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PubMed2005

Large cell neuroendocrine carcinoma of the uterine cervix with cytogenetic analysis by comparative genomic hybridization: a case study.

Large cell neuroendocrine carcinoma (LCNEC) of the uterine cervix is a newly introduced category of the revised World Health Organization classification. We reported a case of cervical LCNEC with cytogenetic analysis by comparative genomic hybridization (CGH). The cervical tumor showed moderately increased mitotic activity (8-14 mitotic figures per 10 high-power fields) and focal necrosis, which made it problematic to differentiate from atypical carcinoid. CGH analysis failed to detect chromosome 11q loss that has been reported to be characteristic of pulmonary atypical carcinoids. Furthermore, chromosome 3q amplification, which has been detected frequently in pulmonary small cell carcinomas and LCNECs but not in pulmonary typical and atypical carcinoids, was the most remarkable chromosomal aberration. Although CGH reports are extremely rare in neuroendocrine tumors of the uterine cervix, specific chromosomal aberrations may be useful in their distinction.

Adult↗

PubMed2003

Comparative study of primary and recurrent ovarian serous carcinomas: comparative genomic hybridization analysis with a potential application for prognosis.

OBJECTIVES: The purpose of this study is to comparatively characterize genomic imbalances in primary and recurrent ovarian serous carcinomas and to identify genomic alterations that may be used as a marker for prognosis. METHODS: Twenty ovarian serous carcinomas were studied by comparative genomic hybridization (CGH). RESULTS: Genomic alterations were found in all of the tumors. The most common regions involving gain of DNA copy numbers are 1q41q44, 8q22q24, 19p12q13.1, 20q12q13, 3q26q29, 12p12p13, 2p22p25, 7p14p21, 5p15.2p15.3, and 17q22q25. The most common regions with loss of DNA copy numbers are Xp11.2q13, 4q31q35, Xp21p22.3, 18q22q23, 13q22q31, 9p22p24, and 16q22q24. High-level gains were detected at chromosomal regions of 1q41q44, 2p22p25, 3q26q29, and 19p12q13.1. Comparative analysis of primary and recurrent tumors showed that gains of 2p22p25, 19p12q13.1, and 20q12q13 and loss of 5q14q22 were more common in the recurrent high-grade tumors. About 85% of the tumors showed increases in DNA copy numbers in the regions (2p and 8q) harboring the myc family gene. Patients with tumor containing fewer than seven chromosomal aberrations showed longer survival time. CONCLUSION: The myc oncogene family may play a role in the pathogenesis of ovarian serous carcinomas. Our study suggests that tumors with gains of 2p22p25, 19p12q13.1, and 20q12q13 and loss of 5q14q22 may be at high risk for recurrence. Furthermore, the patients' survival time inversely correlates with the numbers of chromosomal alterations found in their tumors. CGH analysis may have a clinical application in predicting prognosis and risk of recurrence in patients with ovarian serous carcinomas.

Aged↗

PubMed2004

Fibrolamellar hepatocellular carcinoma occurring 5 years after hepatocellular adenoma in a 14-year-old girl: a case report with comparative genomic hybridization analysis.

An unusual case of fibrolamellar carcinoma of the liver developed 5 years after removal of a hepatocellular adenoma in a 14-year-old girl belonging to a family with Carney syndrome. Both tumors were studied by light and electron microscopy, flow cytometry, and comparative genomic hybridization. The first tumor, removed at the age of 9, was a bulky well-circumscribed liver mass composed of large eosinophilic cells with a focal pseudoglandular pattern but without cytologic atypia or sclerosis. A diagnosis of hepatocellular adenoma was rendered. Five years later, another hepatic tumor was removed from the right lobe. Microscopic examination revealed polygonal cells, each with a large amount of eosinophilic cytoplasm and a round nucleus with a conspicuous nucleolus. These cells were arranged in nests and strands and separated by bands of dense fibrous tissue, leading to a diagnosis of fibrolamellar carcinoma. Comparative genomic hybridization analysis revealed no genetic alteration in the adenoma; however, several chromosomal aberrations (loss of chromosome regions 1p and 4p and gains of chromosome regions 6q, 13q, and Xq) were detected in the fibrolamellar carcinoma. To our knowledge, this is the first report of an association between hepatocellular adenoma and fibrolamellar carcinoma.

Adenoma, Liver Cell↗

PubMed2001

[Key technologies in image analysis of comparative genomic hybridization].

