Intra-tumour genetic heterogeneity is the result of ongoing evolutionary change within each cancer. The expansion of genetically distinct sub-clonal populations may explain the emergence of drug resistance, and if so, would have prognostic and predictive utility. However, methods for objectively quantifying tumour heterogeneity have been missing and are particularly difficult to establish in cancers where predominant copy number variation prevents accurate phylogenetic reconstruction owing to horizontal dependencies caused by long and cascading genomic rearrangements. To address these challenges, we present MEDICC, a method for phylogenetic reconstruction and heterogeneity quantification based on a Minimum Event Distance for Intra-tumour Copy-number Comparisons. Using a transducer-based pairwise comparison function, we determine optimal phasing of major and minor alleles, as well as evolutionary distances between samples, and are able to reconstruct ancestral genomes. Rigorous simulations and an extensive clinical study show the power of our method, which outperforms state-of-the-art competitors in reconstruction accuracy, and additionally allows unbiased numerical quantification of tumour heterogeneity. Accurate quantification and evolutionary inference are essential to understand the functional consequences of tumour heterogeneity. The MEDICC algorithms are independent of the experimental techniques used and are applicable to both next-generation sequencing and array CGH data.
The study of intra-tumour genetic heterogeneity (for short: heterogeneity) is now a major focus of cancer genomics research [1]–[12] due to its potential to provide prognostic information [13]–[15] and to explain mechanisms of drug resistance [16]–[19]. Quantifying tumour heterogeneity and understanding its aetiology crucially depends on our ability to accurately reconstruct the evolutionary history of cancer cells within each patient. In many cancers, such as high-grade serous ovarian cancer (HGSOC), most of this heterogeneity is not reflected in point mutations but in genomic rearrangements and endoreduplications that lead to aberrant copy-number profiles [20], [21]. In these cases tree inference is hindered by unknown phasing of parental alleles and horizontal dependencies between adjacent genomic loci. Therefore heterogeneity and evolutionary divergence are typically quantified using ad-hoc thresholds [19] and tree inference is often done subjectively [11]. Approaches developed to address this problem include a graph theoretical approach on signed reversals to order rearrangement events [22], but this requires detailed annotation of rearrangements in the data that may not be available, and the algorithm does not generally infer global trees representing cancer evolution within a patient. The TuMult algorithm [23] deals with underlying computational complexity by considering only breakpoints — locations on the genome where the copy-number changes — and by using total copy-number without phasing of parental alleles. While simplifying the computational problem, this approach discards potentially informative data. Our aim is to establish numerical quantification of tumour heterogeneity per patient from copy-number profiles that can routinely be acquired from clinical samples. To this end, we have developed MEDICC (Minimum Event Distance for Intra-tumour Copy-number Comparisons), a method for accurate inference of phylogenetic trees from unsigned integer copy-number profiles. MEDICC specifically addresses the following challenges associated with copy-number-based phylogeny estimation: It makes use of the full copy-number information across both parental alleles by phasing copy-number variants, i. e. assigning them to one of the two physical alleles such that the overall evolutionary distance is minimal. It estimates evolutionary distances, thereby dealing with horizontal dependencies between adjacent genomic loci and with multiple overlapping events by using efficient heuristics. It therefore works on complete copy-number profiles instead of breakpoints which allows the reconstruction of ancestral genomes. It implements statistical tests for molecular clock (homogeneous branch lengths), star topology (phylogenetic structure) and tests for the relationship between clonal subpopulations to provide informative summary statistics for the reconstructed evolutionary histories and tumour heterogeneity. MEDICC was designed to work on integer copy-number profiles that can routinely be obtained from single nucleotide polymorphism (SNP) arrays [24] or paired-end sequencing [25], [26]. In both cases DNA content is quantified relative to a diploid normal in windows along the genome. SNPs distinguish the two parental alleles via the B-allelic frequency, i. e. the amount of DNA assigned to the B allele relative to the total DNA amount at that specific genomic locus. The resulting profile comprises two vectors of integer copy-numbers, representing the absolute number of copies of that particular genomic segment in the two alleles. However, without any external linkage information these vectors contain no information about which copy-numbers belong together on the same allele [11]. By convention (and for each genomic segment independently), the larger of the two copy-numbers is termed the major and the other the minor copy-number (Figure 1 left). The process of finding the correct assignment of major and minor copy-number to the two parental alleles is called phasing. In contrast to nucleotide substitution models where sites in a sequence are modelled as independent and identically distributed [27], copy-number events often overlap and range across many adjacent genomic regions. Therefore, finding the correct phasing is essential to accurately estimate evolutionary distances (Figure 2A), which additionally requires a model capable of dealing with these horizontal dependencies. We developed MEDICC and successfully applied it to the analysis of a novel dataset of 170 copy-number profiles of patients undergoing neo-adjuvant chemotherapy for HGSOC as described in our accompanying clinical study [28]. In the following we give a more detailed description of the data and problems that MEDICC addresses. We then introduce the MEDICC modelling framework that guides all steps of the algorithm and which is then explained in detail. We finish with a demonstration of MEDICC on a real-world example of a case of endometrioid cancer and give simulation results that compare it to competing methods.
