scholarly journals Leptospire Genomic Diversity Revealed by Microarray-Based Comparative Genomic Hybridization

2012 ◽  
Vol 78 (9) ◽  
pp. 3045-3050 ◽  
Author(s):  
Broderick Eribo ◽  
Sirima Mingmongkolchai ◽  
Tingfen Yan ◽  
Padunsri Dubbs ◽  
Karen E. Nelson
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Comparative Genomic Hybridization ◽  
Virulence Factors ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Leptospira Interrogans ◽  
Genomic Hybridization ◽  
Content Type ◽  
Reference Genomes

ABSTRACTComparative genomic hybridization was used to compare genetic diversity of five strains ofLeptospira(Leptospira interrogansserovars Bratislava, Canicola, and Hebdomadis andLeptospira kirschneriserovars Cynopteri and Grippotyphosa). The array was designed based on two available sequencedLeptospirareference genomes, those ofL. interrogansserovar Copenhageni andL. interrogansserovar Lai. A comparison of genetic contents showed thatL. interrogansserovar Bratislava was closest to the reference genomes whileL. kirschneriserovar Grippotyphosa had the least similarity to the reference genomes. Cluster analysis indicated thatL. interrogansserovars Bratislava and Hebdomadis clustered together first, followed byL. interrogansserovar Canicola, before the twoL. kirschneristrains. Confirmed/potential virulence factors identified in previous research were also detected in the tested strains.

scholarly journals Chromosomal Regions in Prostatic Carcinomas Studied by Comparative Genomic Hybridization, Hierarchical Cluster Analysis and Self-Organizing Feature Maps

2002 ◽  
Vol 24 (4-5) ◽  
pp. 167-179 ◽  
Author(s):  
Torsten Mattfeldt ◽  
Hubertus Wolter ◽  
Danilo Trijic ◽  
Hans‐Werner Gottfried ◽  
Hans A. Kestler
Keyword(s):  
Cluster Analysis ◽  
Comparative Genomic Hybridization ◽  
Hierarchical Cluster Analysis ◽  
Hierarchical Cluster ◽  
Data Matrix ◽  
Comparative Genomic ◽  
Feature Maps ◽  
Genomic Hybridization ◽  
A Genome ◽  
Self Organizing

Comparative genomic hybridization (CGH) is an established genetic method which enables a genome‐wide survey of chromosomal imbalances. For each chromosome region, one obtains the information whether there is a loss or gain of genetic material, or whether there is no change at that place. Therefore, large amounts of data quickly accumulate which must be put into a logical order. Cluster analysis can be used to assign individual cases (samples) to different clusters of cases, which are similar and where each cluster may be related to a different tumour biology. Another approach consists in a clustering of chromosomal regions by rewriting the original data matrix, where the cases are written as rows and the chromosomal regions as columns, in a transposed form. In this paper we applied hierarchical cluster analysis as well as two implementations of self‐organizing feature maps as classical and neuronal tools for cluster analysis of CGH data from prostatic carcinomas to such transposed data sets. Self‐organizing maps are artificial neural networks with the capability to form clusters on the basis of an unsupervised learning rule. We studied a group of 48 cases of incidental carcinomas, a tumour category which has not been evaluated by CGH before. In addition we studied a group of 50 cases of pT2N0‐tumours and a group of 20 pT3N0‐carcinomas. The results show in all case groups three clusters of chromosomal regions, which are (i) normal or minimally affected by losses and gains, (ii) regions with many losses and few gains and (iii) regions with many gains and few losses. Moreover, for the pT2N0‐ and pT3N0‐groups, it could be shown that the regions 6q, 8p and 13q lay all on the same cluster (associated with losses), and that the regions 9q and 20q belonged to the same cluster (associated with gains). For the incidental cancers such clear correlations could not be demonstrated.

scholarly journals Survey of Genomic Diversity among Enterococcus faecalis Strains by Microarray-Based Comparative Genomic Hybridization

