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PubMed2004

Array comparative genomic hybridization analysis of genomic alterations in breast cancer subtypes.

In this study, we performed high-resolution array comparative genomic hybridization with an array of 4153 bacterial artificial chromosome clones to assess copy number changes in 44 archival breast cancers. The tumors were flow sorted to exclude non-tumor DNA and increase our ability to detect gene copy number changes. In these tumors, losses were more frequent than gains, and gains in 1q and loss in 16q were the most frequent alterations. We compared gene copy number changes in the tumors based on histologic subtype and estrogen receptor (ER) status, i.e., ER-negative infiltrating ductal carcinoma, ER-positive infiltrating ductal carcinoma, and ER-positive infiltrating lobular carcinoma. We observed a consistent association between loss in regions of 5q and ER-negative infiltrating ductal carcinoma, as well as more frequent loss in 4p16, 8p23, 8p21, 10q25, and 17p11.2 in ER-negative infiltrating ductal carcinoma compared with ER-positive infiltrating ductal carcinoma (adjusted P values < or = 0.05). We also observed high-level amplifications in ER-negative infiltrating ductal carcinoma in regions of 8q24 and 17q12 encompassing the c-myc and c-erbB-2 genes and apparent homozygous deletions in 3p21, 5q33, 8p23, 8p21, 9q34, 16q24, and 19q13. ER-positive infiltrating ductal carcinoma showed a higher frequency of gain in 16p13 and loss in 16q21 than ER-negative infiltrating ductal carcinoma. Correlation analysis highlighted regions of change commonly seen together in ER-negative infiltrating ductal carcinoma. ER-positive infiltrating lobular carcinoma differed from ER-positive infiltrating ductal carcinoma in the frequency of gain in 1q and loss in 11q and showed high-level amplifications in 1q32, 8p23, 11q13, and 11q14. These results indicate that array comparative genomic hybridization can identify significant differences in the genomic alterations between subtypes of breast cancer.

Adult↗
PubMed2026

Genomic insights into Aeromonas infections in diarrheal patients: high diversity, emerging resistance, and potential outbreak in Beijing.

BACKGROUND: Aeromonas species are ubiquitous aquatic bacteria that have emerged as significant foodborne enteric pathogens worldwide, yet their genomic landscape in clinical settings remains poorly delineated, particularly in Beijing. METHODS: To address this gap, we performed active surveillance for Aeromonas among 691 consecutive diarrheal outpatients in a Beijing district from January to December 2024. Isolates were recovered using enrichment culture coupled with PCR screening and identified by MALDI-TOF MS. Antimicrobial susceptibility was tested against 17 agents. Whole-genome sequencing was conducted on all isolates, enabling average nucleotide identity (ANI) analysis, comprehensive annotation of antimicrobial resistance and virulence genes, multilocus sequence typing (MLST), and core-genome SNP (cgSNP)-based phylogenetics. RESULTS: Aeromonas was detected in 3.3% (23/691) of patients, with Aeromonas veronii (56.52%, 13/23) and Aeromonas caviae (26.09%, 6/23) predominating. Co-infections with other enteric pathogens occurred in 65.2% of positive cases. Resistance rates were notably high for ampicillin/ampicillin-sulbactam (78.26%), nalidixic acid (56.52%), and ertapenem (21.73%), and 65.21% of isolates were multidrug-resistant. Genotypic-phenotypic concordance was robust, with &#x3b2;-lactamase genes ampS (60.87%) and blaCEPH-A3 (47.83%) being most prevalent. Strikingly, mcr-3.25 and mcr-3.3, which belong to the mcr family (originally described as mobile colistin resistance genes), were identified in 8.70% of isolates, exhibiting perfect correlation with phenotypic resistance. Plasmer analysis suggested both mcr genes to be chromosomally encoded. Comparative genomic analysis of virulence-associated genes revealed striking species-specific specialization: A. veronii predominantly carried complete T3SS clusters (61.5%), A. caviae and Aeromonas enteropelogenes were enriched in T6SS genes, and a single A. dhakensis isolate possessed an extensive arsenal including T3SS, T6SS, and a full RTX toxin cluster. MLST resolved the 23 isolates into 22 sequence types, 18 of which were novel. Phylogenetic reconstruction identified a tight monophyletic cluster of three A. veronii isolates (9-27 SNP differences) recovered within a 96-h window, suggestive of a potential cluster that warrants further epidemiological investigation. Comparative genomic analysis of the rare species Aeromonas allosaccharophila demonstrated that the Beijing clinical isolate S14 differs from the U.S. clinical strain ATCC 35942 by 42,099 SNPs, confirming its distinct genetic lineage. CONCLUSION: Collectively, this study delineates high genetic diversity, emerging chromosomal colistin resistance, and species-specific virulence specialization among Aeromonas isolates from diarrheal patients in Beijing. The detection of a potential outbreak cluster and a rare clinical isolate underscores the power of genomics-based surveillance for detecting and mitigating foodborne pathogen threats.

