Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data

doi:10.1093/bioinformatics/bti611

Bioinformatics. Author manuscript; available in PMC 2010 February 10.

Published in final edited form as:

Bioinformatics. 2005 October 1; 21(19): 3763.

Published online 2005 August 4. doi: 10.1093/bioinformatics/bti611

PMCID: PMC2819184

NIHMSID: NIHMS171393

Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data

Weil R. Lai,¹ Mark D. Johnson,² Raju Kucherlapati,¹ and Peter J. Park^1,³^*

¹Harvard-Partners Center for Genetics and Genomics, 77 Avenue Louis Pasteur, Boston, MA, 02115

²Department of Neurological Surgery, Brigham and Women's Hospital and Harvard Medical School, 75 Francis St, Boston, MA, 02115

³Children's Hospital Informatics Program, 300 Longwood Ave, Boston, MA, 02115

^*to whom correspondence should be addressed

Contact: peter_park/at/harvard.edu

The publisher's final edited version of this article is available free at Bioinformatics

See other articles in PMC that cite the published article.

Abstract

Motivation:

Array Comparative Genomic Hybridization (CGH) can reveal chromosomal aberrations in the genomic DNA. These amplifications and deletions at the DNA level are important in the pathogenesis of cancer and other diseases. While a large number of approaches have been proposed for analyzing the large array CGH data sets, the relative merits of these methods in practice are not clear.

Results:

We compare eleven different algorithms for analyzing array CGH data. These include both segment detection methods and smoothing methods, based on such diverse techniques as mixture models, Hidden Markov Models, maximum likelihood, regression, wavelets, genetic algorithms, and others. We compute the Receiver Operating Characteristic (ROC) curves using simulated data to quantify sensitivity and specificity for various levels of signal-to-noise ratio and different sizes of abnormalities. We also characterize their performance on chromosomal regions of interest in a real data set obtained from patients with Glioblastoma Multiforme. While comparisons of this type are difficult due to possibly sub-optimal choice of parameters in the methods, they nevertheless reveal general characteristics that are helpful to the biological investigator.

INTRODUCTION

Locating chromosomal aberrations in genomic DNA samples is an important step in understanding the pathogenesis of many diseases. This is especially true in cancer, and an enormous amount of effort and resources has been dedicated to the detailed characterization of the chromosomal abnormalities in the development and progression of various cancers. Amplification or deletion of chromosomal segments can lead to abnormal mRNA transcript levels and results in the malfunctioning of cellular processes.

Array Comparative Genomic Hybridization (CGH) is a technique for measuring such changes (Solinas-Toldo et al., 1997; Pinkel et al., 1998). See Pinkel and Albertson (2005) for a review. The main difference between array CGH and mRNA expression profiling is that genomic DNA rather than mRNA transcripts are hybridized in array CGH. As the resolution of the arrays has improved over the years, array CGH has become a powerful tool. As a high-throughput technique, it offers many advantages over other cytogenetic techniques such as Fluorescence in Situ Hybridization (FISH). Whereas early experimental techniques were only able to detect chromosomal changes at the whole chromosomal or whole arm level, the CGH arrays using BAC (Bacterial Artificial Chromosome) clones have been widely used subsequently, with the resolution on the order of 1Mb (Pinkel et al., 1998). These arrays generally contain many regions with known oncogenes and tumor suppressor genes, and can be iteratively designed in a locus-specific manner to identify candidate genes in a small region. More recently, cDNA and oligonucleotide arrays have become popular for CGH (Pollack et al., 1999; Brennan et al., 2004). The shorter probes on these new arrays may not be as robust as BACs for large segments, but they offer much higher resolution (on the order of 50 – 100 Kb). In particular, oligonucleotide arrays allow design flexibility and greater coverage, and they appear to provide sufficient sensitivity (Brennan et al., 2004). Tiling or custom arrays are also available now for even finer resolution of specific regions and allow the detection of micro-amplifications and deletions (Lucito et al., 2003; Ishkanian et al., 2004).

