Assembly of microarrays for genome-wide measurement of DNA copy number

Copy number gain at 8q12.1-q22.1 is associated with a malignant tumor phenotype in salivary gland myoepitheliomas

Salivary gland myoepithelial tumors are relatively uncommon tumors with an unpredictable clinical course. More knowledge about their genetic profiles is necessary to identify novel predictors of disease. In this study, we subjected 27 primary tumors (15 myoepitheliomas and 12 myoepithelial carcinomas) to genome-wide microarray-based comparative genomic hybridization (array CGH). We set out to delineate known chromosomal aberrations in more detail and to unravel chromosomal differences between benign myoepitheliomas and myoepithelial carcinomas. Patterns of DNA copy number aberrations were analyzed by unsupervised hierarchical cluster analysis. Both benign and malignant tumors revealed a limited amount of chromosomal alterations (median of 5 and 7.5, respectively). In both tumor groups, high frequency gains (> or =20%) were found mainly at loci of growth factors and growth factor receptors (e.g., PDGF, FGF(R)s, and EGFR). In myoepitheliomas, high frequency losses (> or =20%) were detected at regions of proto-cadherins. Cluster analysis of the array CGH data identified three clusters. Differential copy numbers on chromosome arm 8q and chromosome 17 set the clusters apart. Cluster 1 contained a mixture of the two phenotypes (n = 10), cluster 2 included mostly benign tumors (n = 10), and cluster 3 only contained carcinomas (n = 7). Supervised analysis between malignant and benign tumors revealed a 36 Mbp-region at 8q being more frequently gained in malignant tumors (P = 0.007, FDR = 0.05). This is the first study investigating genomic differences between benign and malignant myoepithelial tumors of the salivary glands at a genomic level. Both unsupervised and supervised analysis of the genomic profiles revealed chromosome arm 8q to be involved in the malignant phenotype of salivary gland myoepitheliomas.

Diagnostic applications of fluorescence in situ hybridization

BACKGROUND

Fluorescence in situ hybridization (FISH) assays are indispensable in diagnostics and research. Routine application of this so-called molecular cytogenetic technique on human chromosomes started in 1986. Since then, a huge variety of different approaches for chromosomal differentiation based on FISH has been described. It was established to characterize marker chromosomes identified in conventional banding analysis as well as cryptic rearrangements not resolved by standard cytogenetics.

OBJECTIVE/METHOD

Even though molecular cytogenetics, like banding cytogenetics for almost 40 years, is often called dead now, it offers unique possibilities of single cell analysis. Thus, a review is presented here on the available diagnostic-relevant FISH methods and probe sets applied in routine pre- and postnatal clinical as well as tumor cytogenetics.

CONCLUSION

Molecular cytogenetics is a fast, straightforward and reliable tool that is indispensable in cytogenetic diagnostics. It is and will continue to be of high clinical impact in diagnostics, especially in the overwhelming majority of routine cytogenetic laboratories that cannot afford and do not need high-throughput chip-based platforms for their daily work.

Indistinguishable genomic profiles and shared prognostic markers in undifferentiated pleomorphic sarcoma and leiomyosarcoma: different sides of a single coin?

Soft tissue sarcoma (STS) diagnostics and prognostics are challenging, particularly in highly malignant and pleomorphic subtypes such as undifferentiated pleomorphic sarcoma (UPS) and leiomyosarcoma (LMS). We applied 32K BAC arrays and gene expression profiling to 18 extremity soft tissue LMS and 31 extremity soft tissue UPS with the aim of identifying molecular subtype signatures and genomic prognostic markers. Both the gains/losses and gene expression signatures revealed striking similarities between UPS and LMS, which were indistinguishable using unsupervised hierarchical cluster analysis and significance analysis for microarrays. Gene expression analysis revealed just nine genes, among them tropomyosin beta, which were differentially expressed. Loss of 4q31 (encompassing the SMAD1 locus), loss of 18q22, and tumor necrosis were identified as independent predictors of metastasis in multivariate stepwise Cox regression analysis. Combined analysis applying loss of 4q31 and 18q22 and the presence of necrosis improved the area under receiver operating characteristic curve for metastasis prediction from 0.64 to 0.86. The extensive genetic similarities between extremity soft tissue UPS and LMS suggest a shared lineage of these STS subtypes and the new and independent genetic prognosticators identified hold promise for refined prognostic determination in high-grade, genetically complex STS.

Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics

Metaplastic breast cancers (MBC) are aggressive, chemoresistant tumors characterized by lineage plasticity. To advance understanding of their pathogenesis and relatedness to other breast cancer subtypes, 28 MBCs were compared with common breast cancers using comparative genomic hybridization, transcriptional profiling, and reverse-phase protein arrays and by sequencing for common breast cancer mutations. MBCs showed unique DNA copy number aberrations compared with common breast cancers. PIK3CA mutations were detected in 9 of 19 MBCs (47.4%) versus 80 of 232 hormone receptor-positive cancers (34.5%; P = 0.32), 17 of 75 HER-2-positive samples (22.7%; P = 0.04), 20 of 240 basal-like cancers (8.3%; P < 0.0001), and 0 of 14 claudin-low tumors (P = 0.004). Of 7 phosphatidylinositol 3-kinase/AKT pathway phosphorylation sites, 6 were more highly phosphorylated in MBCs than in other breast tumor subtypes. The majority of MBCs displayed mRNA profiles different from those of the most common, including basal-like cancers. By transcriptional profiling, MBCs and the recently identified claudin-low breast cancer subset constitute related receptor-negative subgroups characterized by low expression of GATA3-regulated genes and of genes responsible for cell-cell adhesion with enrichment for markers linked to stem cell function and epithelial-to-mesenchymal transition (EMT). In contrast to other breast cancers, claudin-low tumors and most MBCs showed a significant similarity to a "tumorigenic" signature defined using CD44(+)/CD24(-) breast tumor-initiating stem cell-like cells. MBCs and claudin-low tumors are thus enriched in EMT and stem cell-like features, and may arise from an earlier, more chemoresistant breast epithelial precursor than basal-like or luminal cancers. PIK3CA mutations, EMT, and stem cell-like characteristics likely contribute to the poor outcomes of MBC and suggest novel therapeutic targets.