Aeromonas↗
PubMed1999

Comparative genomic hybridization analysis of genetic alterations associated with malignant progression of meningioma.

Little is known about genetic alterations during malignant progression of meningioma. We used comparative genomic hybridization (CGH) in 20 patients (13 with typical, 4 with atypical and 3 with anaplastic meningiomas) to investigate the genetic pathway underlying the development of meningioma. Typical meningiomas displayed only a few genetic changes such as monosomy 22. Anaplastic meningiomas manifested more aberrations than typical meningiomas, frequently exhibiting losses of 1p, 2p, 6q, chromosome 10 and 14q, and gain of 20q, in addition to monosomy 22. The average number of alteration sites in each patient with typical meningioma was significantly less than those in each patient with atypical (p < 0.01) and with anaplastic meningioma (p < 0.05). Anaplastic meningiomas showed the chromosomal changes seen in atypical meningiomas together with other aberrations. These CGH findings suggest that losses of 1p, 2p, 6q, chromosome 10 and 14q, and gain of 20q are genetic changes implicated in the malignant progression of meningioma.

Adult↗
PubMed2004

[Comparative genomic hybridization analysis of nasopharyngeal carcinoma drug-resistant cell CNE2/DDP and its parent cell CNE2].

BACKGROUND & OBJECTIVE: Developed from fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH) is a new molecular and cellular technique,used to examine the genomic imbalances,especially the loss and amplification of chromosomes,and to locate these alterations in certain chromosome regions. For a comprehensive understanding of the possible differences in genomic DNA between nasopharyngeal carcinoma drug-resistant and drug-sensitive cells, we analyzed the genomic DNA of a nasopharyngeal carcinoma drug-resistant cell line CNE2/DDP and its parent cell line CNE2 with CGH. METHODS: Genomic DNA was extracted from CNE2/DDP and CNE2 cells, as well as from normal placenta tissue. Fluorescent random primed labeling method was used to label the DNA probes (CNE2 and CNE2/DDP cells with green fluorescein-12-dUTP and normal placenta tissue with red tetramethylrhodamine-5-dUTP). The labeled DNA probes were then co-hybridized with normal lymphocyte metaphase chromosomes. Signals were taken by charge coupled device (CCD) and processed with Quips CGH Program after fluorescent hybridization. The green-to-red fluorescent ratio was calculated automatically and showed with graphs. RESULTS: There were extensive chromosome changes in CNE2, mainly the gain of 1q, 3q, 5p, 6p, 7p, 8q, 9q, 11p, 12q and 19q, and the loss of 4q, 12p, 13p, 14p, 15p, 18, 20q, 21p and 22. However, the CNE2/DDP cells, which come from the CNE2, showed a relatively normal karyotype except loss of 8p and gain of 8q and 19q. Consistent result was achieved after the CNE2/DDP cells were cultured in the medium free of any drugs for over one month. It appears that the CNE2/DDP cell has relative normal and much more stable chromosome constitution than its parent CNE2 cell. CONCLUSION: The CNE2/DDP is a single drug-resistant clone selected from CNE2,which is a blend of sub-clones that have different sorts of chromosome number and structure. It strongly suggests that the appearance of tumor drug-resistance is mainly a select process in which the would-be drug-resistant cell clone be selected from unfavorable survival condition.