The resultant high-throughput array CGH data have prompted the development of various algorithms for data analysis, as briefly reviewed in the next section. However, while there have been numerous publications introducing new methods, the relative strengths and weaknesses of these methods are difficult to discern, due to the complexity of the algorithms and the lack of software with visualization tools. This problem is exacerbated by nondescript titles and abstracts of the articles and their lack of extensive performance comparisons to existing methods. This is especially true from the perspective of the biologist who must choose an algorithm for the data set of interest. The purpose of this paper is to compare the algorithms that have been published so that the user can quickly gain an overview of the array CGH algorithms and their performance. Both simulated data and real data obtained from glioblastoma samples are used for evaluating the algorithms.

METHODS

Basic Issues & Algorithms

Array CGH data consist of the log-ratios of normalized intensities from disease vs control samples, indexed by the physical location of the probes on the genome. The goal is to identify regions of concentrated high or low log-ratios. In general, these regions of interest can be very small; some microdeletions may only contain a single probe. Because attempting to identify such small regions can result in too many false positives, information from consecutive probes are used to identify larger regions with more confidence.

The first analytical methods were simple yet intuitive and often effective, involving smoothing of the ratio profiles and applying a reasonable threshold to determine if the average ratio over a potential region signified an amplification or a deletion. For instance, a moving average was used to process the ratios, and a ‘normal vs normal’ hybridization was used to compute a threshold level (Pollack et al., 2002). In another study, a simple maximum likelihood method was used to fit a mixture of three Gaussian distributions corresponding to gain, loss, and normal regions (Hodgson et al., 2001).

Broadly, there are two estimation problems. One is to infer the number and statistical significance of the alterations; the other is to locate their boundaries accurately. The many available methods differ in the ways in which each part is modeled and the two are combined. In general, the formulation of a model-based method presumes a sequence of piecewise constant segments, as a function of various parameters such as the number of breakpoints, their locations, and the mean/variance of the distributions for each segment. Then the maximization of a function, typically a log-likelihood, is used to estimate the model parameters from the data. In the likelihood, a penalty term for the number of segments is often included to avoid too fine a partition which tends to increase the likelihood. Models differ in their distributional assumptions and the incorporation of penalty terms.

Subsequently, more complicated methods for denoising and estimating the spatial dependence were derived. Genomic amplifications and deletions are assumed to cover multiple probes in general, and an effective incorporation of this spatial structure is a key component in any algorithm. For instance, a quantile smoothing method based on the minimization of errors in L₁ norms (sum of absolute errors) rather than L₂ norm (sum of squared errors) is shown to give sharper boundaries between segments (Eilers and de Menezes, 2005). Another promising smoothing algorithm is a denoising by wavelets (Hsu et al., 2005), a nonparametric technique that appears to handle abrupt changes in the profiles well. A simple and more common approach is based on robust locally weighted regression and smoothing scatterplots (lowess), introduced in Cleveland (1979). This has been used previously in other works such as in Beheshti et al. (2003).

In Olshen and Venkatraman (2002); Olshen et al. (2004), the binary segmentation method (Sen and Srivastava, 1975) is modified to allow splits into either two or three segments. In this algorithm, termed Circular Binary Segmentation (CBS), the maximum of a likelihood ratio statistic is used recursively to detect narrower segments of aberration. In Jong et al. (2003, 2004), a genetic search algorithm is used to maximize a likelihood with a penalty term containing the number of breakpoints. In Hupe et al. (2004), a more complex likelihood function with weights determined adaptively is used to solve the estimation problem locally based on data smoothed by the Adaptive Weights Smoothing procedure (Polzehl and Spokoiny, 2000). A likelihood method with a different penalty function is used in Picard et al. (2005) for the number of segments to avoid underestimation on the number of segments. It is pointed out that a distribution assumption can have an importance consequence in a model: a homogeneous variance assumption among different regions, for example, tends to lead to a more segmented profile in order to satisfy the variance assumption. In Daruwala et al. (2004), a Poisson distribution is used to model the number of segments and this is incorporated as an additional component in the likelihood. (This last method was not available publicly.)

