Chromosomal Comparative Genomic Hybridization Research Articles

Microarray comparative genomic hybridization detection of chromosomal imbalances in uterine cervix carcinoma

BackgroundChromosomal Comparative Genomic Hybridization (CGH) has been applied to all stages of cervical carcinoma progression, defining a specific pattern of chromosomal imbalances in this tumor. However, given its limited spatial resolution, chromosomal CGH has offered only general information regarding the possible genetic targets of DNA copy number changes.MethodsIn order to further define specific DNA copy number changes in cervical cancer, we analyzed 20 cervical samples (3 pre-malignant lesions, 10 invasive tumors, and 7 cell lines), using the GenoSensor microarray CGH system to define particular genetic targets that suffer copy number changes.ResultsThe most common DNA gains detected by array CGH in the invasive samples were located at the RBP1-RBP2 (3q21-q22) genes, the sub-telomeric clone C84C11/T3 (5ptel), D5S23 (5p15.2) and the DAB2 gene (5p13) in 58.8% of the samples. The most common losses were found at the FHIT gene (3p14.2) in 47% of the samples, followed by deletions at D8S504 (8p23.3), CTDP1-SHGC- 145820 (18qtel), KIT (4q11-q12), D1S427-FAF1 (1p32.3), D9S325 (9qtel), EIF4E (eukaryotic translation initiation factor 4E, 4q24), RB1 (13q14), and DXS7132 (Xq12) present in 5/17 (29.4%) of the samples.ConclusionOur results confirm the presence of a specific pattern of chromosomal imbalances in cervical carcinoma and define specific targets that are suffering DNA copy number changes in this neoplasm.

Copy number gains on 22q13 in adenoid cystic carcinoma of the salivary gland revealed by comparative genomic hybridization and tissue microarray analysis

Adenoid cystic carcinoma (ACC) of the salivary gland is a neoplasm characterized by slow but inevitable local progression and terminal hematogenous metastasis. To detect novel imbalanced chromosomal regions associated with tumorigenesis, we used chromosomal comparative genomic hybridization to screen 27 ACC. The most common aberration was copy number gain of 22q13 (nine cases) followed by gains of 16p (seven cases) and 17q (four cases) and copy number losses on 6q (six cases). To further delineate the prevalence of 22q13 copy number gains in ACC, fluorescence in situ hybridization was performed for five bacterial/phage artificial chromosome (BAC/PAC) probes from the 22q13 consensus region with 57 ACC on a tissue microarray. The overall prevalence of copy number gains on 22q13 was 30% of the tumors in the fluorescence in situ hybridization analysis, irrespective of histologic differentiation (cribriform/tubular vs. solid) or tumor event (primary vs. recurrent). We therefore assume that copy number gain of 22q13 is a novel frequent finding in ACC that may be involved in the initial pathogenesis of this neoplasm by proto-oncogene activation.

Clinical Outcome Correlations of Genomic Gains and Losses in Diffuse Large B-Cell Lymphoma by Array-CGH.

Conventional karyotype and chromosomal comparative genomic hybridization (CGH) studies of diffuse large B-cell lymphoma (DLBCL) have revealed few chromosomal abnormalities associated with outcome. In order to evaluate the association between genomic copy number changes in DLBCL and clinical outcome at a higher resolution, we assayed a panel of 64 newly-diagnosed DLBCL specimens by array-CGH. For each specimen, the respective patient had a known response to anthracycline-based therapy, and the median follow-up was 5-years. Forward and reverse hybridizations were performed for all specimens to avoid dye-bias, using BAC/PAC arrays with 1-4 Mb resolution coverage of the genome (Spectral Genomics). After customized normalization, the circular binary segmentation (CBS) algorithm was used to identify regional copy number changes along each chromosome in each specimen. Of the 64 specimens, 59 (92%) displayed regional copy number changes. The frequency of gain/loss of each clone for all 64 specimens was then calculated based on the CBS results, and, additionally, based on singleton clone changes if they were outside of CBS-defined regions. Clones displaying change ≥ in 10% of specimens for at least two contiguous clones were further considered as recurrent sites for clinical correlations. 27 sites of recurrent gain and 25 sites of recurrent loss were identified. Association between loss or gain of sites and International Prognostic Index (IPI) were evaluated using Fisher's exact test, and associations between loss or gain of sites and time to treatment failure (TTF) and overall survival (OS) were tested using the log-rank test. Table 1 lists the sites as independent markers that were significant at p < 0.05. Of these sites, five (with asterisk) were found to significantly predict outcome after stratifying by IPI using the stratified log-rank test. It is noted that 6 of the sites were 5 Mb or less in size, facilitating the identification of target genes. Losses of chromosome 7 (8–13 Mb) and chromosome 13 (56.7–63 Mb) were found to contribute to IPI prediction of outcome, but were not significantly associated with clinical features as independent markers. In summary, array-CGH has lead to the identification of several genetic markers with prognostic significance in DLBCL, which in some cases are of a size amenable for target gene identification.Significant Genetic Markers Associated with Clinical OutcomeChrom.Start (Mb)End (MB)Change# of casesIPITTFOS178.279.1Loss19Better22.44.1Loss8Worse*30.272.3Gain14BetterBetter3101.3136Gain18LowBetter3154.7188.7Gain18LowBetterBetter662.2170.5Loss32LowBetterBetter718.819.2Loss11Better*98.313Loss13Better983.996.3Gain9Better9122.1132.8Gain12BetterBetter*120133.3Gain31High160.14.7Gain13Better1633.835.6Loss7Worse*Worse*1943.163.7Gain13BetterBetter

