with

a mutation rate either: uniform in length (Uniform), derived from experimentally determined

chromatin contact probabilities (HiC) or derived from contact probability in the fractal

globular chromatin architecture (FG). We note that the FG model specifies a contact

probability that depends on the distance between genomic loci, but does not include

positional differences at a given distance.

We also took into account possible deleterious effects of SCNAs due to purifying selection,

which can lead to a reduced probability of fixation (see Eq. 1). Deleterious effects of SCNAs

on cellular fitness may arise from the disruption of genes or regulatory regions; as such, we

expect longer SCNAs to be more deleterious. A relationship between SCNA length and its

deleterious effect on cellular fitness is supported by the observation that whole-arm SCNAs

are less likely for longer chromosomal arms1, as well as an observation of linearly

decreasing bacterial growth rate with longer amplifications19. If we assume that the

deleterious effect of an SCNA increases linearly with its length L, and consider the somatic

evolution of cancer as a Moran process15,20, we find that the probability of fixation decays

roughly exponentially with length at a rate that reflects the strength of purifying selection

(see Eq. 4, Fig. 1B). Combining the effects of purifying selection on fixation probability

with the mutational models leads to the following six models: Uniform, Uniform+sel, HiC,

HiC+sel, FG, FG+sel, with no fitting parameters for models without selection and a single

fitting parameter for selection, where the additional parameter is penalized via BIC.

Model selection provides two major results (Fig. 3): First, among models of SCNA

generation, a model that follows the chromosomal contact probability of the fractal globule

(~ 1/L) significantly outperforms other models. Second, since considering purifying

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selection helps fit the observed roll-over in the number of SCNAs at longer distances (L

>20Mb, Fig. 1B), every model is significantly improved when purifying selection is taken

into account (p < .001 via bootstrapping), suggesting that SCNAs experience purifying

selection. We note that the additional decline in the number of SCNA at long distances

could possibly be due to alternative chromatin-independent mechanisms that further disfavor

the formation of exceptionally long SCNAs. Figure 3 presents log-likelihood ratios of the

models (with and without purifying selection) with respect to the uniform model. If models

are fit on a chromosome-by-chromosome basis (Supplementary Fig. 2) we observe that for

long chromosomes, the FG model fits better than purifying selection alone. We also find that

the best-fit parameter describing purifying selection is proportional to chromosome length

(Supplementary Fig. 2A). Since smaller values for the best-fit parameter correspond to

stronger purifying selection, these two results suggest that short, gene-rich, chromosomes

may experience greater purifying selection. However, we note that purifying selection

proportional to the genomic length of an SCNA fits the data better than purifying selection

proportional to the number of genes affected by an SCNA (Supplementary Fig. 3).

Permutation analysis supports the connection between SCNAs and experimentally

determined three-dimensional chromatin architecture

We next tested whether the position-specific structure of chromosomal contacts observed in

experimental HiC data, and absent for the FG, was evident in the SCNA landscape. The test

was performed using permutation analysis (Fig. 4). Since both the probability of observing

an SCNA with a given length and intra-chromosomal contact probability in HiC depend

strongly on distance L, we permuted SCNAs in a way that preserves this dependence but

destroys the remaining fine structure. This is achieved by randomly reassigning SCNA

starting locations within the same chromosomal arm, while keeping their lengths fixed. We

find that HiC fits the observed SCNAs much better than it fits permuted SCNAs (Fig. 4, p<.

001). Similar analysis within individual chromosomes shows that the fit is better for 18 of

the 22 autosomal chromosomes, except for chromosomes 10, 11, 16, and 19, and is

significantly better (p<.01) for nine chromosomes 1, 2, 4, 5, 7, 8, 13, 14, and 17 (Fig. 4B).

While the observed amplification and deletions each separately fit better on average than

their permuted counterparts (Supplementary Fig. 5), deletions fit considerably better than

amplifications (p<0.001 vs. p<0.05).