In a more local approach (Myers et al., 2004), an edge filter is used to detect the approximate location of edges, and an EM algorithm is used to place them more precisely. In Lingjaerde et al. (2005), a simple smoothing is done using signs of neighbors, and significance is determined by comparing both the width and height of the observed segments to their joint null distribution. A dynamic programming approach is used in Autio et al. (2003), but this was not part of our study because the associated MATLAB package was difficult to port to our platform.

A different kind of modeling approach involves the Hidden Markov models (HMMs), in which the underlying copy numbers are the hidden states with certain transition probabilities (Snijders et al., 2003; Sebat et al., 2004; Fridlyand et al., 2004). In Wang et al. (2005), a simple but effective method based on hierarchical clustering along the chromosomes is used to identify regions of interest and the False Discovery Rate (FDR) is used as a selection criterion.

Evaluation Method

Evaluating the relative performance of these methods is complicated by several problems. One difficulty is that the goals of different algorithms are not the same. For example, those with an emphasis on the smoothing part may simply return the log-ratios without determining which ones are significant. More comprehensive methods may return the coordinates of only the statistically significant segments with or without the estimated average log-ratio per segment. One may require a ‘normal vs normal’ sample as a control while another may not. When necessary, we simulated the control samples by Gaussian noise with zero mean and a variance estimated from the tested data using the median absolute deviation.

In terms of implementation, the primary issue was that not every algorithm was implemented in publicly available software. All our calculations were carried out in the statistical language R (R Development Core Team, 2004), since this was the dominant platform for the software packages. But other algorithms were implemented in MATLAB, a JAVA application, or an executable file. When the code could be ported easily from MATLAB to R, such as the algorithm in Picard et al. (2005), this was carried out. When a program allowed a relatively simple interface, as was the case with the algorithms in Jong et al. (2004), Myers et al. (2004), and Lingjaerde et al. (2005), it was used for computations.

The most appropriate way to compare these algorithms on simulated data was to calculate the Receiver Operating Characteristic (ROC) curves. Because different algorithms were tuned at different sensitivity levels, it was important to examine the trade-off between sensitivity and specificity in each case. This approach adjusts for the differences arising from identifying different numbers of segments in each algorithm. We have used the default parameters for each algorithm, as most users will be doing. If no default parameters were available, we used the steps suggested in the program documentation or the papers describing the method to select the parameter values. We have not attempted to adjust the parameters to improve the performance, due to the large number of algorithms and the large number of scenarios under which they were tested. This issue is further discussed in Discussion. The general properties are nonetheless apparent, even if the parameters were suboptimal.

RESULTS

First, we tested the algorithms on simulated data of various abnormality widths and noise levels. To generate ROC curves corresponding to a particular aberration width and noise level, we calculated the true positive rates (TPR) and the false positive rates (FPR) as we varied the threshold for determining an aberration. We also tested the algorithms on cDNA microarray data containing measurements from 26 different primary Glioblastoma Multiforme (GBM) tumors (Bredel et al., 2005).

Simulated Data

We calculated the ROC profiles of each algorithm for aberration widths of 5, 10, 20, and 40 probes and signal-to-noise ratios (SNR) of 1, 2, 3, and 4. SNR was defined as the mean magnitude of the aberration (i.e., signal) divided by the standard deviation of the superimposed Gaussian noise. Figure 1 illustrates the kind of profiles examined in this simulation. For each aberration width and SNR, we generated 100 artificial chromosomes, each consisting of 100 probes and with the square-wave signal profile added to the center of the chromosome. The performance of the algorithms for the aberrations at the boundaries was not examined here.