2007 ◽  
Vol 73 (7) ◽  
pp. 2207-2217 ◽  
Author(s):  
Ågot Aakra ◽  
O. Ludvig Nyquist ◽  
Lars Snipen ◽  
Turid S. Reiersen ◽  
Ingolf F. Nes
Keyword(s):  
Enterococcus Faecalis ◽  
Comparative Genomic Hybridization ◽  
Antibiotic Resistance Genes ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Mobile Dna ◽  
Genomic Hybridization ◽  
Promising Tool ◽  
Plasmid Genes ◽  
Harsh Conditions

ABSTRACT We have compared nine Enterococcus faecalis strains with E. faecalis V583 by comparative genomic hybridization using microarrays (CGH). The strains used in this study (the “test” strains) originated from various environments. CGH is a powerful and promising tool for obtaining novel information on genome diversity in bacteria. By CGH, one obtains clues about which genes are present or divergent in the strains, compared to a reference strain (here, V583). The information obtained by CGH is important from both ecological and systematic points of view. CGH of E. faecalis showed considerable diversity in gene content: Compared to V583, the percentage of divergent genes in the test strains varied from 15% to 23%, and 154 genes were divergent in all strains. The main variation was found in regions corresponding to exogenously acquired or mobile DNA in V583. Antibiotic resistance genes, virulence factors, and integrated plasmid genes dominated among the divergent genes. The strains examined showed various contents of genes corresponding to the pTEF1, pTEF2, and pTEF3 genes in V583. The extensive transport and metabolic capabilities of V583 appeared similar in the test strains; CGH indicated that the ability to transport and metabolize various carbohydrates was similar in the test strains (verified by API 50 CH assays). The contents of genes related to stress tolerance appeared similar in V583 and the nine test strains, supporting the view of E. faecalis as an organism able to resist harsh conditions.

Comparative genomic hybridization analysis of craniopharyngiomas

2003 ◽  
Vol 98 (1) ◽  
pp. 162-164 ◽  
Author(s):  
Shlomit Rienstein ◽  
Eric F. Adams ◽  
David Pilzer ◽  
Ayala Aviram Goldring ◽  
Boleslaw Goldman ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Molecular Mechanisms ◽  
Genetic Alterations ◽  
Genomic Alteration ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Dna Copy Number ◽  
Content Type ◽  
Fine Print

Object. Craniopharyngioma is the most common childhood brain tumor and is thought to arise from embryonic remnants of the Rathke pouch. Some craniopharyngiomas are monoclonal in origin and hence presumably harbor somatic genetic alterations, although the precise molecular mechanisms involved in craniopharyngioma development are unknown. The goal of this study was to identify genetic alterations in craniopharyngiomas. Methods. To gain insight into the molecular mechanisms involved in development of these tumors, the authors analyzed nine adamantinomatous craniopharyngiomas by using comparative genomic hybridization. Six tumors (67%) displayed at least one genomic alteration, and three had six or more alterations. Only two tumors displayed a decrease in DNA copy number, and in all others an increase in DNA copy number was noted. Conclusions. The authors conclude that a subset of craniopharyngiomas consists of monoclonal tumors arising from activation of oncogenes located at specific chromosomal loci.

Analysis of von Hippel—Lindau mutations with comparative genomic hybridization in sporadic and hereditary hemangioblastomas: possible genetic heterogeneity

2002 ◽  
Vol 97 (4) ◽  
pp. 977-982 ◽  
Author(s):  
Johanna M. M. Gijtenbeek ◽  
Bram Jacobs ◽  
Sandra H. E. Sprenger ◽  
Marc J. Eleveld ◽  
Ad Geurts van Kessel ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Molecular Mechanisms ◽  
Chromosome 3 ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Content Type ◽  
Von Hippel Lindau ◽  
Chromosome 3P ◽  
Chromosomal Imbalances ◽  
Fine Print