Finally, we examined the possible influence of chromosomal compartments (domains, as

determined in2) on the landscape of SCNAs by fitting models where SCNA formation is

favored if both ends are in the same type of domain (see Methods). Maximizing the

likelihood of this two-parameter FG+domains model demonstrated a marginal increase in the

BIC-corrected likelihood above the FG model for deletions, and not for amplifications

(Supplemental Fig. 8 and 9). The best-fitting domain strength parameter values favored

small (10–20%) increases in the relative probability of intra-domain SCNAs. Additionally,

the best-fitting FG+domains model shows a smaller amount of position-specific information

than HiC, as determined by permutation tests (Supplemental Fig. 8).

Discussion

Our genome-wide analysis of HiC measurements and cancer SCNA finds multiple

connections between higher-order genome architecture and re-arrangements in cancer.

Using an incisive likelihood-based BIC framework, we found that: (1) probability of a 3D

contact between two loci based on the FG model explains the length distribution of SCNA

better than other mechanistic models or than a model of purifying selection alone; (2)

comparisons with permuted data demonstrate the significant connection between megabase-

level position-specific 3D chromatin structure observed in HiC and SCNA; (3) a

multiplicative model favoring intra-domain SCNAs provides little improvement beyond the

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FG model and has less position-specific information than HiC; (4) SCNA data reflect

mutational mechanisms and purifying selection, in addition to commonly considered

positive selection.

These results argue strongly for the importance of 3D chromatin organization in the

formation of chromosomal alterations. While the distribution of SCNAs could conceivably

depend on a complicated mutation and selection landscape, which is merely correlated with

3D genomic structure, a direct explanation via 3D genomic contacts is more parsimonious.

Along these lines, two recent experimental studies of translocations suggest that physical

proximity is among the key determinants of genomic rearrangements21,22. Additionally, a

genome-wide analysis of translocations across cancers demonstrates an enrichment of

translocations among chromosomal loci with greater numbers of experimentally determined

chromosomal contacts23.

Genomic architecture may vary with cancer cell type of origin and the specific chromatin

states of these cells24,25, thus influencing the set of observed SCNAs in each cancer type; for

example, re-arrangement breakpoints in prostate cancer were found to correlate with loci in

specific chromatin states of prostate epithelial cells8. In fact, if HiC data matching the tumor

cell-types of origin for the set of observed SCNAs becomes available, we may find that the

cell-type specific experimental 3D contacts fit the observed distribution of SCNAs better

than the fractal globule model. Despite this limitation, when we perform a permutation

analysis on SCNAs grouped by cancer lineage (epithelial, hematopoietic, sarcomas and

neural), we still find that HiC fits the observed SCNAs significantly better than it fits

permuted SCNAs consistently across cancer lineages for deletions, but not for

amplifications (Supplementary Fig. 6).

Differences between amplifications and deletions (Supplementary Figs. 4, 5, 6) may reflect

differences in the strength of selection and mechanisms of genomic alteration: conceivably a

simple loss of a chromosomal loop could lead to a deletion, while amplifications may occur

through more complicated processes17 and may require interactions with homologous and

non-homologous chromosomes that are not necessarily directly related to intra-chromosomal

spatial proximity during interphase.

Our results suggest that a comprehensive understanding of mutational and selective forces

acting on the cancer genome, not limited to positive selection of cancer-associated genes, is

important for explaining the observed distribution of SCNAs. Furthermore, comparing

model goodness-of-fits for the distribution of SCNAs argues that purifying selection is a

common phenomenon, and that many SCNAs in cancer may be mildly deleterious

“passenger mutations” (reviewed in26,27). We note that while we find evidence for both

chromatin organization and purifying selection in the length distribution of SCNAs, in our

best-fitting model, 3D chromatin architecture explains a factor of ~100 in relative

frequencies of SCNAs, whereas purifying selection contributes an additional factor of ~3 for

long SCNAs (L > 20–100Mb) and has little effect on the frequency of shorter SCNAs (L <

20Mb). Presumably, mechanisms other than purifying selection could lead to additional

suppression of excessively long SCNAs. However, the observed exponential rollover in the

number of SCNAs at long distances is unlikely to be caused by limitations arising from

SCNA mapping, since whole-arm SCNAs are successfully detected at high frequencies.