Fig. 1

Array-CGH algorithms on simulated aberrations of increasing width. Illustrated here as an example are the signal profiles consisting of five aberrations of 2, 5, 10, 20, and 40 probes long with an amplitude of 1. Gaussian noise N(0, .25²) was added onto (more ...)

TPR was defined as the number of probes inside the aberration whose fitted values are above the threshold level divided by the number of probes in the aberration. FPR was defined as the number of probes outside the aberration whose fitted values are above the threshold level divided by the total number of probes outside the aberration. In order to compute the ROC curve, we varied the threshold value for aberration from the minimum log-ratio value to the maximum. (This is equivalent to moving the x-axis cutoff value in a mixture distribution.) Each threshold value results in a TPR and a FPR, represented by a point on the ROC curve. A set of TPRs and FPRs were then plotted to reveal the algorithm's ROC profile for the particular aberration width and SNR (see Figure 2). We also computed confidence intervals around each ROC curve (not shown) but there did not appear to be significant differences among the methods.

Fig. 2

Receiver operating characteristic (ROC) curves for array CGH algorithms measured at different aberration widths and signal-to-noise ratios (SNR). The x-axis is the false positive rate and the y-axis is the true positive rate. Red is CGHseg (Picard et (more ...)

We note that TPR and FPR are informative in understanding how an algorithm performs in estimating the boundary of the altered region. When the algorithm over-estimates the boundary, FPR increases while TPR remains fixed; when it under-estimates the boundary, TPR decreases while FPR remains fixed. We also note that FPR estimates depend on the size of the aberration relative to that of the chromosome. Therefore, FPR should be used only for measuring relative performance among different methods given a fixed aberration size.

The default parameters in the software were used except in the following cases where the parameters had to be chosen by the user. For quantile smoothing, we followed the suggestion of Eilers and de Menezes (2005) to use two-fold cross-validation to estimate the value of λ that minimizes the overall penalty term; this gave us a λ of 1.5. For the wavelet denoising algorithm, we chose soft Stein's Unbiased Risk Estimate thresholding with a maximum wavelet coefficient level of 3 based on results given in their paper. For lowess, we used a smoothing window of 10 probes and defined the smoothing span as the size of the smoothing window divided by the number of non-missing log-ratios in the chromosome. For the genetic algorithm (Jong et al., 2003), we deselected the option to filter out log-ratios with a threshold value of 0.75 so that their program will consider all data points in the analysis. For Analysis of Copy Errors (Lingjaerde et al., 2005), we chose results for the estimated false discovery rate closest to 0.001.

As shown in Figure 2, most algorithms did well in the case of detecting the existence and the width of aberrations for the large changes and high SNRs (upper left panels). For the cases of smaller aberrations and low SNRs, the smoothing methods (i.e., wavelets, lowess, quantile regression) gave better detection results (higher TPR and lower FPR) than other methods. The smoothing algorithms followed low amplitude and local trends in the data better than the other algorithms which were less sensitive to such features.

Among the methods that perform estimation (indicated by ‘E’ in Table 1), the homoscedastic algorithm in Picard et al. (2005) appeared to perform better than other methods. However, none of the algorithms reliably detected the aberrations with small width and low SNR because the signal is too weak to differentiate from the noise. Compared to other algorithms, the CLAC algorithm tended to overestimate the boundaries of the aberrations. The mean smoothing step in CLAC appeared to reduce noise in the artificial chromosome data at the expense of blurring the edges of the boundaries. The ChARM algorithm did not detect the presence of aberrations in every artificial chromosome even in the large width, high SNR case, irrespective of the cutoff p-values for the mean and sign tests. We suspect that this may be due to the fact that its boundary detection step is local and decoupled from the overall estimation.

Table 1

List of algorithms tested in this paper. For the last column, ‘S’ and ‘E’ indicate that the algorithm has a step for smoothing and estimation, respectively. Three methods (Quantreg, Wavelet, and Lowess) are for smoothing (more ...)