We model the evolution of copy-number profiles through a series of simple operations that increase or decrease copy-numbers by one (Figure 3A). They map to real genomic rearrangements that have an observable effect on copy-number profiles in the following way: terminal and interstitial deletions, as well as unbalanced translocations, are single deletion events; tandem and inverted duplications are single amplification events; and breakage fusion bridges are dual events involving a duplication and a deletion (copy number decrease on one locus and increase on the second) [22]. We use a finite-state automaton (FSA) representation of genomic profiles and finite-state transducers (FST) [30] for modelling and efficient computing of the minimum-event distance based on these genomic events (Figure 3B). Transducers have earlier been proposed as an efficient way of modeling indels on trees [31]–[33], a problem closely related to the one discussed here. Before going through the three steps of the reconstruction process in detail it is necessary to introduce some terminology; for a more thorough introduction into transducer theory see [30], [34], [35] and references therein. We assessed reconstruction accuracy using simulated data generated by the SimCopy R package [43] (see Methods). Random coalescent trees were generated with APE [44]. To create an unbiased simulation scenario, genome evolution was simulated using increasing evolutionary rates on the sequence level using five basic genomic rearrangement events: deletion, duplication, inverted duplication, inversion and translocation (for details see Methods). Once the simulations were complete, copy-numbers were counted for each genomic segment and these copy-number profiles were used for tree inference using the following three methods: i) BioNJ [45] tree reconstruction on a matrix of Euclidean distances computed directly on the copy-numbers, ii) breakpoint-based tree-inference using the TuMult software [23] and iii) MEDICC. TuMult additionally requires array log-intensities as input. In order to keep the comparisons unbiased, noiseless log ratios simulating CGH array intensities for TuMult were directly computed from the copy-number profiles. To assess the relative abilities of the methods to correctly recover the evolutionary relationships of the simulated copy-number profiles, reconstruction accuracy was measured in quartet distance [46] between the true and the reconstructed tree. Quartet distance was chosen as it only considers topological differences; branch lengths have widely different meanings in the methods tested and as such are not comparable. This simulation strategy is based on basic biological principles, independent of the methods compared and a priori does not favour any of them. All simulations were repeated to cover a wide parameter range, yielding qualitatively similar results. The simulation results clearly show the improvement in reconstruction accuracy of MEDICC over naive approaches (BioNJ on Euclidean distances) and competing methods (TuMult) (Figure 4A). In general, reconstruction accuracies increase with increasing evolutionary rates. Especially when the amount of phylogenetic information is limited, MEDICC outperforms other methods by a significant margin. This may be because of two reasons: firstly, in contrast to other methods MEDICC is capable of phasing the parental alleles, thereby making much more effective use of the phylogenetic information compared to methods that work on total copy-number alone. Secondly, due to efficient and accurate heuristics, MEDICC can deal with the horizontal dependencies imposed by overlapping genomic events of arbitrary size and accurately computes distances between them. To assess the accuracy of the implemented CFG-based phasing method, for each reconstructed tree phased alleles were compared to the original simulated alleles. MEDICC correctly phased of all genomic loci across all simulations (Figure 4C). We additionally evaluated the runtime of the complete algorithm on our simulation scenario which consisted of 100 genomic segments after compression and found it to take on average 5 minutes for a full reconstruction on a UNIX based Intel (R) Xeon (R) CPU E5-2670 at 2. 60 GHz. Intra-tumour heterogeneity is a loose concept that describes the amount of genomic difference between multiple cells or samples of the same tumour. Two types of heterogeneity often of interest are spatial and temporal heterogeneity. For example, spatial differences might be observed from separate biopsies of a primary cancer and a distant metastasis. Other changes may occur between different time points, for example before and after chemotherapy. Average distances between subsets of samples might be computed by any method that returns dissimilarities between samples by simple averaging. However, clinical datasets are often noisy due to normal contamination and immune response such as leukocyte infiltration. As for example a sample with exceptionally low cellularity can lead to errors during segmentation, more robust measures of distances between aggregated subsets of samples are desirable that are not easily skewed by outliers. As described earlier, the matrix of pairwise minimum-event distances inferred by MEDICC can directly be transformed into a kernel matrix [38], [33] which maps samples to a high-dimensional mutational landscape. We reduce the dimensionality of this landscape through kernel principal components analysis [47] where we can use spatial statistics to derive numerical measures of heterogeneity for each patient. In the following section