Cell Line, Tumor↗
PubMed2006

Psittacid herpesvirus 1 and infectious laryngotracheitis virus: Comparative genome sequence analysis of two avian alphaherpesviruses.

Psittacid herpesvirus 1 (PsHV-1) is the causative agent of Pacheco's disease, an acute, highly contagious, and potentially lethal respiratory herpesvirus infection in psittacine birds, while infectious laryngotracheitis virus (ILTV) is a highly contagious and economically significant avian herpesvirus which is responsible for an acute respiratory disease limited to galliform birds. The complete genome sequence of PsHV-1 has been determined and compared to the ILTV sequence, assembled from published data. The PsHV-1 and ILTV genomes exhibit similar structural characteristics and are 163,025 bp and 148,665 bp in length, respectively. The PsHV-1 genome contains 73 predicted open reading frames (ORFs), while the ILTV genome contains 77 predicted ORFs. Both genomes contain an inversion in the unique long region similar to that observed in pseudorabies virus. PsHV-1 is closely related to ILTV, and it is proposed that it be assigned to the Iltovirus genus. These two avian herpesviruses represent a phylogenetically unique clade of alphaherpesviruses that are distinct from the Marek's disease-like viruses (Mardivirus). The determination of the complete genomic nucleotide sequences of PsHV-1 and ILTV provides a tool for further comparative and functional analysis of this unique class of avian alphaherpesviruses.

Amino Acid Sequence↗
PubMed2004

[Comparative genomic hybridization analysis of laryngeal carcinoma].

In order to find out the genes involved in the tumorigenesis of laryngeal carcinoma, we analyzed 18 laryngeal carcinoma with comparative genomic hybridization. Results show that each one has different degree of variances, included gains and losses of partial and whole chromosome. Each case has 12.9 abnormal regions averagely; losses are more than gains, equal to 7.2 and 5.7 per case respectively. Main regions are gains in chromosomes 3q (78%), 5p (61%), 11q (56%), 1q (50%), 8p (44%), 8q (39%) and 15q (39%), and losses of 3p (70%), 5q (78%), 9p (67%), 13q (50%), 1p (44%) and 14q (39%). There are many specific gains and losses in several chromosomes,especially the increase of copy number karyotype in 1p13-21(8/18), 3p21-23 (14/18), 5p21-22 (14/18), 9p12-pter (10/18) and 13q21-31 (8/18), while the decrease in 1q11-21 (11/18), 3q15-21 (12/18), 8p22-24 (6/18), 11q12-13 (8/18), 15q21-23 (7/18), 18p11 (8/18) are the characteristic varieties. These results suggest that there are oncogene, tumor suppressor gene and other associated genes involved in the tumorigenesis.

Acid Anhydride Hydrolases↗
PubMed2005

Microarray comparative genomic hybridisation analysis of intraocular uveal melanomas identifies distinctive imbalances associated with loss of chromosome 3.

Defining regions of genomic imbalance can identify genes involved in tumour development. Conventional cytogenetics has identified several nonrandom copy number alterations (CNA) in uveal melanomas (UVM), which include monosomy 3, chromosome 6 abnormalities and gain of 8q. To gain further insight into the CNAs and define the regions involved more precisely we analysed 18 primary UVMs using 1 Mb BAC microarray comparative genomic hybridisation (CGH). Our analysis showed that the most common genomic imbalances were 8q gain (78%), 6p gain (67%) and monosomy 3 (56%). Two distinct CGH profiles could be delineated on the basis of the chromosome 3 status. The most common genetic changes in monosomy 3 tumours, in our study, were gain of 8q11.21-q24.3, 6p25.1-p21.2, 21q21.2-q21.3 and 21q22.13-q22.3 and loss of 1p36.33-p34.3, 1p31.1-p21.2, 6q16.2-q25.3 and 8p23.3-p11.23. In contrast, disomy 3 tumours showed recurrent gains of only 6p25.3-p22.3 and 8q23.2-q24.3. Our approach allowed definition of the smallest overlapping regions of imbalance, which may be important in the development of UVM.