Glioblastoma Multiforme (GBM) Data

There are 26 samples representing primary GBMs in the glioma data from Bredel et al. (2005). GBM is a particularly malignant type of brain tumor, with a median patient survival time of a year. The samples were co-hybridized with pooled human controls onto custom spotted cDNA microarrays. The scanned raw data were downloaded from the Stanford Microarray Database (http://smd.stanford.edu). For the purpose of this paper, the array data were normalized by print-tip group, intensity-dependent normalization with the Limma package (Smyth, 2004). Of the 41,421 elements on each array, we were able to link 33,599 of them to chromosomal positions using mapped EST data from the hg16 build of the UCSC Genome Browser (http://genome.ucsc.edu). Missing values in each array were removed to avoid the effect of imputed values in subsequent analyses.

Though noisy (standard deviation of the log-ratios for each array ranges from 0.35 to 0.9), the GBM data contained a mixture of larger, low amplitude regions of gains/losses and smaller, high amplitude regions of amplifications/deletions. These types of copy number alterations represent the types of aberrations the array CGH algorithms should detect. Two examples representing a broad, low amplitude change and a smaller, high amplitude one are examined in the following paragraphs.

Numerous regions of gains/losses have been found in many microarray studies on gliomas (Koschny et al., 2002). For instance, gain of chromosome 7 and losses of chromosomes 10 and of large portions of 13 and 22 have been observed in GBMs previously. These gains and losses may be the effect of uncontrolled mitotic events from point mutations of oncogenes and tumor-suppressing genes. In the sample GBM31, there exists a large region of loss on chromosome 13. The overall magnitude of the loss is very low because not all tumor cells in a given sample have the same types of gains and losses. It may also be due to the presence of connective tissues and other non-tumor cells in the sample. As a consequence of sample heterogeneity, the signal is diluted, thus complicating the detection procedure for the algorithms.

As can be seen in Figure 3, most algorithms in the study detected the proximal loss of chromosome 13 of GBM31. CGHseg, GLAD, CBS, GA all clearly identified nearly identical regions. All three smoothing algorithms showed the same general trend but the global loss was obscured by the local features. These algorithms performed well in detecting the smaller aberrations in the simulated data, but they were not as useful for a global view. HMM did not separate chromosome 13 into two regions. In addition to detecting the loss, GLAD identified numerous single-probe outliers. Such outliers can either indicate a real focal aberration, some type of polymorphism, or an experimental artifact (e.g., bad probe). CLAC and ACE detected the region of loss as a series of smaller losses. Many smaller regions within chromosome 13 that CLAC and ACE did not detect as losses coincided with localized positive spikes in log-ratios.

Fig. 3

Array-CGH profile of chromosome 13 in a Glioblastoma Multiforme sample (GBM31). This chromosome has a partial loss of low magnitude. Most algorithms in the study detect the loss. In particular, CGHseg, GLAD, CBS, and GA clearly identify the region.

The GBM data also contained numerous amplifications. Several amplifications, such as those around PDGFRA, CDK4, and MDM2, have been well-studied in GBMs (Kraus et al., 2002). The amplification at the EGFR locus has been implicated in other tumors, and it is clearly present in GBMs, as shown in Figure 4. In this GBM29 sample, there appeared to be at least three high amplitude amplifications around EGFR. The algorithms CGHseg, quantreg, GLAD, wavelet, and GA detected all three high amplifications. Because there are only 4 probes separating the first two amplifications, methods such as CLAC, CBS, Lowess, and ACE combined the first two amplifications together. It is possible that these two amplifications were in fact a single one, but mapping the probes to their physical positions suggested that they are likely to be two separate aberrations.

