Use Of Comparative Genomic Hybridization Research Articles

Association of IMMP2L deletion with neurodevelopmental disorders: new case report and review of the literature.

The inner mitochondrial membrane peptidase subunit 2-like protein, the IMMP2L gene in 7q31.1, have been associated with different neurodevelopmental disorders, including autism spectrum disorders, attention deficit/hyperactivity disorder and Gilles de la Tourette's syndrome (GTS). Since the use of comparative genomic hybridization as essential tool in the diagnostic workup of neurodevelopmental disorders, recurrent microdeletions CNV's were identified in IMMP2L gene. We report here a 3 years old girl presenting since early life with complex motor tics, developmental delay, and other various cognitive/behavioral disturbances. Array CGH analysis showed a 331 Kb de novo pathogenic heterozygous deletion at 7q31.1 into the IMMP2L gene, involving exons 1 to 3. We discuss the functions of IMMP2L gene suggesting that his disruption may act as high-risk factor for neurodevelopmental disorders and movement disorders.

Chromosomal imbalances detected in NTRK-rearranged sarcomas by the use of comparative genomic hybridisation.

NTRK-rearranged sarcomas are emerging as a distinct class of sarcomas of particular importance in the era of targeted therapy. The aim of this study was to use array comparative genomic hybridisation (aCGH) to explore the cytogenetic profile of six adult soft tissue sarcomas harbouring NTRK gene fusions. aCGH was performed on six adult soft tissue sarcomas with proven NTRK rearrangements [NTRK1, n=1 (TPM3-NTRK1); NTRK2, n=1 (MTMR2-NTRK2); NTRK3, n=4 (two ETV6-NTRK3; two with unknown partners). The morphological patterns of these cases included inflammatory myofibroblastic tumour-like, fibrosarcoma/malignant peripheral nerve sheath tumour-like, and Ewing sarcoma-like. On the basis of the number of chromosomal copy number variations (CNVs), ranging from two to 15 per sample, NTRK-associated sarcomas could be subdivided into two groups: one with a relatively simple karyotype (n=2; median of three genomic alterations), and those with a more complex karyotype (n=4; median of 11 genomic imbalances). Recurrent chromosomal CNVs included gains at chromosomes 6p, 1q, 7 (whole chromosome), and 12p, and losses at chromosomes 10q, 13q, 19q, and 9p. NTRK-rearranged sarcomas constitute a heterogeneous group of tumours that can show a relatively simple or a complex karyotype. Although there were some, but inconsistent, associations between karyotype complexity and morphology, our study showed that a more complex karyotype in this group of tumours appeared to correlate with more aggressive clinical behaviour. Gains at chromosome 6p and 1q were the most common recurrent genomic alterations, being present in 67% of the samples (4/6), followed by gains at chromosome 7, which were present in 50% of the samples (3/6).

Comparative Genomic Hybridization (CGH) in Genotoxicology.

In the past two decades, comparative genomic hybridization (CGH) and array CGH have become indispensable tools in clinical diagnostics and toxicological risk assessment. Initially developed for the genome-wide screening of chromosomal imbalances, that is, copy-number variations in tumor cells, both CGH and array CGH have been employed in genotoxicology and most recently in toxicogenomics. The latter allows a multi-end point analysis of how particular genes react to toxic agents, revealing changes in signaling pathways and other underlying molecular mechanisms. This chapter provides background on the use of CGH and array CGH in the context of genotoxicology, and also a protocol for conventional CGH, so that the basic principles of this methodology can be better understood. Conventional and array CGH investigate DNA expression patterns, copy-number variations across the whole genome, and loss of heterozygosity after genotoxic damage. Array CGH is still cost-intensive but produces exponentially more data, requiring suitable analytical algorithms and sophisticated bioinformatic analysis. As toxicogenomics is an emerging sub-discipline of toxicology research, effectively evaluating toxicogenomic microarray data can be hugely advantageous for human risk assessment, even though international regulatory guidelines on toxicogenomics have yet to be fully agreed and implemented.