Comparative genomic hybridization has become a new technique in molecular-cytogenetics, and it has found significant applications in tumor pathology. Image analysis is an important part of comparative genomic hybridization. It analyzes the fluorescent images by many steps and finally determines whether there is any abnormality in the copy number of the test tumor tissue. This paper expatiates on the key steps in the image analysis of comparative genomic hybridization, including background correction, chromosome segmentation, chromosome axis determination, karyotyping and determining ratio profile. The future trend is also discussed.

Cytogenetics↗

PubMed2006

Similarity and differences in the Lactobacillus acidophilus group identified by polyphasic analysis and comparative genomics.

A set of lactobacilli were investigated by polyphasic analysis. Multilocus sequence analysis, DNA typing, microarray analysis, and in silico whole-genome alignments provided a remarkably consistent pattern of similarity within the Lactobacillus acidophilus complex. On microarray analysis, 17 and 5% of the genes from Lactobacillus johnsonii strain NCC533 represented variable and strain-specific genes, respectively, when tested against four independent isolates of L. johnsonii. When projected on the NCC533 genome map, about 10 large clusters of variable genes were identified, and they were enriched around the terminus of replication. A quarter of the variable genes and two-thirds of the strain-specific genes were associated with mobile DNA. Signatures for horizontal gene transfer and modular evolution were found in prophages and in DNA from the exopolysaccharide biosynthesis cluster. On microarray hybridizations, Lactobacillus gasseri strains showed a shift to significantly lower fluorescence intensities than the L. johnsonii test strains, and only genes encoding very conserved cellular functions from L. acidophilus hybridized to the L. johnsonii array. In-silico comparative genomics showed extensive protein sequence similarity and genome synteny of L. johnsonii with L. gasseri, L. acidophilus, and Lactobacillus delbrueckii; moderate synteny with Lactobacillus casei; and scattered X-type sharing of protein sequence identity with the other sequenced lactobacilli. The observation of a stepwise decrease in similarity between the members of the L. acidophilus group suggests a strong element of vertical evolution in a natural phylogenetic group. Modern whole-genome-based techniques are thus a useful adjunct to the clarification of taxonomical relationships in problematic bacterial groups.

Genetic Variation↗

PubMed2004

DNA microarrays for comparative genomics and analysis of gene expression in Trypanosoma cruzi.

Trypanosoma cruzi presents high genetic diversity and parasite isolates show remarkable differences in biological parameters. In this study, we evaluated whether DNA microarrays containing CL Brener cDNAs can be used for comparative genomics and for the analysis of gene expression in T. cruzi. We constructed a prototype microarray with 710 expression sequence tags of CL Brener and 20 sequences of T. cruzi strains. These probes represent 665 unique genes. Results from four hybridisations with genomic DNA of Silvio (T. cruzi I) and CL Brener (hybrid genotype) identified 9.3% of the probes (68/730) differentially represented in the two genomes. Data from eight hybridisations with cDNA obtained from three independent parasite harvests of Silvio and CL Brener disclosed 84 sequences of 730 (11.5%) that showed statistical significant (P < or = 0.01) changes in expression (1.6-6.5-fold). Some of the array-identified sequences were confirmed by Southern and Northern blot analysis. Only 20% of the probes with increased expression in Silvio or CL Brener presented higher hybridisation with genomic DNA of either strain. Approximately 2.5% (18/730) and 9.0% (65/730) of the probes were differentially expressed (P < or = 0.01), respectively, in epimastigotes and metacyclic trypomastigotes of two T. cruzi II strains isolated from chronic chagasic patients. Microarrays identified several sequences for which differences in gene copy number and/or in the levels of RNA transcripts were previously demonstrated by different approaches. The data indicate that DNA microarrays are a useful tool for comparative studies between strains and provide further evidence for a high level of post-transcriptional regulation of RNA abundance in T. cruzi.

Adaptation, Physiological↗

PubMed2001

Characterization of chromosome aberrations associated with soft-tissue leiomyosarcomas by twenty-four-color karyotyping and comparative genomic hybridization analysis.