Genomic disorders ten years on

It is now becoming generally accepted that a significant amount of human genetic variation is due to structural changes of the genome rather than to base-pair changes in the DNA. As for base-pair changes, knowledge of gene and genome function has been informed by structural alterations that convey clinical phenotypes. Genomic disorders are a class of human conditions that result from structural changes of the human genome that convey traits or susceptibility to traits. The path to the delineation of genomic disorders is intertwined with the evolving technologies that have enabled the resolution of human genome analyses to continue increasing. Similarly, the ability to perform high-resolution human genome analysis has fueled the current and future clinical implementation of such discoveries in the evolving field of genome medicine.

Co-amplified genes at 8p12 and 11q13 in breast tumors cooperate with two major pathways in oncogenesis

Co-amplification at chromosomes 8p11-8p12 and 11q12-11q14 occurs often in breast tumors, suggesting possible cooperation between genes in these regions in oncogenesis. We used high resolution array comparative genomic hybridization (array CGH) to map the minimal amplified regions. The 8p and 11q amplicons are complex and consist of at least four amplicon cores at each site. Candidate oncogenes mapping to these regions were identified by combining copy number and RNA and protein expression analyses. These studies also suggested that CCND1 at 11q13 induced expression of ZNF703 mapping at 8p12, which was subsequently shown to be mediated via the Rb/E2F pathway. Nine candidate oncogenes from 8p12 and four from 11q13 were further evaluated for oncogenic function. None of the genes individually promoted colony formation in soft agar or collaborated with each other functionally. On the other hand, FGFR1 and DDHD2 at 8p12 cooperated functionally with MYC, while CCND1 and ZNF703 cooperated with a dominant negative form of TP53. These observations highlight the complexity and functional consequences of the genomic rearrangements that occur in these breast cancer amplicons, including transcriptional cross-talk between genes in the 8p and 11q amplicons, as well as their cooperation with major pathways of tumorigenesis.

Microarray-based comparative genomic hybridization using sex-matched reference DNA provides greater sensitivity for detection of sex chromosome imbalances than array-comparative genomic hybridization with sex-mismatched reference DNA

In array-comparative genomic hybridization (array-CGH) experiments, the measurement of DNA copy number of sex chromosomal regions depends on the sex of the patient and the reference DNAs used. We evaluated the ability of bacterial artificial chromosomes/P1-derived artificial and oligonucleotide array-CGH analyses to detect constitutional sex chromosome imbalances using sex-mismatched reference DNAs. Twenty-two samples with imbalances involving either the X or Y chromosome, including deletions, duplications, triplications, derivative or isodicentric chromosomes, and aneuploidy, were analyzed. Although concordant results were obtained for approximately one-half of the samples when using sex-mismatched and sex-matched reference DNAs, array-CGH analyses with sex-mismatched reference DNAs did not detect genomic imbalances that were detected using sex-matched reference DNAs in 6 of 22 patients. Small duplications and deletions of the X chromosome were most difficult to detect in female and male patients, respectively, when sex-mismatched reference DNAs were used. Sex-matched reference DNAs in array-CGH analyses provides optimal sensitivity and enables an automated statistical evaluation for the detection of sex chromosome imbalances when compared with an experimental design using sex-mismatched reference DNAs. Using sex-mismatched reference DNAs in array-CGH analyses may generate false-negative, false-positive, and ambiguous results for sex chromosome-specific probes, thus masking potential pathogenic genomic imbalances. Therefore, to optimize both detection of clinically relevant sex chromosome imbalances and ensure proper experimental performance, we suggest that alternative internal controls be developed and used instead of using sex-mismatched reference DNAs.

Array-based genomics in glioma research

Over the years, several relevant biomarkers with a potential clinical interest have been identified in gliomas using various techniques, such as karyotype, microsatellite analysis, fluorescent in situ hybridization and chromosome comparative genomic hybridization. Despite their pivotal contribution to our understanding of gliomas biology, clinical application of these approaches has been limited by technological and clinical complexities. In contrast, genomic arrays (array-based comparative genomic hybridization and single nucleotide polymorphisms array) have emerged as promising technologies for clinical use in the setting of gliomas. Indeed, their feasibility and reliability have been rigorously assessed in gliomas and are discussed in this review. The well-known genomic biomarkers in gliomas are in fact readily and reliably identified using genomic arrays. Moreover, it detects a multitude of new cryptic genomic markers, with potential biological and/or clinical significances. The main studies dedicated to genomic characterization of gliomas using genomic arrays are reviewed here. Interestingly, several recurrent genomic signatures have been reported by different teams, suggesting the validity of these genomic patterns. In light of this, genomic arrays are relatively simple and cost-effective techniques whose implementation in molecular diagnostic laboratories should be encouraged as a valuable clinical tool for management of glioma patients.

Genomic analyses reveal global functional alterations that promote tumor growth and novel tumor suppressor genes in natural killer-cell malignancies

Natural killer (NK)-cell malignancies are among the most aggressive lymphoid neoplasms with very poor prognosis. We performed array comparative genomic hybridization analysis on a number of NK cell lines and primary tumors to gain better understanding of the pathogenesis and tumor biology of these malignancies. We also obtained transcriptional profiles of genes residing in these regions and compared them with normal and activated NK cells. Only 30-50% of the genes residing in the gained or deleted regions showed corresponding increased or decreased expression. However, many of the upregulated genes in regions of gain are functionally important for the proliferation and growth of the neoplastic population. Genes downregulated in regions of loss included many transcription factors or repressors, tumor suppressors or negative regulators of the cell cycle. The minimal common region of deletion in 6q21 included three known genes (PRDM1, ATG5 and AIM1) showing generally low expression. Mutations resulting in truncated PRDM1 and changes in conserved amino-acid sequences of AIM1 were detected. Highly methylated CpG islands 5' of PRDM1 and AIM1 correlated with low expression of the transcripts. Reversal of methylation by Decitabine induced expression of PRDM1 and cell death. In conclusion, we have shown a general tumor-promoting effect of genetic alterations and have identified PRDM1 as the most likely target gene in del6q21. ATG5, an essential gene for autophagy and AIM1, a gene implicated in melanoma, may also participate in the functional abnormalities.