Object. Hemangioblastomas (HBs) occur sporadically or as a manifestation of von Hippel—Lindau (VHL) disease. In the majority of VHL-related HBs, inactivation of the VHL tumor suppressor gene (TSG), which is located on chromosome 3p25–26, is found. The VHL gene is assumed to be involved also in the development of sporadic HBs. In a previous study of chromosomal aberrations of sporadic HBs, multiple chromosomal imbalances were found in the majority of tumors. The aim of this study was to analyze further both sporadic HBs and VHL-related HBs to determine if these histopathologically identical tumors have a different genetic background. Methods. Sixteen sporadic HBs and seven VHL-related HBs were identified by clinical criteria and analyzed. Comparative genomic hybridization was used to screen for chromosomal imbalances throughout the entire HB genome. Additionally, mutation analysis of the VHL gene was performed using direct sequencing. Loss of chromosome 3 and multiple other chromosomal imbalances were found in the sporadic HBs, although only one imbalance, a loss of chromosome 3, was detected in the seven VHL-related HBs. Somatic VHL gene mutations were found in one third of sporadic HBs, whereas a mutation of the VHL gene was detected in all VHL-related HBs. Conclusions. These results indicate that the molecular mechanisms underlying sporadic HBs and VHL-related HBs are different. Inactivation of the VHL gene is probably not the most important event in the tumorigenesis of sporadic HBs. Other mechanisms of inhibition of VHL protein function, or inactivation of other TSGs, on chromosome 3p or on other chromosomes, might be important in the development of sporadic HBs.

Investigating the role of pneumococcal neuraminidase A activity in isolates from pneumococcal haemolytic uraemic syndrome

2013 ◽  
Vol 62 (11) ◽  
pp. 1735-1742 ◽  
Author(s):  
Andrew Smith ◽  
Calum Johnston ◽  
Donald Inverarity ◽  
Mary Slack ◽  
Gavin K. Paterson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Young Children ◽  
Comparative Genomic Hybridization ◽  
Haemolytic Uraemic Syndrome ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Neuraminidase Activity ◽  
Atypical Haemolytic Uraemic Syndrome ◽  
Significant Difference

Streptococcus pneumoniae diseases are a rare but increasingly recognized trigger of atypical haemolytic uraemic syndrome (HUS) in young children and associated with a higher mortality rate than diarrhoea-associated HUS. This study aimed to determine the importance of neuraminidase A (NanA) and genomic diversity in the pathogenesis of pneumococcal HUS (pHUS). We investigated the nanA gene sequence, gene expression, neuraminidase activity and comparative genomic hybridization of invasive pneumococcal disease (IPD) isolates from patients with pHUS and control strains matched by serotype and sequence type (ST), isolated from patients with IPD but not pHUS. The nanA sequence of 33 isolates was determined and mutations at 142 aa positions were identified. High levels of diversity were observed within the NanA protein, with mosaic blocks, insertions and repeat regions present. When comparing nanA allelic diversity with ST and disease profile in the isolates tested, nanA alleles clustered mostly by ST. No particular nanA allele was associated with pHUS. There was no significant difference in overall neuraminidase activity between pHUS isolates and controls when induced/uninduced with N-acetylneuraminic acid. Comparative genomic hybridization showed little difference in genetic content between the pHUS isolates and the controls. Results of gene expression studies identified 12 genes differentially regulated in all pHUS isolates compared with the control. Although neuraminidase enzyme activity may be important in pHUS progression and contribute to pathogenesis, the lack of a distinction between pHUS isolates and controls suggests that host factors, such as acquired abnormalities of the alternative complement cascade in young children, may play a more significant role in the outcome of pHUS.

scholarly journals Extensive Genomic Diversity in Pathogenic Escherichia coli and Shigella Strains Revealed by Comparative Genomic Hybridization Microarray

2004 ◽  
Vol 186 (12) ◽  
pp. 3911-3921 ◽  
Author(s):  
Satoru Fukiya ◽  
Hiroshi Mizoguchi ◽  
Toru Tobe ◽  
Hideo Mori
Keyword(s):  
Escherichia Coli ◽  
Comparative Genomic Hybridization ◽  
Cell Envelope ◽  
Genome Structure ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Phylogenic Tree ◽  
E Coli ◽  
K 12