Data on the chromosome aberrations associated with leiomyosarcomas of soft tissues are limited, complex, and incomplete. The aim of this study was to characterize genetic aberrations associated with this tumor group, to identify consistent regions of involvement and to determine correlations with clinical outcome. Chromosomes were prepared from 10 primary soft-tissue leiomyosarcoma samples, and preparations from four of them, plus the cell line SK-LMS-1, were suitable for analysis using 24-color karyotyping by multifluor fluorescence in situ hybridization. This method allowed rearranged chromosomes to be characterized, which would not have been possible by banding analysis alone. The remaining six chromosome preparations were analyzed using standard Giemsa banding. The chromosome imbalances associated with all the samples were determined by comparative genomic hybridization analysis. Taken together, the results show both intra- and intertumor heterogeneity and considerable complexity. Although no highly consistent rearrangements were found, some regions of the genome frequently were involved, including 1q21, 5p14-pter, and 20q13, which likely harbor genes that play a role in the pathogenesis of soft-tissue leiomyosarcomas. There were no obvious correlations between the chromosomal changes identified and available clinical details.

Adult↗

PubMed2026

Whole-genome safety assessment of Loigolactobacillus coryniformis WBB05 and identification of a candidate gene for aerobic reuterin production.

This study reports on the safety profile of Loigolactobacillus coryniformis WBB05 for food industry applications and identifies glycerol-3-phosphate oxidase (GlpO) as a candidate gene associated with aerobic reuterin production. The safety of L. coryniformis WBB05 was evaluated through whole-genome sequencing, phenotypic analysis of haemolytic activity and determination of minimum inhibitory concentrations (MICs) of antibiotics. Comparative genomic analysis was performed to identify candidate genetic determinants for aerobic reuterin production. The draft genome (2.83 Mb, 179 contigs) harboured no known virulence factors, acquired antimicrobial resistance (AMR) genes or biogenic amine biosynthetic genes. Prophage analysis identified only one incomplete prophage region, and four CRISPR-Cas systems (212 spacers) were consistent with phage defence capacity. Secondary metabolite analysis revealed biosynthetic gene clusters encoding a coagulin-like bacteriocin. No β-haemolytic activity was observed. The MICs of all antibiotics tested were below the European Food Safety Authority cut-off values except for kanamycin (128 mg/L), although no acquired AMR genes were detected. Comparative genomic analysis revealed that L. coryniformis WBB05 possesses two putative copies of GlpO, a gene not detected in publicly available genomes of Limosilactobacillus reuteri, which produces reuterin only under anaerobic conditions. These findings support the use of L. coryniformis WBB05 as a safe adjunct culture for dairy applications and highlight GlpO as a candidate determinant of aerobic reuterin production. Further studies comparing GlpO-positive and GlpO-negative strains under aerobic and anaerobic conditions are warranted to confirm the role of GlpO.

Loigolactobacillus coryniformis↗

PubMed1995

Comparative genomic hybridization analysis of human sarcomas: II. Identification of novel amplicons at 6p and 17p in osteosarcomas.

Using comparative genomic hybridization (CGH), we have identified and mapped regions of DNA amplification in primary and metastatic osteosarcomas. Samples were obtained from four patients and ten independent xenografts. Sixty-four percent of the tumors showed increased DNA-sequence copy numbers, affecting 23 different chromosomal sites. Most of these regions were not previously associated with the development and/or progression of these tumors. Amplicons originating from 1q21-q23, 6p, 8q23-qter, and 17p11-p12 were observed most frequently. The 6p and 17p11-p12 amplicons seem to be specific for osteosarcomas, indicating that these regions may harbor genes relevant for the development of these tumors.

Animals↗

PubMedDate not supplied

[Computer searching of new targets for antimicrobial drugs based on comparative analysis of genomes].

The progress in genome research allows to use genomic databases for drug discovery. The major interest consists in their usage for searching of new molecular targets for new drugs. It is especially important in the area of new antimicrobial drugs creation. In recent years, the applicability of genome analysis for solution of this problem was shown by different authors. We propose an approach for searching new targets for antimicrobial drugs based upon comparative analysis of genomes and samples from molecular databases. For each protein encoded by the target microorganism genome the conformance to a number of medico-biological and technological requirements was tested. The obtained evaluations were used for selection of potential targets. The approach was implemented in the original software GenMesh. It was successfully tested with known targets of drugs against tuberculosis when correct valuations were obtained. The attempt of new targets selection for design of new drugs against tuberculosis was done with reliable results.

Anti-Infective Agents↗

PubMed1998

Establishing germ cell origin of undifferentiated tumors by identifying gain of 12p material using comparative genomic hybridization analysis of paraffin-embedded samples.