A new classification method using array Comparative Genome Hybridization data, based on the concept of Limited Jumping Emerging Patterns

Background

Classification using aCGH data is an important and insufficiently investigated problem in bioinformatics. In this paper we propose a new classification method of DNA copy number data based on the concept of limited Jumping Emerging Patterns. We present the comparison of our limJEPClassifier to SVM which is considered the most successful classifier in the case of high-throughput data.

Results

Our results revealed that the classification performance using limJEPClassifier is significantly higher than other methods. Furthermore, we show that application of the limited JEP's can significantly improve classification, when strongly unbalanced data are given.

Conclusion

Nowadays, aCGH has become a very important tool, used in research of cancer or genomic disorders. Therefore, improving classification of aCGH data can have a great impact on many medical issues such as the process of diagnosis and finding disease-related genes. The performed experiment shows that the application of Jumping Emerging Patterns can be effective in the classification of high-dimensional data, including these from aCGH experiments.

MSMAD: a computationally efficient method for the analysis of noisy array CGH data

MOTIVATION

Genome analysis has become one of the most important tools for understanding the complex process of cancerogenesis. With increasing resolution of CGH arrays, the demand for computationally efficient algorithms arises, which are effective in the detection of aberrations even in very noisy data.

RESULTS

We developed a rather simple, non-parametric technique of high computational efficiency for CGH array analysis that adopts a median absolute deviation concept for breakpoint detection, comprising median smoothing for pre-processing. The resulting algorithm has the potential to outperform any single smoothing approach as well as several recently proposed segmentation techniques. We show its performance through the application of simulated and real datasets in comparison to three other methods for array CGH analysis.

IMPLEMENTATION

Our approach is implemented in the R-language and environment for statistical computing (version 2.6.1 for Windows, R-project, 2007). The code is available at: http://www.iba.muni.cz/~budinska/msmad.html.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Identification of DNA copy number aberrations by array comparative genomic hybridization in patients with ruptured intracranial aneurysms

We aimed to use array comparative genomic hybridization (CGH) to identify chromosomal loci that contribute to the pathogenesis of ruptured intracranial aneurysms (IAs) in a Korean population and to confirm the results using real-time polymerase chain reaction (PCR). Twenty-three patients with ruptured IAs were enrolled in this study. Array CGH revealed copy number aberrations in 19 chromosomal regions. Chromosomal gains were identified at a high frequency in regions 1p12, 4q24, 5p15.31, 5p15.33, 6p12.2, 6q22.33, 7p21.1, 9q22.1, 10q24.32, 10q26.3, 12q13.13, 17p12, 18q12.3, 18q23, 19p13.3, 20q13.33, 21q11.2, and 21q22.3, whereas chromosomal losses were identified at 15q11.2 and 22q11.21. Real-time PCR confirmed the results of the array CGH studies of the COL6A2, GRIN3B, MUC17, and PRODH genes. This is the first study to identify candidate regions by array CGH in patients with IAs. The identification of genes that may predispose an individual to the development of IAs may lead to a better understanding of the mechanism of IA formation. Multicenter studies comparing cohorts of patients of different ethnicities are needed to better understand the mechanism of IA formation.

Fluorescence in situ hybridization techniques in medical diagnostics

BACKGROUND

Fluorescence in situ hybridization (FISH) has become a well-established method in medical diagnostics. FISH methods complement conventional cytogenetic banding techniques and offer extra clinical applications. FISH is based on the binding of complementary, single-stranded fluorescence-labeled nucleic acid sequences to the fixed and denatured target DNA of metaphases, interphase nuclei or isolated DNA sequences (BACs, oligonucleotides).

OBJECTIVE

The intent of this article is to review the development of molecular cytogenetic techniques available at present and to summarize the most efficient and appropriate use of these techniques in medical diagnostics. The technical aspects and most important applications of FISH assays are described.

CONCLUSION

FISH is bridging the gap between conventional cytogenetic banding analysis and molecular genetic DNA studies. The use of FISH techniques enhances the correct interpretation of numerical and structural chromosome aberrations.

Molecular analysis of multifocal prostate cancer by comparative genomic hybridization

BACKGROUND

Prostate cancer is often multifocal and shows histological heterogeneity among different tumor foci within the same prostate. We analyzed the origin and molecular basis of multifocal prostate cancer and genomic alterations associated with tumor progression.

METHODS

We examined 45 multifocal prostate cancer foci from 22 radical prostatectomy specimens by comparative genomic hybridization (CGH). Laser capture microdissection (LCM) was used to gather cancer cells from frozen prostate specimens.

RESULTS

Frequent chromosomal alternations were losses of 2q21-24 (22.2%), 6q14-22 (60.0%), 8p12-22 (35.6%), 13q14-31 (44.4%) and 16q13-24 (24.4%) and gains of 8q21.3-24.3 (37.8%) and 7q21-33 (20.0%). Frequency of losses of 8p12-22 and 16q13-24 and gains of 8q21.3-24.3 were significantly higher in tumors with high Gleason score (GS) than in those with low GS (P < 0.01, P < 0.05, and P < 0.01, respectively). Tumors with losses of 8p12-22 or 13q14-31 displayed larger volume than those without such losses (P < 0.05 and P < 0.01, respectively). In comparison between different tumor foci within the same prostate, chromosomal alterations did not show completely the same pattern between any tumor foci, except for one case in which two of the three foci displayed no chromosomal abnormalities. More malignant tumors (high GS or extracapsular invasion) displayed significantly higher frequency of losses of 8p12-22 (P < 0.05).