ABSTRACT Escherichia coli, including the closely related genus Shigella, is a highly diverse species in terms of genome structure. Comparative genomic hybridization (CGH) microarray analysis was used to compare the gene content of E. coli K-12 with the gene contents of pathogenic strains. Missing genes in a pathogen were detected on a microarray slide spotted with 4,071 open reading frames (ORFs) of W3110, a commonly used wild-type K-12 strain. For 22 strains subjected to the CGH microarray analyses 1,424 ORFs were found to be absent in at least one strain. The common backbone of the E. coli genome was estimated to contain about 2,800 ORFs. The mosaic distribution of absent regions indicated that the genomes of pathogenic strains were highly diversified becasue of insertions and deletions. Prophages, cell envelope genes, transporter genes, and regulator genes in the K-12 genome often were not present in pathogens. The gene contents of the strains tested were recognized as a matrix for a neighbor-joining analysis. The phylogenic tree obtained was consistent with the results of previous studies. However, unique relationships between enteroinvasive strains and Shigella, uropathogenic, and some enteropathogenic strains were suggested by the results of this study. The data demonstrated that the CGH microarray technique is useful not only for genomic comparisons but also for phylogenic analysis of E. coli at the strain level.

scholarly journals Cluster Analysis of Comparative Genomic Hybridization (CGH) Data Using Self-Organizing Maps: Application to Prostate Carcinomas

2001 ◽  
Vol 23 (1) ◽  
pp. 29-37 ◽  
Author(s):  
Torsten Mattfeldt ◽  
Hubertus Wolter ◽  
Ralf Kemmerling ◽  
Hans‐Werner Gottfried ◽  
Hans A. Kestler
Keyword(s):  
Cluster Analysis ◽  
Comparative Genomic Hybridization ◽  
Genetic Material ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Self Organizing Maps ◽  
Data Set ◽  
A Genome ◽  
Self Organizing

Comparative genomic hybridization (CGH) is a modern genetic method which enables a genome‐wide survey of chromosomal imbalances. For each chromosome region, one obtains the information whether there is a loss or gain of genetic material, or whether there is no change at that region. Usually it is not possible to evaluate all 46 chromosomes of a metaphase, therefore several (up to 20 or more) metaphases are analyzed per individual, and expressed as average. Mostly one does not study one individual alone but groups of 20–30 individuals. Therefore, large amounts of data quickly accumulate which must be put into a logical order. In this paper we present the application of a self‐organizing map (Genecluster) as a tool for cluster analysis of data from pT2N0 prostate cancer cases studied by CGH. Self‐organizing maps are artificial neural networks with the capability to form clusters on the basis of an unsupervised learning rule, i.e., in our examples it gets the CGH data as only information (no clinical data). We studied a group of 40 recent cases without follow‐up, an older group of 20 cases with follow‐up, and the data set obtained by pooling both groups. In all groups good clusterings were found in the sense that clinically similar cases were placed into the same clusters on the basis of the genetic information only. The data indicate that losses on chromosome arms 6q, 8p and 13q are all frequent in pT2N0 prostatic cancer, but the loss on 8p has probably the largest prognostic importance.

Detection of chromosomal imbalances in central neurocytomas by using comparative genomic hybridization

2000 ◽  
Vol 93 (1) ◽  
pp. 77-81 ◽  
Author(s):  
Xiao-Lu Yin ◽  
Jesse Chung-Sean Pang ◽  
Angela Bik-Yu Hui ◽  
Ho-Keung Ng
Keyword(s):  
Dna Sequence ◽  
Comparative Genomic Hybridization ◽  
Dna Sequences ◽  
Immunohistochemical Analysis ◽  
Comparative Genomic ◽  
Fluorescence Intensity Ratio ◽  
Genomic Hybridization ◽  
Metaphase Chromosomes ◽  
Content Type ◽  
Fine Print

Object. Central neurocytomas are rare neuronal tumors commonly found in the intraventricular regions. Little is known about the tumorigenesis of these neoplasms. The aim of this study was to provide an overview of genetic imbalances in central neurocytomas.Methods. In this study, comparative genomic hybridization was used to identify DNA sequence copy number changes (losses and gains) in a series of 10 central neurocytomas. Tumor DNA and normal reference DNA were differentially labeled and allowed to cohybridize to normal metaphase chromosomes. After hybridization and fluorescent staining of the bound DNA, regions of gain or of loss of DNA sequences were detected as changes in the tumor/normal fluorescence intensity ratio along the target metaphase chromosomes. A gain of DNA sequence was detected in chromosomes 2p, 10q, and 18q. A protooncogene, Bcl2, which maps to 18q21, was evaluated by immunohistochemical analysis to determine its role in the formation of central neurocytomas.Conclusions. In this study the authors identified recurrent genetic changes on chromosomes 2p, 10q, and 18q in central neurocytomas and highlighted chromosomal regions for additional mapping and cloning of candidate genes that are important in the development of central neurocytomas.