Fig. 4

Array-CGH profile of the three amplifications around EGFR in GBM29. CGHseg, quantreg, GLAD, wavelet, and GA detects all three amplifications. CLAC, CBS, Lowess, and ACE detect the first two amplifications as one larger region. ChARM detects the amplification (more ...)

CLAC, ACE, and ChARM all use mean smoothing as an initial step to denoise the data. Mean smoothing increases SNR at the cost of blurring the edges of the boundaries. Because of the blurring, CLAC detected the amplifications as two, larger adjacent amplifications. ACE does not merge the amplifications the way CLAC did, as it has an additional step to compensate for the blurring in identifying the boundaries. More sophisticated smoothing methods appear to perform better in general.

ChARM detected the three amplifications as one large region of gain. However, when each region was manually tested for significance in their software, all regions were marked as significant by their mean and sign tests. This indicated that the boundary detection part should be improved. HMM did not detect any of the three amplifications, even though it detected smaller regions in the simulated data. Singular matrices in the iterations were often the source of problems.

DISCUSSION

For processing a large number of high-resolution arrays, the speed of the algorithms becomes an issue. The simple smoothing algorithms such as lowess and wavelets are the fastest, while Hidden Markov Model and Circular Binary Segmentation are the slowest. The fast local algorithms are (N), where N is the number of probes along the chromosome, and slow ones, which require long-range information, are generally (N²). For the typical BAC arrays, speed is not a concern, but it can be a problem for high-density oligonucleotide arrays.

A particularly helpful feature for future implementations of some algorithms would be to estimate the statistical significance of the detected copy number changes and then rank them accordingly. Some current implementations simply return the processed profiles but do not ‘call’ the detected regions as significant or not. When the genome-wide profile is scanned for potentially new regions of interest, quantitative statistics about the aberrations are critical in order to decide which region to pursue for further examination. The false discovery rate appears to be a natural framework, but only two of the algorithms (CLAC and ACE) have incorporated this so far.

There is an inherent difficulty in comparisons of complicated algorithms. Each method has its own set of parameters that must be tuned properly, and this often requires a detailed understanding of the algorithm. It is therefore possible for the proponents of one algorithm to argue that their method did not perform adequately simply because the parameters were not set at an optimal level. This is especially true when the developers of different algorithms were interested in arrays of different resolutions and noise levels, or were motivated by different types of biological problems. For example, researchers working on well-characterized cancers might be more interested in focal aberrations, whereas those working on less characterized cancers might be interested in broad changes. To the extent that this is true, the results of our analysis here should be taken with caution, and it is incumbent upon the user to understand the characteristics of each method. On the other hand, if the algorithm is very sensitive to the changes in parameters or if the complexity of the algorithm does not allow the user to determine the correct parameters easily, that may be legitimately viewed as a weakness.

There are several ways in which these algorithms can be improved. First, further refining of the methodology especially in the pre-processing of the data would be beneficial. We have found that some segmentation methods, especially CGHseg (Picard et al., 2005) and CBS (Olshen et al., 2004), appear to perform consistently well. When the noise is high, smoothing methods appear to work well, although their output is more difficult to interpret. An optimal combination of the smoothing step and the segmentation step may result in improved performance. Second, one piece of information that was not considered in any of the methods discussed here is the physical distance of the probes along the genome; uniform spacing is assumed currently. If two probes indicating the same direction of change are very far apart, the probability that they refer to the same alteration should be lower than if they had been closer. It is not clear how much improvement could result by incorporating this information, but it can only help, if done correctly. Third, because multiple samples are usually analyzed at the same time, it is important to summarize the overall results in a clear fashion. Although those aberrations present in a small fraction of patients can be important, those occurring with a higher frequency are more likely candidates for research. Finally, user-friendly software with visualization tools and links to other databases would be helpful. Currently, these functionalities are present only for a small number of programs implementing the algorithms. An investigator is more likely to be interested in a region if a gene is present in the region, and even more so if it is an oncogene. Links to such information would be invaluable.

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