The sensitivity and relevance of comparative genomic approaches to chromosome

rearrangements can only increase as additional HiC-type datasets become available. Future

studies will be able to address the importance of different 3D structures to the observed

chromosomal rearrangements across cell types and cell states. Perhaps even more

importantly, cancer genomic sequencing data will allow for significantly more detailed

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analyses than the current array-based approaches, allowing for greater mechanistic insight

into SCNA formation. In particular, high-throughput whole-genome sequencing data will

allow for both a high-resolution analysis of interchromosomal rearrangements and yield

insight into the interplay between sequence features, chromatin modifications, and 3D

genomic structure.

Methods

Constructing heatmaps

We generated SCNA heatmaps from the data of Beroukhim et al.1 who reported a total of

75,700 amplification and 55,101 deletion events across 3,131 cancer specimens; reported

events are those with inferred copy number changes >.1 or <!.1, due to experimental

limitations. We restricted our analysis to intra-arm SCNAs which do not start/end near

telomeric/centromeric regions separated by more than one megabase bin, giving a set of

39,568 SCNAs (26,022 amplifications and 13,546 deletions). We note that SCNAs starting/

ending in centromeres/telomeres (which include full-arm gain/loss) display a very different

pattern of occurrence from other focal SCNAs, particularly in terms of their length

distribution, which may indicate a different mutational mechanism. Requiring a separation

of greater than one megabase bin is due to resolution limits of both SCNA and HiC data (see

Supplementary Fig. 1 for details). SCNA matrices are constructed by counting the number

of amplifications or deletions starting at Mb i and ending at Mb j of the same chromosomes.

Similarly, HiC heatmaps were generated by counting the number of reported interactions2

between Mb i and j of the same chromosome in human cell line GM06690.

Mutational and Evolutionary Models of SCNA

To test the respective contributions of mutational and selective forces on the distribution of

SCNAs, we consider the probability of observing at SCNA that starts and end at i and j

(1)

as the product of the probability of a mutation, i.e. an SCNA to occur in a single cell μij, and

the probability to have this mutation fixed in the population of cancer cells π(L), where L = |

i − j is the SCNA length. The mutation probability μij depends on the model that describes

the process leading to chromosomal alterations: (Uniform) two ends of an alteration are

drawn randomly from the same chromosomal arm, giving

probability of an alteration depends on the probability of a 3D contact between the ends as

; (HiC) the

given by HiC data,

probability of 3D contact according to the fractal globule model, i.e. on SCNA length L:

; (FG) the probability of alteration depends upon the

. The probability of fixation depends on the fitness of a mutated cell as

compared to non-mutated cells (see below). Each mutational model is considered by itself

and in combination with purifying selection, giving six models: Uniform, HiC, FG,

Uniform+sel, HiC+sel, and FG+sel. For example,

additional parameter describing selection is accounted for using BIC (described below).

. The

We also examined a mutational model which combines the effects of chromosomal

compartments as determined by HiC2 with the FG model (FG+domains). Domains are brought

into our models by assuming different likelihoods of SCNA ends to be located active-active,

active-inactive and inactive-inactive domains (two independent parameters). This domain

structure is then multiplied by the fractal globule contact probability,

where Dij = 1 if i and j are in different domains, Dij = κ if i and j are both in an open

,

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domain, and Dij = ν if i and j are both in a closed domain. We exclude chromosomes 4, 5,

and 15 for the domain analysis, as these chromosomes have a poor correspondence between

HiC domains (as determined in the original analysis of HiC2) and the HiC contact map.

Effects of Selection on the Probability of Fixation

Two major selective forces act on SCNAs: positive selection on SCNAs that amplify an

oncogene or delete a tumor suppressor, and purifying selection that acts on all alterations.

Purifying selection results from the deleterious effects of an SCNA that deletes or amplifies

genes and regulatory regions of the genome that are not related to tumor progression. We

assume that deleterious effect of an SCNA, and the resulting reduction in cells fitness ΔF, is

proportional to SCNA length: |ΔF| ∝ L.