Clinical use of monopronucleated zygotes following blastocyst culture and preimplantation genetic screening, including verification of biparental chromosome inheritance

In assisted reproduction, embryos derived from monopronucleated (1PN) zygotes are considered abnormal and unsuitable for clinical use. Outcomes of 1PN-derived embryos designated for preimplantation genetic screening (PGS) were analysed. These embryos, especially from intracytoplasmic sperm injection (ICSI), were found to have a low developmental potential; 1PN and 2PN day 5 blastocyst development for IVF was 14.8% versus 36.4% (P < 0.0001), and for ICSI, 6.6% versus 34.0% (P < 0.0001), respectively. With the use of comparative genomic hybridization or next-generation sequencing, PGS was successfully carried out for 74 IVF and 32 ICSI 1PN-derived blastocysts, revealing adjusted abnormality rates of 39.7% and 40.6%, respectively. Additionally, 24 female 1PN-derived blastocysts underwent testing for biparental inheritance, with one ICSI-derived embryo demonstrating paternal only contribution, thus presenting a risk for complete hydatidiform molar pregnancy. Single embryo transfer of 20 IVF and six ICSI 1PN-derived blastocysts with no detectable abnormalities resulted in nine clinical pregnancies. Six have been delivered and three are ongoing, with no anomalies reported to date. The limitation of this study is that pronuclear status was determined through one static observation. The results suggest that 1PN-derived embryos, in which euploidy and biparental inheritance have been established, can provide a source of clinically useful embryos.

Molecular karyotyping of cell-free DNA from blastocoele fluid as a basis for noninvasive preimplantation genetic screening of aneuploidy

The discovery of DNA fragments in the blastocoele fluid is promising for the development of new noninvasive methods for the preimplantation genetic diagnosis of chromosomal diseases. However, to date there are no data confirming the concordance between the molecular karyotype of cell-free DNA from blastocoele fluid and the blastocyst cells per se. This paper reports on this concordance according to the results of molecular-cytogenetic analysis of the chromosomal set with the use of comparative genomic hybridization.

Increased ALK1 copy number and renal cell carcinoma—a case report

There have been recent reports of a rare variant of renal cell carcinoma associated with upregulation of the anaplastic lymphoma kinase gene (ALK) arising as a consequence of chromosomal translocations. The tumours were described as having a characteristic morphology. Here, we describe a case with similar morphology characterised by eosinophilic cells, abundant intracytoplasmic lumina and scattered large ganglion-like tumour cells. There was focal staining for ALK demonstrated by immunohistochemistry. However, rather than exhibiting a chromosomal translocation involving ALK, the use of FISH and a break-apart probe demonstrated that there was increased copy number of intact 2p23, the chromosomal region containing the ALK gene. Furthermore, the use of comparative genomic hybridisation showed increase of the whole of chromosome 2 along with chromosomes 6 and 17. There was no evidence of loss of 3p nor of trisomy of 7 associated with clear cell and papillary carcinoma, respectively. We suggest that this demonstrates a novel mechanism of upregulation of ALK activity by increased copy number occurring during the development of a renal carcinoma with the characteristic ALK-associated morphology.

Array CGH Phylogeny: How accurate are Comparative Genomic Hybridization-based trees?

BackgroundArray-based Comparative Genomic Hybridization (CGH) data have been used to infer phylogenetic relationships. However, the reliability of array CGH analysis to determine evolutionary relationships has not been well established. In most CGH work, all species and strains are compared to a single reference species, whose genome was used to design the array. In the accompanying work, we critically evaluated CGH-based phylogeny using simulated competitive hybridization data. This work showed that a limited number of conditions, principally the tree topology and placement of the reference taxon in the tree, had a strong effect on the ability to recover the correct tree topology. Here, we add to our simulation study by testing the use of CGH as a phylogenetic tool with experimental CGH data from competitive hybridizations between N. crassa and other Neurospora species. In the discussion, we add to our empirical study of Neurospora by reanalyzing of data from a previous CGH phylogenetic analysis of the yeast sensu stricto complex.ResultsArray ratio data for Neurospora and related species were normalized with loess, robust spline, and linear ratio based methods, and then used to construct Neighbor-Joining and parsimony trees. These trees were compared to published phylogenetic analyses for Neurospora based on multilocus sequence analysis (MLSA). For the Neurospora dataset, the best combination of methods resulted in recovery of the MLSA tree topology less than half the time. Our reanalysis of a yeast dataset found that trees identical to established phylogeny were recovered only by pruning taxa - including the reference taxon - from the analysis.ConclusionOur results indicate that CGH data can be problematic for phylogenetic analysis. Success fluctuates based on the methods utilized to construct the tree and the taxa included. Selective pruning of the taxa improves the results - an impractical approach for normal phylogenetic analysis. From the more successful methods we make suggestions on the normalization and post-normalization methods that work best in estimating genetic distance between taxa.