we demonstrate MEDICC on a case from the CTCR-OV03 clinical study [54]. This case had advanced endometrioid ovarian carcinoma and was treated with platinum-based neoadjuvant chemotherapy. After three cycles of chemotherapy the patient had stable disease based on RECIST assessment, pre- and post-chemotherapy CT imaging and a reduction of the tumour response marker CA125. She then underwent interval debulking surgery but had residual tumour of cm at completion. After six moths she progressed with platinum-resistant disease and died one month later. Out of 20 biopsy samples 18 satisfied quality control for tumour cellularity and array quality. The dataset included 14 omentum samples, two samples from the vaginal vault (VV) and two samples from the external surface of the bladder (BL). The BL and VV samples were taken prior to chemotherapy and the omental samples were collected at interval-debulking surgery after three cycles of chemotherapy. All samples were copy-number profiled with Affymetrix SNP 6. 0 arrays and segmented and compressed using PICNIC [24] and CGHregions [55]. Pairwise evolutionary distances between all samples were estimated with MEDICC. The distance distribution was tested for the molecular clock hypothesis using MEDICCquant and showed strong non-clock like behaviour (, Figure 6A). Tree reconstruction was performed by MEDICC using the Fitch-Margoliash algorithm Fitch1967. MEDICCquant detected a high degree of clonal expansion () as can be seen in the strong spatial clustering of samples on the mutational landscape (Figure 6B). MEDICC counted a median of 204 genomic events relative to the diploid and a median of 146 between all pairwise comparisons. Tree reconstruction showed good support values for the omental and BL/VV subclades, suggesting strong spatial heterogeneity. The patient also showed strong temporal heterogeneity, as there were large evolutionary distances between samples before and after neoadjuvant chemotherapy (temporal heterogeneity index 3. 78, Figure 6B). However, temporal and spatial heterogeneity in this case are indistinguishable because the BL/VV samples coincide with the biopsy samples, whereas all omentum samples were taken at surgery. Ancestral reconstructions using MEDICC showed loss-of-heterozygosity (LOH) events on chromosome 17q (see internal node profiles in Figure 6A) that often coincide with deleterious mutations in BRCA1 and TP53 [56]. The most prominent contributors to the clonal expansions of the subgroup surrounding sample S01 seemed to be chromosomal amplifications on chromosomes 6,8, 11 and 14; as well as LOH on chromosome 15. We also detected large LOH events on chromosomes 4,5, 9,10,13,14,16 and 17 (Figure 6C).
While significant progress has been made recently to understand tumour heterogeneity through extensive multiple sampling studies and experimental efforts, few algorithms have been developed to target the specific questions raised by such datasets. MEDICC is our contribution to better reconstruct the evolutionary histories of cancer within a patient and propose unbiased quantification of heterogeneity and the degree of clonal expansion. We have shown the success of these efforts in simulations and their utility in the example discussed in this article. More detailed analyses of clinical cases that also elaborate on the connection between clonal expansions and patient outcome can be found in our clinical study [28]. It is important to note that both the clonal expansion index and the proposed measure for average evolutionary distance between subsets of samples are based solely on pairwise distances and the implicit feature space projection and not on the reconstructed trees. This is advantageous as e. g. for the temporal heterogeneity index the subsets of samples that are compared are not necessarily monophyletic clades in the tree. As discussed above we attribute the increase in reconstruction accuracy mainly to two factors. First, MEDICC makes efficient use of the available phylogenetic information by phasing parental alleles using the minimum evolution criterion, which has to our knowledge not been attempted before. Second, MEDICC models actual genomic events that change copy-number and incorporates biological constraints such as loss-of heterozygosity, which is not the case in breakpoint-based approaches. The loss of reconstruction accuracy of TuMult relative even to naive approaches using Euclidean distances is most likely due to the fact that TuMult was designed for fewer leaf nodes (typically around 4; Letouze, personal communication). It is worth stressing that, unlike its competitors, MEDICC is not linked to a specific data collection platform. Data from SNP arrays can be used, as well as sequencing-based datasets or any other method that returns absolute copy numbers. It is further worth noting that an increase in, the maximum allelic copy-number, first of all increases the alphabet size but not the complexity of the algorithms. However, increasing also increase the number of states in the tree FST and hence the memory demands on the elementary FST operations determinisation and minimisation [34] that are used when constructing. This effectively caps at a value of for the time being. Future work will focus on reductions of algorithmic complexity as well as the integration of SNV data into the reconstruction process. Another important aspect is subclonality within a physical sample which may not easily lead to integer-based copy number inference. Instead of fully clonal integer CN profiles we are working on an extension that allows for mixtures of cells to be