Adult↗
PubMed2003

Comparative genomic hybridization analysis of bilateral hyperplasia of usual type of the breast.

Hyperplasia of usual type (HUT) is part of the spectrum of benign proliferative disease in the breast and confers an increased risk of developing invasive cancer. Its role as a putative precursor of invasive ductal carcinomas in the breast is, however, controversial. HUT is occasionally seen bilaterally but it is not clear whether there is a genetic predisposition to the process. This study has analysed 14 cases of bilateral HUT in the breast (28 independent lesions) by comparative genomic hybridization (CGH) analysis to define DNA copy number changes and to investigate any commonality in these genetic alterations. The mean number of alterations seen was 1.6 (46/28) in all lesions, with common losses at chromosomes 1p, 16p, 17q, and 22q. Bilaterally, only five alterations were seen in common across both lesions in both breasts, but no single locus was altered preferentially. These data indicate that a proportion of HUT in the breast are indeed clonal, neoplastic proliferations which exhibit genetic alterations in common with invasive breast cancer, albeit at very low levels. The limited data from these experiments do not reveal a specific predisposition locus.

Breast↗
PubMed2005

Array comparative genomic hybridization analysis of uterine leiomyosarcoma.

PURPOSE: Using a genome-wide array-based comparative genomic hybridization (array-CGH), DNA copy number changes in uterine leiomyosarcoma were analyzed. MATERIALS AND METHODS: We analyzed 4 cases of uterine leiomyoma and 7 cases of uterine leiomyosarcoma. The paraffin-fixed tissue samples were microdissected under microscope and DNA was extracted. Array-based CGH and fluorescence in situ hybridization (FISH) were carried out with Genome database (Gene Ontology). RESULTS: Uterine leiomyoma showed no genetic alterations, while all of 7 cases of uterine leiomyosarcoma showed specific gains and losses. The percentage of average gains and losses were 4.86% and 15.1%, respectively. The regions of high level of gain were 7q36.3, 7q33-q35, 12q13-12q15, and 12q23.3. And the regions of homozygous loss were 1p21.1, 2p22.2, 6p11.2, 9p21.1, 9p21.3, 9p22.1, 14q32.33, and 14q32.33 qter. There were no recurrent regions of gain, but recurrent regions of loss were 1p21.1-p21.2, 1p22.3-p31.1, 9p21.2-p22.2, 10q25-q25.2, 11q24.2-q25, 13q12-q12.13, 14q31.1-q31.3, 14q32.32-q32.33, 15q11-q12, 15q13-q14, 18q12.1-q12.2, 18q22.1-q22.3, 20p12.1, and 21q22.12-q22.13. In the high level of gain regions, BAC clones encoded HMGIC, SAS, MDM2, TIM1 genes. Frequently gained BAC clone-encoded genes were TIM1, PDGFR-beta, REC Q4, VAV2, FGF4, KLK2, PNUTL1, GDNF, FLG, EXT1, WISP1, HER-2, and SOX18. The genes encoded by frequently lost BAC clones were LEU1, ERCC5, THBS1, DCC, MBD2, SCCA1, FVT1, CYB5, and ETS2/E2. A subset of cellular processes from each gene was clustered by Gene Ontology database. CONCLUSION: Using array-CGH, chromosomal aberrations related to uterine leiomyosarcoma were identified. The high resolution of array-CGH combined with human genome database would give a chance to find out possible target genes present in the gained or lost clones.

Adult↗
PubMed2005

Array-based comparative genomic hybridization analysis of recurrent chromosome 15q rearrangements.