CONCLUSIONS

These results suggest that tumor foci within the same prostate represent independent tumors with differing clonal origin and that loss of 8p12-22 represents an important determinant of prostate cancer progression.

Application of array-based comparative genome hybridization in children with developmental delay or mental retardation

Children with developmental delay or mental retardation (DD/MR) are commonly encountered in child neurology clinics, and establishing an etiologic diagnosis is a challenge for child neurologists. Among the etiologies, chromosomal imbalance is one of the most important causes. However, many of these chromosomal imbalances are submicroscopic and cannot be detected by conventional cytogenetic methods. Microarray-based comparative genomic hybridization (array CGH) is considered to be superior in the investigation of chromosomal deletions or duplications in children with DD/MR, and has been demonstrated to improve the diagnostic detection rate for these small chromosomal abnormalities. Here, we review the recent studies of array CGH in the evaluation of patients with idiopathic DD/MR.

Epigenetic silencing of the kinase tumor suppressor WNK2 is tumor-type and tumor-grade specific

Both genetic and epigenetic mechanisms contribute to meningioma development by altering gene expression and protein function. To determine the relative contribution of each mechanism to meningioma development, we used an integrative approach measuring copy number and DNA methylation changes genomewide. We found that genetic alterations affected 1.9%, 7.4%, and 13.3% of the 691 loci studied, whereas epigenetic mechanisms affected 5.4%, 9.9%, and 10.3% of these loci in grade I, II, and III meningiomas, respectively. Genetic and epigenetic mechanisms rarely involved the same locus in any given tumor. The predilection for epigenetic rather than genetic silencing was exemplified at the 5' CpG island of WNK2, a serine-threonine kinase gene on chromosome 9q22.31. WNK2 is known to negatively regulate epidermal growth factor receptor signaling via inhibition of MEK1 (mitogen-activated protein kinase kinase 1), and point mutations have been reported in WNK1, WNK2, WNK3, and WNK4. In meningiomas, WNK2 was aberrantly methylated in 83% and 71% of grade II and III meningiomas, respectively, but rarely in a total of 209 tumors from 13 other tumor types. Aberrant methylation of the CpG island was associated with decreased expression in primary tumors. WNK2 could be reactivated with a methylation inhibitor in IOMM-Lee, a meningioma cell line with a densely methylated WNK2 CpG island and lack of WNK2 expression. Expression of exogenous WNK2 inhibited colony formation, implicating it as a potential cell growth suppressor. These findings indicate that epigenetic mechanisms are common across meningiomas of all grades and that for specific genes such as WNK2, epigenetic alteration may be the dominant, grade-specific mechanism of gene inactivation.

Clinicopathological features and global genomic copy number alterations of pilomyxoid astrocytoma in the hypothalamus/optic pathway: comparative analysis with pilocytic astrocytoma using array-based comparative genomic hybridization

Pilomyxoid astrocytoma is a recently identified variant of pilocytic astrocytoma. We studied 11 circumscribed astrocytomas with focal (n=5) or diffuse (n=6) pilomyxoid features and compared them with 17 pilocytic astrocytomas from the hypothalamic/chiasmatic region in children. In one patient, a tumor that recurred after initial surgery had changed from pure-form pilomyxoid astrocytoma to the mixed form. The presence of a pilomyxoid area was associated with shorter survival. Next, we compared the comprehensive genome copy number changes in the pilomyxoid astrocytoma (n=4) with those in pilocytic astrocytoma (n=6) cases by array-based comparative genomic hybridization. The number of lost clones was larger in pilomyxoid astrocytoma than in pilocytic astrocytoma. Clones located in chromosome 8q24.3 were frequently gained in pilocytic astrocytoma (four of six) and in pilomyxoid astrocytoma (one of four). Clones located in 9p24.3 and 15q26.3 were lost in all of the pilomyxoid astrocytomas and in five of the pilocytic astrocytomas. Those in 8p23.3 showed a copy number loss in three of the pilomyxoid astrocytomas and four of the pilocytic astrocytomas. The frequency of copy number changes was significantly different between pilomyxoid astrocytoma and pilocytic astrocytoma in 47 (3.6%) clones, 20 of them having been located in 2p, 10 in 2q, and 11 in 3q. An unsupervised hierarchical clustering analysis classified the cases into three clusters: one pilomyxoid astrocytoma patient into one cluster, two pilomyxoid astrocytoma patients into another cluster, and six pilocytic astrocytoma patients and one pilomyxoid astrocytoma patient into the third cluster. In conclusion, the presence of mixed-form pilomyxoid astrocytoma, the acquisition of pilocytic astrocytoma features in a recurrent tumor in pure-form pilomyxoid astrocytoma, and the above results of the genome-wide gene copy number analysis suggest that pilomyxoid astrocytoma might be a pathologically and genetically related, aggressive variant of pilocytic astrocytoma with partially different genetic alterations.

ITCH is a putative target for a novel 20q11.22 amplification detected in anaplastic thyroid carcinoma cells by array-based comparative genomic hybridization

Anaplastic thyroid carcinoma (ATC) is one of the most virulent of all human malignancies, with a mean survival time among patients of less than 1 year after diagnosis. To date, however, cytogenetic information on this disease has been very limited. During the course of a program to screen a panel of ATC cell lines for genomic copy-number aberrations using array-based comparative genomic hybridization, we identified a high-level amplification of the ITCH gene, which is mapped to 20q11.22 and belongs to the homologous to the E6-associated protein carboxylterminus ubiquitin ligase family. The expression of ITCH was increased in 4 of 14 ATC cell lines (28.6%), including 8305C in which there was a copy-number amplification of this gene, and six of seven primary cases (85.7%). Among the primary thyroid tumors, a considerable number of ITCH high expressers was found in ATC (40/45, 88.9%), papillary thyroid carcinoma (25/25, 100%), and papillary microcarcinoma (25/25, 100%). Furthermore, knockdown of ITCH by specific small interfering RNA significantly inhibited the growth of ITCH-overexpressing cells, whereas ectopic overexpression of ITCH promoted growth of ATC cell lines with relatively weak expression. These observations indicate ITCH to be the most likely target for 20q11.22 amplification and to play a crucial role in the progression of thyroid carcinoma.