represented effectively, allowing for the computation of expected sequence similarities between mixtures of cancer genomes. Additionally, it would certainly be desirable to move from the current minimum-evolution approach to a full probabilistic model with specific probabilities for amplification and deletion events. Event probabilities could then be trained by expectation-maximisation. However, this significantly increases the computational complexity of the algorithm, which demands the development of new heuristics that constrain the size of intermediate results of the reconstruction process. Another consequence of this minimum-evolution approach is that all events are weighted equally, independent of their size, while computing evolutionary distances. During ancestral reconstruction, however, if two possible ancestors would yield the same total number of events in the tree, the algorithm prefers shorter events over longer ones to reduce the ambiguity when determining ancestral genomes. Preferring shorter events is a direct consequence of our minimum evolution approach. However, if two genomes differ by a focal deletion in a key gene that confers a substantial fitness advantage, this fitness-increasing mutation will most likely not be visible when determining the clonal expansion index due to its relative small evolutionary distance to the other genomes. Future work might explore the possibility of weighting individual events based on their genomic position and the potential oncogenes and tumour suppressors contained therein. Lastly, MEDICC is subject to the same limitations as classical algorithms for phylogenetic reconstructions. Strong convergent evolution, i. e. two genomes becoming similar due to selection even though they diverged early, can in theory mislead the reconstruction process. However, this problem is typically more pronounced for point mutations than for copy-number changes. Two convergent copy-number events that occurred independently must by chance have the same start and end locus on the genome to be considered identical, which is much less likely than two point mutations occurring by chance at the same genomic position, due to the far greater number of possible outcomes of each event.
Coalescent trees were simulated using the APE R package [44]. Simulation of genome evolution on these trees was performed by custom code, released as the SimCopy R package [43]. SimCopy relies on the PhyloSim package [57] in order to perform the simulations on the level of abstract “genomic regions”. The genomic regions are encoded in a sequence of integers, with the sign representing their orientation. The package then uses modified PhyloSim processes in order to simulate deletion, duplication, inversion, inverted duplication and translocation events happening with rates specified by the user. The number of genomic regions affected by each of these events is modelled by truncated Geometric+1 distributions. After simulating genome evolution, copy-number profiles are reported for leaf and internal nodes. Genomes were simulated using 15 leaf nodes, a root size of 100 segments and an average event length of 12 segments to allow for overlapping events. Event rates covered the following set: Individual event rates were modified with the following factors: deletions: , duplications: , inverted duplications: , inversions: , translocations: . All parameters were chosen such that the leaf node copy-number distributions are similar in shape to copy-number distributions from experimental data in the clinical study [28]. All FST and FSA algorithms were implemented using OpenFST [40]. MEDICC was written in Python, while implementation of time-critical parts used C. For the Fitch-Margoliash implementations we used the Phylip package [58]. MEDICC is available at https: //bitbucket. org/rfs/medicc and has been tested on Windows and UNIX-based systems. The quantitative analysis of MEDICC results was done in R and all necessary functions are implemented in the MEDICCquant package included in the MEDICC distribution. Spatial statistics were computed using the spatstat package [52], and for kernel manipulations the kernlab package was used [59].
Cancer is a disease of random mutation and selection within the cellular genomes of an organism. As a result, when advanced disease is diagnosed, the cells comprising the tumour show a great amount of variability on the genomic level, a phenomenon termed intra-tumour genetic heterogeneity. Heterogeneity is thought to be one of the main reasons why tumors become resistant to therapy, and thus hinders personalised medicine approaches. If we want to understand tumour heterogeneity and its connection to resistance development we need to quantify it, which implies reconstructing the evolutionary history of cancer within the patient. Unfortunately, so far, methods for accurate reconstructions of these particular evolutionary trees and for quantification of heterogeneity have been missing. We here present MEDICC, a method that uses a minimum evolution criterion to compare cancer genomes based on genomic profiles of DNA content (copy-number profiles). It enables accurate reconstruction of the history of the disease and quantifies heterogeneity. It is specifically designed to deal with diploid human genomes, in that it disentangles genomic events on both parental alleles and includes a variety of accompanying algorithms to test for shapes of the evolutionary trees as well as the rate at which the cancer evolves.
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Phylogenetic Quantification of Intra-tumour Heterogeneity