Structural and numerical abnormalities resolved in one-step analysis: the most common chromosomal rearrangements detected by comparative genomic hybridization in childhood acute lymphoblastic leukemia

Comparative genomic hybridization (CGH) is a technique that permits detection of chromosomal imbalances. This method allows the detection of gains and losses of genetic material at a resolution lower than 5 Mb. The limitations of conventional cytogenetic studies, such as morphologically insufficient quality of metaphases or the mitotic index, can be eliminated by use of CGH. It is particularly important in the diagnosis of leukemias, and CGH could be a useful tool enabling more precise cytogenetic analysis of leukemic cells. A group of 89 children with acute lymphoblastic leukemia was studied by means of CGH using bone marrow obtained from all consecutive pediatric patients. CGH experiments were performed according to the manufacturer's instruction with minor modifications. In addition, each sample was examined with standard GTG technique and fluorescence in situ hybridization. The conventional cytogenetics failed in 12 patients (13.5%), and 22 patients (24.7%) had a normal karyotype. Structural and numerical changes were found in 55 cases (61.8%) displaying a different abnormalities including deletions, trisomies, tetrasomies, isochromosomes, and markers with unknown origin. However, all samples were successfully analyzed by CGH. We have shown that high-resolution comparative genomic hybridization analysis is a reliable and relatively quick one-step method to identify main aberrations that would not be detected by either conventional G banding or by conventional fluorescence in situ hybridization. It should be considered to establish CGH as a routine analysis for screening patients with acute lymphoblastic leukemia.

The Use of Comparative Genomic Hybridization and Fluorescent in Situ Hybridization in Postmortem Pathology Investigation of Congenital Malformations

Chromosomal abnormalities are an important cause of multiple congenital anomalies (MCA). However, conventional cytogenetic analysis using culture is unsuccessful in 10% to 40% of the cases. The purpose of this study was to examine if retrospective chromosomal analysis was possible on paraffin-embedded autopsy material with new techniques, including comparative genomic hybridization (CGH) and fluorescent in situ hybridization (FISH). We investigated 92 patients, including 71 patients with MCA, 17 patients with an isolated congenital anomaly, and 4 normal controls, by conventional CGH analysis and/or FISH. The karyotype was known in 52 cases, of which 26 patients were normal and 26 had chromosomal anomalies. Comparative genomic hybridization or FISH confirmed all but 2 cases, which were not interpretable. In 40 patients the karyotype was unknown but could be analyzed successfully in 36 cases (90%) by CGH. In this series, we found 1 additional chromosomal aberration, 45,X (Turner syndrome). Furthermore, we examined the postmortem material of 12 patients by FISH, confirming a known abnormal karyotype in 9 patients, an abnormal karyotype found by CGH in 1 case, and confirming DiGeorge syndrome (22q11 deletion) in twins. Comparative genomic hybridization and FISH are reliable techniques with which to perform retrospective genetic analysis on paraffin-embedded autopsy material.

Interstitial microduplication of Xp22.31: Causative of intellectual disability or benign copy number variant?

The use of comparative genomic hybridization (CGH) and single nucleotide polymorphism (SNP) arrays has dramatically altered the approach to identification of genetic alterations that can explain intellectual disability and /or congenital anomalies. However, the discovery of numerous copy number changes with benign or unknown clinical significance has made interpretation problematic. Submicroscopic duplication of Xp22.31 has been reported as either a possible cause of intellectual disability and/or developmental delay or a benign variant. Here we report 29 individuals with the microduplication found as part of microarray analysis of 7793 samples submitted to an international group of 13 clinical laboratories. The referral reasons varied and included developmental delay, intellectual disability, autism, dysmorphic features and/or multiple congenital anomalies. The size of the Xp22.31 duplication varied between 149 kb and 1.74 Mb and included the steroid sulfatase ( STS) gene with the male to female ratio of 0.7. Duplication within this segment is seen at a frequency of 0.15% in a healthy control population, whereas a frequency of 0.37% was observed in our cohort of individuals with abnormal phenotypes. We present a detailed comparison of the breakpoints, inheritance, X-inactivation and clinical phenotype in our cohort and a review of the literature for a total of 41 patients. To date, this report is the largest compilation of clinical and array data regarding the microduplication of Xp22.31 and will serve to broaden the knowledge of regions involving copy number variation (CNV).