Gene copy number analysis for family data using semiparametric copula model

Gene copy number changes are common characteristics of many genetic disorders. A new technology, array comparative genomic hybridization (a-CGH), is widely used today to screen for gains and losses in cancers and other genetic diseases with high resolution at the genome level or for specific chromosomal region. Statistical methods for analyzing such a-CGH data have been developed. However, most of the existing methods are for unrelated individual data and the results from them provide explanation for horizontal variations in copy number changes. It is potentially meaningful to develop a statistical method that will allow for the analysis of family data to investigate the vertical kinship effects as well. Here we consider a semiparametric model based on clustering method in which the marginal distributions are estimated nonparametrically, and the familial dependence structure is modeled by copula. The model is illustrated and evaluated using simulated data. Our results show that the proposed method is more robust than the commonly used multivariate normal model. Finally, we demonstrated the utility of our method using a real dataset.

Array CGH data modeling and smoothing in Stationary Wavelet Packet Transform domain

Background

Array-based comparative genomic hybridization (array CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thousands of loci and the reliable detection of local one-copy-level variations. Characterization of these DNA copy number changes is important for both the basic understanding of cancer and its diagnosis. In order to develop effective methods to identify aberration regions from array CGH data, many recent research work focus on both smoothing-based and segmentation-based data processing. In this paper, we propose stationary packet wavelet transform based approach to smooth array CGH data. Our purpose is to remove CGH noise in whole frequency while keeping true signal by using bivariate model.

Results

In both synthetic and real CGH data, Stationary Wavelet Packet Transform (SWPT) is the best wavelet transform to analyze CGH signal in whole frequency. We also introduce a new bivariate shrinkage model which shows the relationship of CGH noisy coefficients of two scales in SWPT. Before smoothing, the symmetric extension is considered as a preprocessing step to save information at the border.

Conclusion

We have designed the SWTP and the SWPT-Bi which are using the stationary wavelet packet transform with the hard thresholding and the new bivariate shrinkage estimator respectively to smooth the array CGH data. We demonstrate the effectiveness of our approach through theoretical and experimental exploration of a set of array CGH data, including both synthetic data and real data. The comparison results show that our method outperforms the previous approaches.

Clinical and molecular studies of patients with characteristics of Opitz G/BBB syndrome shows a novel MID1 mutation

Opitz G/BBB syndrome is characterized by midline abnormalities such as hypertelorism, cleft palate, and hypospadias. This syndrome is heterogeneous with an X-linked recessive form caused by mutations in the MID1 gene at band Xp22.3. However, mutations in MID1 have only been identified in 47% of familial cases of X-linked Opitz G/BBB syndrome, and 13% of sporadic cases. We performed a phenotype-genotype analysis of a group of nine new patients with clinical characteristics commonly seen in Opitz G/BBB syndrome, and of previously reported patients. We identified a novel mutation in exon 9 of the MID1 gene, c.1941insTGAGTCATCATCC, leading to a premature termination codon at amino acid 514 in a patient with hypertelorism, apparently low-set ears, a short philtrum, bilateral cleft of lip and palate and hypospadias. This mutation affects the PRY domain of the C-terminus of the MID1 protein.

An oncogenic role for the multiple endocrine neoplasia type 1 gene in prostate cancer

Prostate cancer is the second leading cause of cancer related deaths in US men, largely because of metastasis, which is ultimately fatal. A better understanding of metastasis biology will lead to improved prognostication and therapeutics. We previously reported 11q13.1 gain was independently predictive of recurrence after radical prostatectomy. Multiple endocrine neoplasia I (MEN1) maps to this region of copy number gain in aggressive prostate tumors and was shown to be the only gene at this locus at increased expression in prostate cancer. Here, we demonstrate an oncogenic role for MEN1 in prostate cancer using a variety of independent assays.

Smoking-related genomic signatures in non-small cell lung cancer

RATIONALE

Tobacco smoking is responsible for 85% of all lung cancers. To further our understanding of the molecular pathogenesis of lung cancer, we determined whether smoking history leads to the emergence of specific genomic alterations found in non-small cell lung cancer (NSCLC).

OBJECTIVES

To identify gene copy number alterations in NSCLCs associated with smoking history or DNA repair capacity.

METHODS

Seventy-five NSCLCs were selected for this study from patients with current, none, or past smoking history, including pack year information. Tissue sections were microdissected, and DNA was extracted, purified, and labeled by random priming before hybridization onto bacterial artificial chromosome (BAC) arrays. Normalized ratios were correlated with smoking history and DNA repair capacity was measured by an in vitro lymphocyte assay in the same patients.

MEASUREMENTS AND MAIN RESULTS

We identified smoking-related genomic signatures in NSCLCs that could be predicted with an overall 74% accuracy. Lung tumors arising from current-smokers had the greatest number of copy number alterations. The genomic regions most significantly associated with smoking were located within 60 regions and were functionally associated with genes controlling the M phase of the cell cycle, the segregation of chromosomes, and the methylation of DNA. Verification of the data is provided from data in the public domain and by quantitative real-time polymerase chain reaction. The associations between genomic abnormalities and DNA repair capacity did not reach statistical significance.

CONCLUSIONS

These findings indicate that smoking history leaves a specific genomic signature in the DNA of lung tumors and suggest that these alterations may reflect new molecular pathways to cancer development.

High-efficiency microarray printer using fused-silica capillary tube printing pins

We describe a contact printing approach for microarrays that uses fused-silica capillary tubes with tapered tips for printing pins and a pressure/vacuum system to control pin loading, printing, and cleaning. The printing process is insensitive to variable environmental factors such as humidity, and the small diameter of the pins allows routine printing from 1536 well source plates. Pin load capacity, 0.2 microL in the current system, is adjustable by controlling pin length. More than 2000 spots can be printed per 0.2-microL pin load (<100 pl/spot), and densities of >12,000 spots/cm(2) are readily achievable. Solutions with a wide range of viscosities and chemical properties can be printed. The system can print tens of thousands of different solutions at high speed, due to the ability to use large numbers of pins simultaneously, and can produce a large number of replicate arrays since all of the solution picked up by the pins is available for deposition.