Genomic rearrangements of chromosome 15q11-q13 cause diverse phenotypes including autism, Prader-Willi syndrome (PWS), and Angelman syndrome (AS). This region is subject to genomic imprinting and characterized by complex combinations of low copy repeat elements. Prader-Willi and Angelman syndrome are caused primarily by 15q11-13 deletions of paternal and maternal origin, respectively. Autism is seen with maternal, but not paternal, interstitial duplications. Isodicentric 15q, most often of maternal origin, is associated with a complex phenotype often including autistic features. Limitations of conventional cytogenetic tests preclude a detailed analysis in most patients with 15q rearrangements. We have developed a microarray for comparative genomic hybridization utilizing 106 genomic clones from chromosome 15q to characterize this region. The array accurately localized all breakpoints associated with gains or losses on 15q. The results confirmed the location of the common breakpoints associated with interstitial deletions and duplications. The majority of idic(15q) chromosomes are comprised of symmetrical arms with four copies of the breakpoint 1 to breakpoint 5 region. Patients with less common breakpoints that are not distinguished by routine cytogenetic methods were more accurately characterized by array analysis. This microarray provides a detailed characterization for chromosomal abnormalities involving 15q11-q14 and is useful for more precise genotype-phenotype correlations for autism, PWS, AS, and idic(15) syndrome.

Chromosome Aberrations↗
PubMedDate not supplied

Genomic profiles in stage I primary non small cell lung cancer using comparative genomic hybridization analysis of cDNA microarrays.

To investigate the genomic aberrations that are involved in lung tumorigenesis and therefore may be developed as biomarkers for lung cancer diagnosis, we characterized the genomic copy number changes associated with individual genes in 14 tumors from patients with primary non small cell lung cancer (NSCLC). Six squamous cell carcinomas (SQCAs) and eight adenocarcinomas (ADCAs) were examined by high-resolution comparative genomic hybridization (CGH) analysis of cDNA microarray. The SQCAs and ADCAs shared common frequency distributions of recurrent genomic gains of 63 genes and losses of 72 genes. Cluster analysis using 57 genes defined the genomic differences between these two major histologic types of NSCLC. Genomic aberrations from a set of 18 genes showed distinct difference of primary ADCAs from their paired normal lung tissues. The genomic copy number of four genes was validated by fluorescence in situ hybridization of 32 primary NSCLC tumors, including those used for cDNA microarray CGH analysis; a strong correlation with cDNA microarray CGH data emerged. The identified genomic aberrations may be involved in the initiation and progression of lung tumorigenesis and, most importantly, may be developed as new biomarkers for the early detection and classification of lung cancer.

Adenocarcinoma↗
PubMed1999

[Comparative genomic hybridization analysis of primary gastric carcinomas].

OBJECTIVE: To investigate whether unknown genes are involved in the tumorigenesis of gastric cancer. METHODS: Fourty-three primary gastric carcinomas were analyzed by comparative genomic hybridization(CGH). RESULTS: A gain in chromosome 3p(8/43), 8q(8/43), 20[20(9/43), 20p(7/43), 20q(4/43)], 12q (16/43), and 13q(12/43) was observed while a loss of 19[19(15/43), 19p (13/43)], 17[17(8/43), 17p(10/43)], 16(10/43) and 1p(11/43) was discovered. CONCLUSION: There were characteristic changes in 3p, 8q, 20, 12q, 13q, 19, 17, 16, and 1p in gastric carcinoma, and some unknown genes located in the above regions might be of importance to gastric carcinoma pathogenesis.

Chromosome Aberrations↗
PubMed2006

Chromosomal imbalances in nasopharyngeal carcinoma: a meta-analysis of comparative genomic hybridization results.

Nasopharyngeal carcinoma (NPC) is a highly prevalent disease in Southeast Asia and its prevalence is clearly affected by genetic background. Various theories have been suggested for its high incidence in this geographical region but to these days no conclusive explanation has been identified. Chromosomal imbalances identifiable through comparative genomic hybridization may shed some light on common genetic alterations that may be of relevance to the onset and progression of NPC. Review of the literature, however, reveals contradictory results among reported findings possibly related to factors associated with patient selection, stage of disease, differences in methodological details etc. To increase the power of the analysis and attempt to identify commonalities among the reported findings, we performed a meta-analysis of results described in NPC tissues based on chromosomal comparative genomic hybridization (CGH). This meta-analysis revealed consistent patters in chromosomal abnormalities that appeared to cluster in specific "hot spots" along the genome following a stage-dependent progression.