Comparative genomic hybridization for the diagnosis of melanoma

Despite advancements in protocols, a subset of melanocytic lesions continues to pose diagnostic challenges. This is particularly true in the pediatric population where certain congenital nevi mimic melanoma. Recently, comparative genomic hybridization (CGH) has been utilized to support diagnoses of melanocytic lesions based on DNA copy number changes. Because distinct differences in copy number changes have been shown to occur in malignant melanoma and benign nevi, CGH can be a useful adjunct when diagnosis based on histology alone is indeterminate. The authors discuss the benefits of using CGH to aid in the diagnosis of melanocytic lesions that are difficult to characterize as malignant or benign based on clinical and histologic features alone. This paper presents a brief clinical report and review of the literature. A 13-year-old Caucasian male presented to an academic tertiary care medical center after a shave biopsy unexpectedly revealed malignant melanoma with positive deep margins. Following complete excisional biopsy, the diagnosis of malignant melanoma with depth of 0.92 mm was confirmed, both by the home institution's pathologist and by consultant dermatopathologists at two separate academic tertiary medical centers. Sentinel lymph node biopsy revealed a small focus of metastatic melanoma, this lead to a left-sided modified radical neck dissection. All nodes removed were negative for disease, and surgical and postsurgical care was uncomplicated. Before proceeding with interferon therapy, CGH was performed on the tissue from the primary lesion. Other than a slight amplification of chromosome 16p, no other aberrations were detected favoring a benign lesion. Ultimately, the diagnosis was amended to compound melanocytic nevus of the nose with benign nevus cell rest in the sentinel node. While histopathologic evaluation is the current gold standard for the diagnosis of melanoma, there are many cases where it is inaccurate. The use of CGH in the evaluation of histologically equivocal lesions may allow certain patients to avoid invasive procedures and associated morbidities. The authors propose that, in these select diagnostically challenging cases, tissue analyses by CGH may be beneficial before proceeding to more invasive procedures such as sentinel node biopsy and complete lymphadenectomy.

Improved detection of aneuploid blastocysts using a new 12-chromosome FISH test

Fluorescence in-situ hybridization (FISH) has been the principal method used for the identification and preferential transfer of chromosomally normal embryos, in the context of both preimplantation genetic diagnosis (PGD) and screening (PGS). Generally, the probe combinations used during PGS have focused on chromosomes frequently identified as abnormal in prenatal samples or material derived from first-trimester spontaneous abortions. Recent data, however, obtained with the use of comparative genomic hybridization (CGH), have suggested that commonly used PGS strategies may fail to detect a large number of aneuploidies affecting preimplantation embryos. Some chromosomes, which have been relatively neglected in PGS protocols thus far, display a disproportionate contribution to embryo aneuploidy and should be prioritized for screening. Using CGH data, it is possible to design new probe combinations that examine between 10 and 12 chromosomes and are capable of accurately diagnosing 89-91% of anomalies seen in embryos. At present, 24-chromosome tests, such as CGH, array CGH or single nucleotide polymorphism arrays, remain relatively costly and, in some cases, are yet to be fully validated. For these reasons, a cost-effective method, capable of accurately detecting almost all aneuploid embryos, represents an attractive alternative to comprehensive chromosome screening approaches.

Molecular diagnosis of a benign proliferative nodule developing in a congenital melanocytic nevus in a 3-month-old infant

Small and intermediate congenital melanocytic nevi have a lifetime risk of developing melanoma estimated to range from 0% to 5%. Secondary benign melanocytic proliferations commonly arise in congenital melanocytic nevi; however, some are difficult to definitively distinguish from malignant melanoma based on clinical features and conventional histology. Herein, we describe the use of comparative genomic hybridization in supporting the diagnosis of a deep penetrating nevus developing within a congenital melanocytic nevus of a 3-month-old infant.