The BAC resource: tools for array CGH and FISH

Bacterial Artificial Chromosome (BAC) vector clones carrying human DNA were chosen as the intermediate templates for the sequencing of the human genome due to their inherent stability and fidelity to the genome sequence from which they were derived. In this unit, we describe a set of protocols for BAC-based array comparative genomic hybridization (aCGH) that comprise the generation of targets for printing solutions onto glass slides, the subsequent hybridization steps, and CGH analysis of a test sample compared to a reference normal sample. The BAC clones through their sequence allow the extent and gene content of numerical aberrations to be delineated by aCGH, and also provide cytogeneticists with tools for subsequent validation or fine mapping studies.

Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors

BACKGROUND

Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine DNA copy number aberrations. Various platforms, brands and underlying technologies are available, facing the user with many choices regarding platform sensitivity and number, localization, and density distribution of probes.

RESULTS

We evaluate three different platforms presenting different nature and arrangement of the probes: The Agilent Human Genome CGH Microarray 44 k, the ROMA/NimbleGen Representational Oligonucleotide Microarray 82 k, and the Illumina Human-1 Genotyping 109 k BeadChip, with Agilent being gene oriented, ROMA/NimbleGen being genome oriented, and Illumina being genotyping oriented. We investigated copy number changes in 20 human breast tumor samples representing different gene expression subclasses, using a suite of graphical and statistical methods designed to work across platforms. Despite substantial differences in the composition and spatial distribution of probes, the comparison revealed high overall concordance. Notably however, some short amplifications and deletions of potential biological importance were not detected by all platforms. Both correlation and cluster analysis indicate a somewhat higher similarity between ROMA/NimbleGen and Illumina than between Agilent and the other two platforms. The programs developed for the analysis are available from http://www.ifi.uio.no/bioinf/Projects/.

CONCLUSION

We conclude that platforms based on different technology principles reveal similar aberration patterns, although we observed some unique amplification or deletion peaks at various locations, only detected by one of the platforms. The correct platform choice for a particular study is dependent on whether the appointed research intention is gene, genome, or genotype oriented.

Microarray-based DNA profiling to study genomic aberrations

High throughput microarrays were initially developed to analyse the expression of many RNA transcripts in parallel. The technology has since been adapted to a variety of applications, one of which is the analysis of the genome to study DNA dosage and sequence content. Advances in microarray fabrication and completion of large-scale genome sequencing projects have enabled the rapid development of affordable array-based methods for high-resolution genome-wide assessment of DNA alterations. This review will describe the evolution of microarray assays to study genomic aberrations and will highlight how they have enabled researchers to gain insight into the biology of human diseases and how they will benefit research in the future.

Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray

PURPOSE

Array comparative genomic hybridization is rapidly becoming an integral part of cytogenetic diagnostics. We report the design, validation, and clinical utility of an oligonucleotide array which combines genome-wide coverage with targeted enhancement at known clinically relevant regions.

METHODS

Probes were placed every 75 kb across the entire euchromatic genome to establish a chromosomal "backbone" with a resolution of approximately 500 kb, which is increased to approximately 50 kb in targeted regions.

RESULTS

For validation, 30 samples showed 100% concordance with previous G-banding and/or fluorescence in situ hybridization results. Prospective array analysis of 211 clinical samples identified 33 (15.6%) cases with clinically significant abnormalities. Of these, 23 (10.9%) were detected by the "targeted" coverage and 10 (4.7%) by the genome-wide coverage (average size of 3.7 Mb). All abnormalities were verified by fluorescence in situ hybridization, using commercially available or homebrew probes using the 32K bacterial artificial chromosome set. Four (1.9%) cases had previously reported imbalances of uncertain clinical significance. Five (2.4%) cases required parental studies for interpretation and all were benign familial variants.

CONCLUSIONS

Our results highlight the enhanced diagnostic utility of a genome-wide plus targeted array design, as the use of only a targeted array would have failed to detect 4.7% of the clinically relevant imbalances.

Molecular profiling of non-small cell lung cancer: of what value in clinical practice?

Future improvements in lung cancer survival are likely to come from delineating its putative oncogenic pathways. The development of microarray technology to perform thousands of simultaneous genetic experiments and the linking of this to clinical information is an imperative for refining our current treatments and developing new ones. This paper reviews the state of this research, describes a typical microarray experiment and the implications for diagnosis and treatment of non-small cell lung cancer.

A fast Bayesian change point analysis for the segmentation of microarray data

MOTIVATION

The ability to detect regions of genetic alteration is of great importance in cancer research. These alterations can take the form of large chromosomal gains and losses as well as smaller amplifications and deletions. The detection of such regions allows researchers to identify genes involved in cancer progression, and to fully understand differences between cancer and non-cancer tissue. The Bayesian method proposed by Barry and Hartigan is well suited for the analysis of such change point problems. In our previous article we introduced the R package bcp (Bayesian change point), an MCMC implementation of Barry and Hartigan's method. In a simulation study and real data examples, bcp is shown to both accurately detect change points and estimate segment means. Earlier versions of bcp (prior to 2.0) are O(n(2)) in speed and O(n) in memory (where n is the number of observations), and run in approximately 45 min for a sequence of length 10 000. With the high resolution of newer microarrays, the number of computations in the O(n(2)) algorithm is prohibitively time-intensive.

RESULTS

We present a new implementation of the Bayesian change point method that is O(n) in both speed and memory; bcp 2.1 runs in approximately 45 s on a single processor with a sequence of length 10,000--a tremendous speed gain. Further speed improvements are possible using parallel computing, supported in bcp via NetWorkSpaces. In simulated and real microarray data from the literature, bcp is shown to quickly and accurately detect aberrations of varying width and magnitude.