An estimated 10% of adult cancer patients present with undifferentiated carcinoma. The diagnosis of germ cell tumor (GCT) in such patients can be difficult but has important implications for patient management. Male testicular GCT is characterized by an isochromosome 12p, i(12p), or additional 12p material, in some cases restricted to the 12p11.2-p12.1 region. A gain of 12p material can indicate that a tumor, which may not be present in the testis, is of germ cell origin. Formalin-fixed, paraffin-embedded samples are the most widely available material for diagnostic analysis and retrospective studies. We have compared the identification of 12p gain in snap-frozen samples with corresponding paraffin-embedded material from three clearly defined testicular GCTs using comparative genomic hybridization analysis. In this preliminary study, paraffin-embedded tumor samples of uncertain histogenesis from seven patients were then analyzed. Tumor samples from three of these patients showed a gain of 12p material, and in one patient, gain was restricted to the 12p11.2-p12 region. The clinical picture and response to therapy were generally consistent with the 12p status, though lack of 12p gain may not exclude a diagnosis of GCT.

Adenocarcinoma↗

PubMed2001

Optimization of DOP-PCR amplification of DNA for high-resolution comparative genomic hybridization analysis.

BACKGROUND: Whole-genome amplification of minute samples of DNA for the use in comparative genomic hybridization (CGH) analysis has found widespread use, but the method has not been well validated. METHODS: Four protocols for degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) and fluorescence labeling were applied to test DNA from normal and K-562 cells. The DNA products were used for CGH analysis. RESULTS: The DOP-PCR-amplified DNA from each protocol produced hybridizations with different qualities. These could be seen primarily as differences in background staining and signal-to-noise ratios, but also as characteristic deviations of normal/normal hybridizations. One DOP-PCR-protocol was further investigated. We observed concordance between CGH results using unamplified and DOP-PCR-amplified DNA. An example of an analysis of an invasive carcinoma of the breast supports the practical value of this approach. CONCLUSIONS: DOP-PCR-amplified DNA is applicable for high- resolution CGH, the results being similar to those of CGH using unamplified DNA.

Breast Neoplasms↗

PubMed1998

Comparative genomic hybridization analysis of lobular carcinoma in situ and atypical lobular hyperplasia and potential roles for gains and losses of genetic material in breast neoplasia.

Lobular carcinoma in situ (LCIS) and atypical lobular hyperplasia (ALH) of the breast are cytologically similar breast lesions that reportedly carry different relative risks of subsequent development of invasive carcinoma. They are frequently multifocal and bilateral. We have identified the chromosomal copy number changes in 31 LCIS and 14 ALH lesions from 28 cases and also the 7 invasive carcinomas that subsequently developed in 6 of these cases. This was achieved by comparative genomic hybridization analysis of microdissected formalin-fixed, paraffin-embedded material. There was no significant difference between the aberrations found in the unilateral versus the bilateral cases of LCIS. Loss of material from 16p, 16q, 17p, and 22q and also gain of material from 6q were found at a similar high frequency in LCIS and ALH. Loss of these genomic regions may indicate the locations of genes that predispose to the development of the lesions, and the results are consistent with LCIS and ALH representing the same genetic stage of development. Comparison of the comparative genomic hybridization results from LCIS/ALH with those from ductal carcinoma in situ and invasive cancer showed some similarities at the chromosomal level, but it also showed significant differences, including gain of 1q and 8q and evidence for genomic amplification, which were not found in LCIS/ALH. A genetic model is postulated for the possible relationships between noninvasive lobular lesions and invasive breast carcinoma, delineating potential roles for specific chromosome copy number changes.

Adult↗

PubMed2000

High resolution comparative genomic hybridisation analysis reveals imbalances in dyschromosomal patients with normal or apparently balanced conventional karyotypes.

A sensitive technique is needed for screening whole genome imbalances in dyschromosomal patients when G-banding shows normal karyotypes or apparently balanced translocations. In this study we performed highly sensitive comparative genomic hybridisation analysis on a number of such cases and revealed chromosomal imbalances in all.

Chromosome Aberrations↗

PubMed2004

CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets.

The advent of DNA microarray technology and the sequencing of multiple vertebrate genomes has provided a unique opportunity for the integration of comparative genomics with high-throughput gene expression analysis. Here we describe the conserved transcription factor binding site (CONFAC) software that enables the high-throughput identification of conserved transcription factor binding sites (TFBSs) in the regulatory regions of hundreds of genes at a time (http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.pl). The CONFAC software compares non-coding regulatory sequences between human and mouse genomes to enable identification of conserved TFBSs that are significantly enriched in promoters of gene clusters from microarray analyses compared to sets of unchanging control genes using a Mann-Whitney U-test. Analysis of random gene sets demonstrated that using our approach, over 98% of TFBSs had false positive rates below 5%. As a proof-of-principle, we have validated the CONFAC software using gene sets from four separate microarray studies and identified TFBSs known to be functionally important for regulation of each of the four gene sets.