Journal Article↗
PubMed1995

Comparative genomic hybridization analysis of human sarcomas: I. Occurrence of genomic imbalances and identification of a novel major amplicon at 1q21-q22 in soft tissue sarcomas.

Comparative genomic hybridization (CGH) was recently developed as a tool to survey entire genomes for variations in DNA sequence copy numbers. We have applied this technique to detect and map amplified regions in 54 soft tissue sarcomas. Aberrations were detected by visual analysis of hybridizations or contrast-enhanced digital images, followed by quantitative digital ratio imaging of the aberrant chromosomes. Several tumors showed increased DNA sequence copy number at 12q14, as expected. However, CGH analysis detected amplification of 12q14 also in some tumors where neither MDM2 nor CDK4 was amplified, suggesting that another as yet unknown gene(s) may drive amplification of this region in sarcomas. Furthermore, a novel recurring amplicon was detected at 1q21-q22. DNA amplifications coinciding with this segment were as frequent as those observed for 12q14, indicating that 1q21-q22-linked gene(s) may also play an important role in the development and/or progression of human soft tissue sarcomas.

Animals↗
PubMed1999

Assessment of genetic changes in hepatocellular carcinoma by comparative genomic hybridization analysis: relationship to disease stage, tumor size, and cirrhosis.

Hepatocellular carcinoma (HCC) is a common and highly malignant tumor that is prevalent in Southeast Asia. Although the etiological factors associated are now well recognized, the interactions between individual factors and the molecular mechanisms by which they lead to cancer remain unclear. Cytogenetic analysis on HCC has been limited because of poor hepatocyte growth in vitro. The recently developed technique of comparative genomic hybridization (CGH), however, permits screening of the entire genome without the need of cell culture. CGH was applied to the study of genomic aberrations in 67 surgically resected samples of HCC, 3 of adenomatous hyperplasia (AH), and 12 of nontumorous cirrhotic liver surrounding the tumors. All samples were from patients of a racially and etiologically homogeneous population in Southern China, where chronic hepatitis B virus infection is the main etiological factor. CGH analysis of the HCC samples revealed frequent copy number gain of 1q (48/67 cases, 72%), 8q (32/67 cases, 48%), 17q (20/67 cases, 30%), and 20q (25/67 cases, 37%) and common losses on 4q (29/67 cases, 43%), 8p (25/67 cases, 37%), 13q (25/67 cases, 37%), and 16q (20/67 cases, 30%). Our finding of a high incidence of 1q gain strongly suggested this aberration was associated with the development of HCC. Genomic abnormalities were detected in 1 of the 3 AH specimens but absent in all 12 cirrhotic tissues surrounding the tumor. Clinical staging classified 3/67 HCC cases as T1, 53 cases as T2, and 11 cases as T3. No significant difference in the pattern of genomic imbalances was detected between stages T2 and T3. A significant copy number loss of 4q11-q23 was, however, identified in those tumors larger than 3 cm in diameter. Of particular interest was the identification of 8q copy number gain in all 12 cases of HCC that arose in a noncirrhotic liver, compared with only 20/55 cases in HCC arising in a cirrhotic liver. We suggest that 8q over-representation is likely associated with a growth advantage and proliferative stimulation that have encouraged malignant changes in the noncirrhotic human liver.

Adult↗
PubMed2001

Comparative genomic hybridization analysis of nasopharygeal carcinoma: consistent patterns of genetic aberrations and clinicopathological correlations.