The probability of fixation is calculated using the Moran process as model of cancer

evolution15,20:

(2)

where ΔF is a relative fitness difference (selection coefficient), N is the effective population

size. For weakly deleterious mutations (ΔF < 0, N|ΔF| ≫ 1, |ΔF| ≪ 1)

(3)

Note that for sufficiently deleterious mutations this leads to an exponentially suppressed

probability of fixation: π(ΔF) ∝ exp(ΔFN) (ΔF < 0), a useful intuitive notion. Assuming a

deleterious effect linear in SCNA length, ΔF = −L/λ, we obtain the probability of fixation

for purifying selection acting on an SCNA

(4)

where C is an arbitrary constant obtained from normalization of P(L), and α = λ/N is a

fitting parameter which quantifies the strength of purifying selection. For gene-based

purifying selection, L is simply replaced by the number of genes altered. Mutations that are

selectively neutral have no length dependence, so π(L) = C, and thus Pij ~ μij.

Controlling for Positive Selection

Positive selection acting on cancer-associated genes (eg. oncogenes and tumor suppressors)

presents a possible confounding factor to our analysis. To establish that our results were

robust to positive selection acting on cancer-associated genes, we analyzed the subset of the

39,568 SCNAs (26,022 amplifications and 13,546 deletions) that do not span highly-

recurrent SCNA regions identified by GISTIC with a false-discovery rate q-value for

alteration of <.25 as listed in Beroukhim et al.1, a collection of 24,310 SCNAs (16,521

amplifications and 7,789 deletions, respectively 63% and 58% of the full set). After SCNAs

spanning highly-recurrent regions are removed, permutations are performed under the

constraint that permuted SCNAs do not cross any of the highly-recurrent regions. Positive

selection can also be somewhat controlled for by setting a threshold on the inferred change

in copy number, to filter SCNAs that may have experienced strong positive selection in

individual cancers. We note that our findings are robust to the subset of chosen SCNAs,

most likely because there are many fewer driver SCNAs than passenger SCNAs

(Supplementary Fig. 7).

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Model Selection using Poisson Log-likelihood, Bayesian Information Criterion

Since the occurrence of a particular SCNA starting at i and ending at j is a rare event, we

evaluate the relative ability of a model to predict the observed distribution of SCNA by

calculating the Poisson Log-likelihood of the data given the model:

(6)

where

SCNAs that start and end at i and j. Since recurrent regions of amplification and deletion are

different, we calculate the log-likelihood separately for amplifications and deletions, and

then aggregate across these two classes of SCNAs. After the log-likelihood is calculated,

models are ranked and model selection is performed using Bayesian Information Criterion

(BIC). BIC penalizes models based upon their complexity, namely their number of

parameters. Penalizing k additional parameters for n observed SCNAs using Bayesian

Information Criterion (BIC) is straightforward:

is dictated by the model as explained above, and SCNAij is the number of

(7)

where models with higher BIC are preferred28. For the permutation analysis, log-likelihood

is calculated in the same way, first for the observed SCNAs, and then for permuted sets of

SCNAs.

Supplementary Material

Refer to Web version on PubMed Central for supplementary material.

Acknowledgments

We thank members of the Mirny Lab for helpful conversations, in particular with Christopher McFarland regarding

purifying selection and Maxim Imakaev regarding fractal globules. We thank Craig Mermel for an introduction to

SCNA data. We thank Vineeta Agarwala, Jesse Engrietz, Rachel McCord, and Job Dekker for helpful comments

and suggestions. This work was supported by the NIH/NCI Physical Sciences Oncology Center at MIT

(U54CA143874)

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Figure 1. 3D proximity as mechanism for SCNA formation

A: Model of how chromosomal architecture and selection can influence observed patterns of

somatic copy-number alterations (SCNAs). First spatial proximity of the loop ends makes an

SCNA more likely to occur after DNA damage and repair. Next, forces of positive selection

and purifying selection act on SCNAs which have arisen, leading to their ultimate fixation or

loss. Observed SCNAs in cancer thus reflect both mutational and selective forces. Inset

illustrates looping in a simulated fractal globule architecture (coordinates from M. Imakaev).