Can comparative genomic hybridization improvein vitrofertilization outcomes?

Fecundity in humans is inefficient, with an estimated 25% chance of successful conception per cycle. in vitro fertilization (IVF) patients and practitioners have to confront such natural inefficiencies in addition to the inherent difficulties of the IVF treatment process. A major contributor to nature’s wastage is oocyte and embryo aneuploidy – estimated to be as high as 70% in some circumstances. Modern IVF practice has no dependable means of selecting viable embryos, but attempts are made to identify nonviable ones – such efforts include aneuploidy screening using fluorescent in situ hybridization (FISH). However, this technology can only assess a limited number of chromosomes routinely, leaving the remainder unexamined. Aside from this limitation, its practice is riddled with deficiencies. To date, aneuploidy screening using FISH has been reported, in a welter of publications, to improve live birth rates; however, in the limited reports involving randomized, controlled trials, FISH has not been proven to be efficacious for embryo selection – one particular reason being that the whole chromosome complement is not amenable for assessment. Comparative genomic hybridization (CGH) was first introduced to IVF in an attempt to overcome this particular problem, with the hope that the transfer of only euploid embryos will improve live birth rates. CGH is not without its own difficulties but, nevertheless, still excites considerable promise as a technology that will eventually significantly improve the outcome of an IVF treatment cycle. This paper reviews the current considerations for the use of CGH, its recent implementation into clinical IVF and the future prospects.

Genomic Structure and Phylogeny of the Plant Pathogen Ralstonia solanacearum Inferred from Gene Distribution Analysis

In the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic beta-proteobacterium Ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. Based on the use of comparative genomic hybridization on a pangenomic microarray for the GMI1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representative of the biodiversity of the R. solanacearum species. This identified a list of 2,690 core genes present in all tested strains. As a corollary, a list of 2,338 variable genes within the R. solanacearum species has been defined. The hierarchical clustering based on the distribution of variable genes is fully consistent with the phylotype classification that was previously defined from the nucleotide sequence analysis of four genes. The presence of numerous pathogenicity-related genes in the core genome indicates that R. solanacearum is an ancestral pathogen. The results establish the long coevolution of the two replicons that constitute the bacterial genome. We also demonstrate the clustering of variable genes in genomic islands. Most genomic islands are included in regions with an alternative codon usage, suggesting that they originate from acquisition of foreign genes through lateral gene transfers. Other genomic islands correspond to genes that have the same base composition as core genes, suggesting that they either might be ancestral genes lost by deletion in certain strains or might originate from horizontal gene transfers.

Medulloblastoma outcome is adversely associated with overexpression of EEF1D, RPL30, and RPS20 on the long arm of chromosome 8

BackgroundMedulloblastoma is the most common malignant brain tumor of childhood. Improvements in clinical outcome require a better understanding of the genetic alterations to identify clinically significant biological factors and to stratify patients accordingly. In the present study, we applied cytogenetic characterization to guide the identification of biologically significant genes from gene expression microarray profiles of medulloblastoma.MethodsWe analyzed 71 primary medulloblastomas for chromosomal copy number aberrations (CNAs) using comparative genomic hybridization (CGH). Among 64 tumors that we previously analyzed by gene expression microarrays, 27 were included in our CGH series. We analyzed clinical outcome with respect to CNAs and microarray results. We filtered microarray data using specific CNAs to detect differentially expressed candidate genes associated with survival.ResultsThe most frequent lesions detected in our series involved chromosome 17; loss of 16q, 10q, or 8p; and gain of 7q or 2p. Recurrent amplifications at 2p23-p24, 2q14, 7q34, and 12p13 were also observed. Gain of 8q is associated with worse overall survival (p = 0.0141), which is not entirely attributable to MYC amplification or overexpression. By applying CGH results to gene expression analysis of medulloblastoma, we identified three 8q-mapped genes that are associated with overall survival in the larger group of 64 patients (p < 0.05): eukaryotic translation elongation factor 1D (EEF1D), ribosomal protein L30 (RPL30), and ribosomal protein S20 (RPS20).ConclusionThe complementary use of CGH and expression profiles can facilitate the identification of clinically significant candidate genes involved in medulloblastoma growth. We demonstrate that gain of 8q and expression levels of three 8q-mapped candidate genes (EEF1D, RPL30, RPS20) are associated with adverse outcome in medulloblastoma.