AVAILABILITY

The R package bcp is available on CRAN (R Development Core Team, 2008). The O(n) version is available in version 2.0 or higher, with support for NetWorkSpaces in versions 2.1 and higher.

Genome-wide DNA copy number predictors of lapatinib sensitivity in tumor-derived cell lines

A common aim of pharmacogenomic studies that use genome-wide assays on panels of cancers is the unbiased discovery of genomic alterations that are associated with clinical outcome and drug response. Previous studies of lapatinib, a selective dual-kinase inhibitor of epidermal growth factor receptor (EGFR) and HER2 tyrosine kinases, have shown predictable relationships between the activity of these target genes and response. Under the hypothesis that additional genes may play a role in drug sensitivity, a predictive model for lapatinib response was constructed from genome-wide DNA copy number data from 24 cancer cell lines. An optimal predictive model which consists of aberrations at nine distinct genetic loci, includes gains of HER2, EGFR, and loss of CDKN2A. This model achieved an area under the receiver operating characteristic curve of approximately 0.85 (80% confidence interval, 0.70-0.98; P < 0.01), and correctly classified the sensitivity status of 8 of 10 head and neck cancer cell lines. This study shows that biomarkers predictive for lapatinib sensitivity, including the previously described copy number gains of EGFR and HER2, can be discovered using novel genomic assays in an unbiased manner. Furthermore, these results show the utility of DNA copy number profiles in pharmacogenomic studies.

Bacterial artificial chromosome-emulation oligonucleotide arrays for targeted clinical array-comparative genomic hybridization analyses

PURPOSE

The goal of this work was to test the ability of oligonucleotide-based arrays to reproduce the results of focused bacterial artificial chromosome (BAC)-based arrays used clinically in comparative genomic hybridization experiments to detect constitutional copy number changes in genomic DNA.

METHODS

Custom oligonucleotide (oligo) arrays were designed using the Agilent Technologies platform to give high-resolution coverage of regions within the genome sequence coordinates of BAC/P1 artificial chromosome (PAC) clones that had already been validated for use in previous versions of clone arrays used in clinical practice. Standard array-comparative genomic hybridization experiments, including a simultaneous blind analysis of a set of clinical samples, were conducted on both array platforms to identify copy number differences between patient samples and normal reference controls.

RESULTS

Initial experiments successfully demonstrated the capacity of oligo arrays to emulate BAC data without the need for dye-reversal comparisons. Empirical data and computational analyses of oligo response and distribution from a pilot array were used to design an optimized array of 44,000 oligos (44K). This custom 44K oligo array consists of probes localized to the genomic positions of >1400 fluorescence in situ hybridization-verified BAC/PAC clones covering more than 140 regions implicated in genetic diseases, as well as all clinically relevant subtelomeric and pericentromeric regions.

CONCLUSIONS

Our data demonstrate that oligo-based arrays offer a valid alternative for focused BAC arrays. Furthermore, they have significant advantages, including better design flexibility, avoidance of repetitive sequences, manufacturing processes amenable to good manufacturing practice standards in the future, increased robustness because of an enhanced dynamic range (signal to background), and increased resolution that allows for detection of smaller regions of change.

Array-based comparative genomic hybridization of mapped BAC DNA clones to screen for chromosome 14 copy number abnormalities in meningiomas

Chromosome 14 loss in meningiomas are associated with more aggressive tumour behaviour. To date, no studies have been reported in which the entire chromosome 14q of meningioma tumour cells has been studied by high-resolution array comparative genomic hybridization (a-CGH). Here, we used a high-resolution a-CGH to define the exact localization and extent of numerical changes of chromosome 14 in meningioma patients. An array containing 807 bacterial artificial chromosome clones specific for chromosome 14q (average resolution of approximately 130 Kb) was constructed and applied to the study of 25 meningiomas in parallel to the confirmatory interphase fluorescence in situ hybridization (iFISH) analyses. Overall, abnormalities of chromosome 14q were detected in 10/25 cases (40%). Interestingly, in seven of these cases, loss of chromosome 14q32.3 was detected by iFISH and confirmed to correspond to monosomy 14 by a-CGH. In contrast, discrepant results were found between iFISH and a-CGH in the other three altered cases. In one patient, a diploid background was observed by iFISH, while monosomy 14 was identified by a-CGH. In the remaining two cases, which showed gains of the IGH gene by iFISH, a-CGH did not detected copy number changes in one case showing a tetraploid karyotype, while in the other tumour, varying genetic imbalances along the long arm of chromosome 14 were detected. In summary, here, we report for the first time, the high-resolution a-CGH profiles of chromosome 14q in meningiomas, confirming that monosomy 14 is the most frequent alteration associated with this chromosome; other numerical abnormalities being only sporadically detected.

Tiling array-CGH for the assessment of genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs

Background

Today, no objective criteria exist to differentiate between individual primary tumors and intra- or intermammary dissemination respectively, in patients diagnosed with two or more synchronous breast cancers. To elucidate whether these tumors most likely arise through clonal expansion, or whether they represent individual primary tumors is of tumor biological interest and may have clinical implications. In this respect, high resolution genomic profiling may provide a more reliable approach than conventional histopathological and tumor biological factors.

Methods

32 K tiling microarray-based comparative genomic hybridization (aCGH) was used to explore the genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs, and was compared with histopathological and tumor biological parameters.

Results

Based on global copy number profiles and unsupervised hierarchical clustering, five of ten (p = 1.9 × 10^-5) unilateral tumor pairs displayed similar genomic profiles within the pair, while only one of eight bilateral tumor pairs (p = 0.29) displayed pair-wise genomic similarities. DNA index, histological type and presence of vessel invasion correlated with the genomic analyses.

Conclusion

Synchronous unilateral tumor pairs are often genomically similar, while synchronous bilateral tumors most often represent individual primary tumors. However, two independent unilateral primary tumors can develop synchronously and contralateral tumor spread can occur. The presence of an intraductal component is not informative when establishing the independence of two tumors, while vessel invasion, the presence of which was found in clustering tumor pairs but not in tumor pairs that did not cluster together, supports the clustering outcome. Our data suggest that genomically similar unilateral tumor pairs may represent a more aggressive disease that requires the addition of more severe treatment modalities, and underscores the importance of evaluating the clonality of multiple tumors for optimal patient management. In summary, our findings demonstrate the importance of evaluating the properties of both tumors in order to determine the most optimal patient management.