Genetic reflection of glioblastoma biopsy material in xenografts: characterization of 11 glioblastoma xenograft lines by comparative genomic hybridization

2000 ◽  
Vol 92 (4) ◽  
pp. 652-658 ◽  
Author(s):  
Judith W. M. Jeuken ◽  
Sandra H. E. Sprenger ◽  
Pieter Wesseling ◽  
Hans J. J. A. Bernsen ◽  
Ron F. Suijkerbuijk ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Tumor Biology ◽  
Point Of View ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Biopsy Material ◽  
Content Type ◽  
Chromosomal Imbalances ◽  
Fine Print

Object. Human tumors implanted as subcutaneous xenografts in nude mice are widely used for the study of tumor biology and therapy. Validation of these models requires knowledge of the genetic makeup of the xenografts. The aim of this study was to establish whether chromosomal imbalances in 11 xenograft lines derived from human glioblastomas multiforme (x-GBMs) are similar to those found in GBM biopsy samples. The authors also studied genetic stability during serial passaging of three xenograft lines.Methods. Chromosomal imbalances in x-GBMs were detected using comparative genomic hybridization (CGH). The authors compared the CGH results in x-GBMs with those in the original GBMs (o-GBMs) that were used to establish three of the xenograft lines and with the GBM biopsy results reported in the literature (l-GBMs). In three xenograft lines two different passages were analyzed.Conclusions. The results show that the chromosomal imbalances in x-GBMs are similar to those in o-GBMs and l-GBMs, indicating that the GBM xenograft lines used were valid models from a genetic point of view. The CGH analysis of two different passages of three xenograft lines indicates that x-GBMs (like l-GBMs) show intratumoral genetic heterogeneity and do not acquire chromosomal imbalances as a result of serial passaging.

Multiple genetic aberrations including evidence of chromosome 11q13 rearrangement detected in pituitary adenomas by comparative genomic hybridization

1999 ◽  
Vol 90 (2) ◽  
pp. 306-314 ◽  
Author(s):  
Andrew K. Metzger ◽  
Gayatry Mohapatra ◽  
Yuriko A. Minn ◽  
Andrew W. Bollen ◽  
Kathleen Lamborn ◽  
...  
Keyword(s):  
Cyclin D1 ◽  
Comparative Genomic Hybridization ◽  
Pituitary Adenomas ◽  
Genetic Material ◽  
Comparative Genomic ◽  
Chromosome 11 ◽  
Genomic Hybridization ◽  
Genetic Aberrations ◽  
Content Type ◽  
Fine Print

Object. This study was conducted to determine whether comparative genomic hybridization (CGH) is a more sensitive method for detecting genetic aberrations than other tests currently in use.Methods. The authors used CGH to examine 40 primary and 13 recurrent adenomas obtained from 52 patients for loss and gain of genetic material. Copy number aberrations (CNAs) were detected in 25 (48%) of the 52 patients studied. The chromosomes affected were, in order of decreasing frequency, 11, 7, X, 1, 8, 13, 5, 14, 2, 6, 9, 10, 12, 3, 18, 21, 4, 16, 15, 19, 22, and Y. Endocrinologically active adenomas were more likely to contain (p = 0.009) and had a greater number (p = 0.003) of CNAs. Of 26 adenomas with CNAs, 18 showed multiple aberrations involving entire chromosomes or chromosome arms. The most frequent CNA involving a chromosome subregion, which was present in four (8%) of 53 adenomas, was the loss of all chromosome 11 material except for a preserved common segment containing 11q13. Immunoperoxidase staining did not detect cyclin D1 expression in those four cases, making cyclin D1 an unlikely target of this rearrangement.Conclusions. These findings indicate that genetic abnormalities are present in pituitary adenomas at a higher rate than previously reported, are associated with endocrinological activity, and often involve several chromosomes. Rearrangement at 11q13 may inactivate a tumor suppressor gene or activate an oncogene that is important in the initiation or progression of sporadic pituitary adenomas.

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