The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella

BackgroundCompelling evidence indicates that Shigella species, the etiologic agents of bacillary dysentery, as well as enteroinvasive Escherichia coli, are derived from multiple origins of Escherichia coli and form a single pathovar. To further understand the genome diversity and virulence evolution of Shigella, comparative genomic hybridization microarray analysis was employed to compare the gene content of E. coli K-12 with those of 43 Shigella strains from all lineages.ResultsFor the 43 strains subjected to CGH microarray analyses, the common backbone of the Shigella genome was estimated to contain more than 1,900 open reading frames (ORFs), with a mean number of 726 undetectable ORFs. The mosaic distribution of absent regions indicated that insertions and/or deletions have led to the highly diversified genomes of pathogenic strains.ConclusionThese results support the hypothesis that by gain and loss of functions, Shigella species became successful human pathogens through convergent evolution from diverse genomic backgrounds. Moreover, we also found many specific differences between different lineages, providing a window into understanding bacterial speciation and taxonomic relationships.

Prenatal Diagnosis of Trisomy 21 with Fetal Cells in Maternal Blood Using Comparative Genomic Hybridization

Objective: This study was undertaken to determine the clinical use of comparative genomic hybridization (CGH) for detection of fetal trisomy 21 from fetal ceIls (nucleated red blood cells; nRBCs) isolated from maternal peripheral venous blood. Methods: Maternal peripheral venous blood samples were collected in sterile tubes containing heparin. After triple density gradient centrifugation, magnetic activated cell sorting using CD45 and CD71 was used to isolate the fetal nRBCs. Fetal nRBCs were successfully isolated from maternal peripheral blood in all cases. After laser-microdissecting fetal nRBCs, degenerate oligonucleotide-primed polymerase chain reaction, and nick translation, DNA size was suitable for hybridization. Results: By CGH analysis, we diagnosed one normal male, one normal female, and one trisomy 21 male fetus. These results were confirmed by amniocentesis. Conclusions: Prenatal diagnosis from fetal cells in maternal peripheral blood by CGH shows clinical promise as an alternative or as a supplement to fluorescence in situ hybridization with chromosome-specific probes but further studies are warranted.

Analysis of chromosomal imbalances in an elderly woman with a giant cell tumour

Giant cell tumour (GCT) remains one of the most obscure and intensely studied bone tumours. In an effort to resolve questions regarding the genesis and clinical outcome of GCT, advances have been made recently in the identification of chromosomal abnormalities implicated in the tumour. Fusion of telomeres is very frequent in GCT, and this process may be associated with chromosome instability and tumour development. However, little emphasis has been placed on chromosomal imbalances in the molecular characterization of this disease. Here, we report the case of an 83-year-old woman diagnosed with GCT where local recurrence was observed after 11 months of the resection. Cytogenetic studies of the GCT showed a modal number of 46 chromosomes with telomeric associations on 11p and dicentric chromosomes. Moreover, clonal abnormalities, such as del(17p) and losses of chromosomes 4, 13 and 18 and gains on chromosome 7, were also detected. Interestingly, comparative genomic hybridisation (CGH) analysis revealed chromosomal imbalances with gains on chromosomes 1p31-q44, 6q12-q23 and 12q15-q22. Thus, the use of CGH expanded the information obtained by conventional cytogenetics and demonstrated that chromosomal imbalances were associated with the recurrence of the GCT.

The cytogenetics of preimplantation human development: insights provided by traditional and novel techniques

Our understanding of the incidence and origin of chromosome abnormalities in human preimplantation embryos is very limited due to the necessary ethical constraints involved in studying such material and the limited data ultimately produced. Several studies have addressed this issue, however, using techniques such as interphase fluorescence in situ hybridisation, modified G-banding preparation and the use of single-cell comparative genomic hybridisation (CGH). This review discusses the use of these techniques in assessing chromosome abnormalities in this, the earliest of human developmental stages. In addition, the prospects for the clinical use of CGH are discussed.