Overexpression of SnoN/SkiL, amplified at the 3q26.2 locus, in ovarian cancers: a role in ovarian pathogenesis

High-resolution array comparative genomic hybridization of 235 serous epithelial ovarian cancers demonstrated a regional increase at 3q26.2 encompassing SnoN/SkiL, a coregulator of SMAD/TGFbeta signaling. SnoN RNA transcripts were elevated in approximately 80% of advanced stage serous epithelial ovarian cancers. In both immortalized normal (TIOSE) and ovarian carcinoma cell lines (OVCA), SnoN RNA levels were increased by TGFbeta stimulation and altered by LY294002 and JNK II inhibitor treatment suggesting that the PI3K and JNK signaling pathways may regulate TGFbeta-induced increases in SnoN RNA. In TIOSE, SnoN protein levels were reduced 15min post TGFbeta-stimulation, likely by proteosome-mediated degradation. In contrast, in OVCA, SnoN levels were elevated 3h post-stimulation potentially as a result of inhibition of the proteosome. To elucidate the role of SnoN in ovarian tumorigenesis, we explored the effects of both increasing and decreasing SnoN levels. In both TIOSE and OVCA, SnoN siRNA decreased cell growth between 20 and 50% concurrent with increased p21 levels. In TIOSE, transient expression of SnoN repressed TGFbeta induction of PAI-1 promoters with little effect on the p21 promoter or resultant cell growth. In contrast to the effects of transient expression, stable expression of SnoN in TIOSE led to growth arrest through induction of senescence. Collectively, these results implicate SnoN levels in multiple roles during ovarian carcinogenesis: promoting cellular proliferation in ovarian cancer cells and as a positive mediator of cell cycle arrest and senescence in non-transformed ovarian epithelial cells.

Clinical array comparative genomic hybridization: a new paradigm

BACKGROUND

Although the clinical utility of array comparative genomic hybridization (aCGH) is undisputed, the implementation of this technology is a unique experience for each laboratory.

OBJECTIVE

Endeavors to construct a bacterial artificial chromosome (BAC)-based CGH microarray targeting microdeletion and duplication syndromes related to mental retardation and developmental delay are described.

METHOD

Covering each chromosome at the 650-band level, the array comprises 1360 BAC clones with emphasis on the subtelomeric and pericentromeric regions and enrichment of genomic hot spots containing genes associated with specific constitutional disorders. During development of the array, fluorescence in situ hybridization (FISH) and end-sequencing analysis eliminated 24% of BACs that were mismapped or cross-hybridized, underscoring the need rigorously to assess arrayed elements. Performance of the BACs was tested further with chromosome-specific add-in experiments.

CONCLUSION

Of the first 500 clinical cases, 54 (11%) showed chromosome abnormalities, which were confirmed by FISH with BACs from the aberrant loci or by conventional cytogenetics. Array CGH is a powerful tool that is now being implemented in the realm of diagnostic testing.

Copy number variant analysis of human embryonic stem cells

Differences between individual DNA sequences provide the basis for human genetic variability. Forms of genetic variation include single-nucleotide polymorphisms, insertions/duplications, deletions, and inversions/translocations. The genome of human embryonic stem cells (hESCs) has been characterized mainly by karyotyping and comparative genomic hybridization (CGH), techniques whose relatively low resolution at 2-10 megabases (Mb) cannot accurately determine most copy number variability, which is estimated to involve 10%-20% of the genome. In this brief technical study, we examined HSF1 and HSF6 hESCs using array-comparative genomic hybridization (aCGH) to determine copy number variants (CNVs) as a higher-resolution method for characterizing hESCs. Our approach used five samples for each hESC line and showed four consistent CNVs for HSF1 and five consistent CNVs for HSF6. These consistent CNVs included amplifications and deletions that ranged in size from 20 kilobases to 1.48 megabases, involved seven different chromosomes, were both shared and unique between hESCs, and were maintained during neuronal stem/progenitor cell differentiation or drug selection. Thirty HSF1 and 40 HSF6 less consistently scored but still highly significant candidate CNVs were also identified. Overall, aCGH provides a promising approach for uniquely identifying hESCs and their derivatives and highlights a potential genomic source for distinct differentiation and functional potentials that lower-resolution karyotype and CGH techniques could miss. Disclosure of potential conflicts of interest is found at the end of this article.

DNA copy number analysis in gastrointestinal stromal tumors using gene expression microarrays

We report a method, Expression-Microarray Copy Number Analysis (ECNA) for the detection of copy number changes using Affymetrix Human Genome U133 Plus 2.0 arrays, starting with as little as 5 ng input genomic DNA. An analytical approach was developed using DNA isolated from cell lines containing various X-chromosome numbers, and validated with DNA from cell lines with defined deletions and amplifications in other chromosomal locations. We applied this method to examine the copy number changes in DNA from 5 frozen gastrointestinal stromal tumors (GIST). We detected known copy number aberrations consistent with previously published results using conventional or BAC-array CGH, as well as novel changes in GIST tumors. These changes were concordant with results from Affymetrix 100K human SNP mapping arrays. Gene expression data for these GIST samples had previously been generated on U133A arrays, allowing us to explore correlations between chromosomal copy number and RNA expression levels. One of the novel aberrations identified in the GIST samples, a previously unreported gain on 1q21.1 containing the PEX11B gene, was confirmed in this study by FISH and was also shown to have significant differences in expression pattern when compared to a control sample. In summary, we have demonstrated the use of gene expression microarrays for the detection of genomic copy number aberrations in tumor samples. This method may be used to study copy number changes in other species for which RNA expression arrays are available, e.g. other mammals, plants, etc., and for which SNPs have not yet been mapped.