Animals↗

PubMed2002

Comparative genomic hybridization analysis of sperm DNA apoptosis after exposure to heat shock.

PURPOSE: A DNA disc chip assay based on comparative genomic hybridization (CGH) was developed to measure sperm DNA integrity. The objective was to correlate DNA integrity of heat-treated sperm with the sperm capacitation index (CI) determined from the sperm penetration assay. METHODS: Basic semen and kinematic parameters were measured (N = 6). Sperm were washed in two-layer colloid suspensions and split portions incubated at either 3 degrees C (control) or 40 degrees C for 4 h. Single-stranded DNA of heated sperm were stained in SYBR Gold and hybridized to bisbenzimide (Hoechst 33342) stained control DNA in a membrane disc. Fluorescent intensities of the discs were measured and correlation analyses with sperm parameters performed. RESULTS: Sperm CI was positively correlated (R = 0.737) with sperm DNA integrity. Two populations of sperm could be discerned: low capacitating sperm that initiated apoptosis and high capacitating sperm unaffected by heat shock treatment. The remaining parameters were not related to sperm DNA stability. CONCLUSIONS: Fragile DNA were found in a population of sperm associated with poor capacitation characteristics and apoptosis was observed after heat treatment. The results suggested that sperm dysfunction might be due to apoptotic sperm DNA resulting from an elevated temperature in the surroundings. The data suggested that the second population of high capacitating sperm induced chaperones such as heat shock proteins hsp 70 to protect against apoptosis.

Apoptosis↗

PubMed1999

Loss of chromosome 13 is the most frequent genomic imbalance in malignant fibrous histiocytomas. A comparative genomic hybridization analysis of a series of 30 cases.

Regional chromosome localizations of DNA copy number imbalances were studied by comparative genomic hybridization in 30 malignant fibrous histiocytomas: 13 primary tumors (2 myxoid, 9 storiform pleomorphic, and 2 with more undifferentiated phenotype) and 17 local recurrences (2 myxoid, 11 storiform pleomorphic, and 4 with more undifferentiated phenotype). Abnormal comparative genomic hybridization (CGH) profiles were observed in 25 tumors (83%). The most frequent gains (ratio > 1.2) corresponded, by order of frequency, to entire Xp, and bands 1q21, 19q13.1, 19p13, 5p13-p14, 1p31, 17p, 18p, 20q, 1p35, 17q23, and 22q12. High levels of gains (ratio > 1.5) were recurrently detected for Xp (10 cases), and in bands 1q21-q22 (8 cases), 3q27 (4 cases), 5p13-p14 (3 cases), 13q32-q34 (3 cases), 15q22-q26 (3 cases), and 17p11-p12 (3 cases). Losses of 13q12-q14 or 13q21 were observed in a large proportion of tumors (17 cases), suggesting that a gene localized in this region could act as a tumor suppressor gene. Losses of 11q23, 2q32, 11p13, 10p, 1q4, 9p2, 16q12, 4q3, 10q25, 3p23, 2p24, and 12p were also recurrently observed. Taken together, these results provide an overview of chromosome imbalances present in MFH, which could be of use for diagnostic purposes. They point to various chromosome regions which may harbor genes important for malignant fibrous histiocytomas (MFH) oncogenesis and progression.

Chromosome Aberrations↗

PubMed2002

Chromosomal imbalances in familial chronic lymphocytic leukaemia: a comparative genomic hybridisation analysis.

A subset of B cell chronic lymphocytic leukaemia (CLL) is familial. Lack of large families makes it attractive to exploit methods in addition to genetic linkage analysis for the identification of a susceptibility locus. One strategy that can localise regions of the genome that may harbour tumour suppressor genes is to identify regions of chromosomal imbalance using comparative genomic hybridisation (CGH) analysis. We examined 24 familial CLL cases by CGH analysis. Losses that are documented as arising frequently in sporadic CLL were observed at a comparable frequency in familial CLL. However, gains and losses in two regions of the X chromosome - Xp11.2-p21 and Xq21-qter - appear more common in familial CLL than in sporadic CLL. This suggests these regions may harbour a susceptibility locus for CLL. There is also some evidence that chromosome regions 2p12-p14 and 4q11-q21 may harbour predisposition genes.

Chromosome Aberrations↗