To define the patterns of genetic imbalances in nasopharyngeal carcinoma (NPC), we studied 30 primary NPC tumors with comparative genomic hybridization (CGH). The common sites of chromosomal gains were found in descending order of frequency in 12p11.2-p12 (36%), 12q14-q21 (33%), 2q24-q31 (23%), 1q31-qter (20%), 3q13 (20%), 1q13.3 (20%), 5q21 (17%), 6q14-q22 (13%), 7q21 (13%), 8q11.2-q23 (13%) and 18q12-qter (13%). The common sites of chromosomal loss were at 3p14-p21 (20%), 11q23-qter (20%), 16q21-qter (17%) and 14q24-qter (13%). Correlation with clinicopathologic features showed that 3p loss was associated with a significantly higher risk of death related to recurrence as compared with patients without 3p loss (50% vs. 9%, P=.029). The presence of 16q loss was associated with more advanced stage tumors (stages I & II: 6% vs. stages III & IV: 33%, P=.046). We conclude that consistent patterns of genetic imbalances can be observed in NPC. Deletion of 3p and 16q were associated with higher risk of tumor recurrence and advanced stage cancer.

Chromosome Aberrations↗
PubMed2000

Comparative genomic hybridization analysis of 38 breast cancer cell lines: a basis for interpreting complementary DNA microarray data.

Breast cancer cell lines provide a useful starting point for the discovery and functional analysis of genes involved in breast cancer. Here, we studied 38 established breast cancer cell lines by comparative genomic hybridization (CGH) to determine recurrent genetic alterations and the extent to which these cell lines resemble uncultured tumors. The following chromosomal gains were observed: 8q (75%), 1q (61%), 20q (55%), 7p (44%), 3q (39%), 5p (39%), 7q (39%), 17q (33%), 1p (30%), and 20p (30%), and the most common losses were: 8p (58%), 18q (58%), 1p (42%), Xp (42%), Xq (42%), 4p (36%), 11q (36%), 18p (33%), 10q (30%), and 19p (28%). Furthermore, 35 recurrent high-level amplification sites were identified, most often involving 8q23 (37%), 20q13 (29%), 3q25-q26 (24%), 17q22-q23 (16%), 17q23-q24 (16%), 1p13 (11%), 1q32 (11%), 5p13 (11%), 5p14 (11%), 11q13 (11%), 17q12-q21 (11%), and 7q21-q22 (11%). A comparison of DNA copy number changes found in the cell lines with those reported in 17 published studies (698 tumors) of uncultured tumors revealed a substantial degree of overlap. CGH copy number profiles may facilitate identification of important new genes located at the hotspots of such chromosomal alterations. This was illustrated by analyzing expression levels of 1236 genes using cDNA microarrays in four of the cell lines. Several highly overexpressed genes (such as RCH1 at 17q23, TOPO II at 17q21-q22, as well as CAS and MYBL2 at 20q13) were involved in these recurrent DNA amplifications. In conclusion, DNA copy number profiles were generated by CGH for most of the publicly available breast cancer cell lines and were made available on a web site (http://www.nhgri.nih.gov/DIR/CGB/++ +CR2000). This should facilitate the correlative analysis of gene expression and copy number as illustrated here by the finding by cDNA microarrays of several overexpressed genes that were amplified.

Breast Neoplasms↗
PubMed2004

Comparative genomic hybridization analysis of pediatric adamantinomatous craniopharyngiomas and a review of the literature.

OBJECT: The purpose of this study was to examine chromosomal gains and losses in 11 pediatric adamantinomatous craniopharyngiomas by using comparative genomic hybridization (CGH), as well as to review the cytogenetic literature that has contributed to the characterization of these tumors. One source of confusion in the cytogenetic and CGH literature concerning craniopharyngioma is that the authors of most studies fail to distinguish between pediatric and later-onset forms of the disease. Thus, this study was focused on pediatric craniopharyngioma. METHODS: To determine an overview of the genetic events leading to the development of these tumors, 10 adamantinomatous craniopharyngiomas were analyzed using CGH; none of the tumor specimens demonstrated gains or losses of DNA sequence. CONCLUSIONS: In view of these findings as well as those published in the majority of previous cytogenetic studies of craniopharyngiomas, the authors conclude that the recurrent acquisition of chromosomal imbalances does not play a major role in tumorigenesis and that chromosomal gains and losses are a relatively rare event in primary tumors of pediatric origin.

Adolescent↗