Two contact points are highlighted by spheres and represent potential end-points of SCNAs.

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B. SCNA length distribution for 60,580 less-recurrent SCNAs (39,071 amplifications,

21,509 deletions) mapped in 3,131 cancer specimens from 26 histological types1. Squares

show mean number of amplification (red) or deletion (blue) SCNAs after binning at 100 kb

resolution (and then averaged over logarithmic intervals). Light magenta lines show ~1/L

distributions. Grey line shows the best fit for purifying selection (Eq 4) with a uniform

mutation rate. Dark purple line shows best fit for deletions for FG+sel.

C: Probability of a contact between two loci distance L apart on a chromosome at 100 kb

resolution. The probability is obtained from intra-chromosomal interactions of 22 human

chromosomes characterized by the HiC method (human cell line GM06690)2. Shaded area

shows range from 5th and 95th percentiles for number of counts in a 100kb bin at a given

distance. The mean contact probability is shown by blue line. Light magenta line shows ~1/

L scaling also observed in the fractal globule model of chromatin architecture. Blue dashed

line provides a baseline for contact frequency obtained as inter-chromosomal contacts in the

same dataset.

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Figure 2. Heatmaps for chromosome 17 at 1 Mb resolution

A. SCNA heatmap: the value for site (i,j) is the number of SCNAs starting at genomic

location i and ending at location j on the same chromosome. Chromosome band structure

from UCSC browser shown on the left side with centromeric bands in red.

B. HiC heatmap: site (i,j) has the number of reported interactions between genomic locations

i and j at Mb resolution. HiC domain structure is shown on the left side. Domains were

determined by thresholding the HiC eigenvector (as in2, white represents open domains,

dark gray represents closed domains).

C. Permuted SCNA heatmap: as in A, but after randomly permuting SCNA locations while

keeping SCNA lengths fixed.

Visually, the true SCNA heatmap is similar to HiC (Pearson’s r = .55, p <.001, see

Supplementary Table S1 for other chromosomes), displaying a “domain” style organization.

Cartoons above the heatmaps illustrate how mapped HiC fragments and SCNA end-points

can be converted into interactions between genomic locations i and j. Since inter-arm

SCNAs, SCNAs with end-points near centromeres or telomeres, and SCNAs < 1Mb were

not considered in our statistical analysis, these areas of the heatmaps are grayed out.

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Figure 3. Selecting a model of SCNA formation

For each model, the log-likelihood ratio (*BIC-corrected log-likelihood ratio) is shown for

the 24,310 observed SCNAs that do not span highly-recurrent SCNA regions listed in1. The

following six models are considered: Uniform, Uniform+sel, HiC, HiC+sel, FG, FG+sel. HiC

model assumes mutation rates proportional to experimentally measured contact

probabilities, while FG model assumes mutation rates proportional to mean contact

probability in a fractal globule architecture (~1/L). Left y-axis presents BIC-corrected log-

likelihood ratio for each model vs. Uniform model. Each model was considered with (+) and

without (−) purifying selection. Right y-axis shows the same data as a fold difference in

likelihood per cancer specimen (sample) vs. Uniform. Error bars were obtained via

bootstrapping: squares represent the median values, bar ends represent the 5th and 95th

percentiles. The FG model significantly outperforms other mutational models of SCNA

formation, and every model is significantly improved when purifying selection is taken into

account.

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Figure 4. Permutation analysis of the relationship between SCNAs and megabase-level structure

of HiC chromosomal interactions

A. Distribution of log-likelihood ratios for randomly permuted SCNAs given HiC vs.

observed SCNAs given HiC over all 22 autosomes. Observed SCNAs (blue arrow) are fit

better by HiC contact probability with p<.001. Permutations are performed by shuffling

SCNA locations while keeping SCNA lengths fixed. B: Distributions of the same log-

likelihood ratios for individual chromosomes (vs their corresponding observed SCNA, blue

line). Squares represent median values, error bars respective represent the range from 5th to

25th percentile and 75th to 95th percentile.

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