Defining minimum genomic regions of imbalance involved in testicular germ cell tumors of adolescents and adults through genome wide microarray analysis of cDNA clones.

Identifying changes in DNA copy number can pinpoint genes that may be involved in tumor development. Here we have defined the smallest overlapping regions of imbalance (SORI) in testicular germ cell tumors other than the 12p region, which has been previously investigated. Definition of the regions was achieved through comparative genomic hybridization (CGH) analysis of a 4559 cDNA clone microarray. A total of 14 SORI were identified, which involved at least five of the 11 samples analysed. Many of these refined regions were previously reported using chromosomal or allelic imbalance studies. The SORI included gain of material from the regions 4q12, 17q21.3, 22q11.23 and Xq22, and loss from 5q33, 11q12.1, 16q22.3 and 22q11. Comparison with parallel chromosomal CGH data supported involvement of most regions. The various SORI span between one and 20 genes and highlight potential oncogenes/tumor suppressor genes to be investigated further.

High-Resolution Analysis of Gene Copy Number Alterations in Human Prostate Cancer Using CGH on cDNA Microarrays: Impact of Copy Number on Gene Expression

Identification of target genes for genetic rearrangements in prostate cancer and the impact of copy number changes on gene expression are currently not well understood. Here, we applied high-resolution comparative genomic hybridization (CGH) on cDNA microarrays for analysis of prostate cancer cell lines. CGH microarrays identified most of the alterations detected by classical chromosomal CGH, as well as a number of previously unreported alterations. Specific recurrent regions of gain (28) and loss (18) were found, their boundaries defined with sub-megabasepair accuracy. The most common changes included copy number decreases at 13% and gains at iq and 5p. Refined mapping identified several sites, such as at 13q (33-44, 49-51, 74-76 Mbp from the p-telomere), which matched with minimal regions of loss seen in extensive loss of heterozygosity mapping studies of large numbers of tumors. Previously unreported recurrent changes were found at 2p, 2q, 3p, 17q (losses), at 3q, 5p, 6p (gains). Integration of genomic and transcriptomic data revealed the role of individual candidate target genes for genomic alterations as well as a highly significant (P < .0001) overall association between copy number levels and the percentage of differentially expressed genes. Across the genome, the overall impact of copy number on gene expression levels was, to a large extent, attributable to low-level gains and losses of copy number, corresponding to common deletions and gains of often large chromosomal regions.

Clustering of Molecular Alterations in Gastroesophageal Carcinomas

Gene expression levels are regulated at many levels. Integration of genome-wide analyses for the study of DNA and RNA provides a unique tool to detect genetic alterations in the cancer genome. In this study, we generated and integrated DNA amplification data from comparative genomic hybridization (CGH) and serial analyses of gene expression (SAGE) in order to obtain a molecular profile of gastroesophageal junction (GEJ) carcinomas. DNA amplifications mapped to specific chromosomal regions and were frequently seen at 1 q, 4q, 5q, 6p, 7p, 8q, 17q, and 20q. Using SAGE, we obtained over 156,432 tags from GEJ adenocarcinomas and normal gastric mucosa. These tags were assigned to UniGene clusters. Chromosomal positions for overexpressed genes were obtained to produce a GEJ carcinoma transcriptome map. A total of 123 genes was significantly overexpressed (more than fivefold; P<.011) in one or more SAGE libraries. This gene overexpression map was integrated and compared to the chromosomal CGH ideogram. Several chromosomal arms that had frequent DNA amplifications showed frequent gene expression alterations such as chromosomes 1 (15 genes), 2 (9 genes), 6 (6 genes), 11 (6 genes), 12 (8 genes), and 17 (13 genes). Despite the relatively large DNA amplification regions, overexpressed genes frequently mapped and clustered to small chromosomal regions at early-replicating (Giemsa light) bands such as 1q21.3 (nine genes), 6p21.3 (five genes), and 17q21 (eight genes). These results provide a comprehensive tool to search for DNA amplifications and overexpressed genes in GEJ carcinoma. The observed phenomenon of the presence of large amplification areas, yet clustering of overexpressed genes to relatively small loci, may suggest a high organization of chromatin and cancer-related genes in the nucleus.

Genetic characterization of bone and soft tissue tumors.

21 During the last 20 years, genetic analyses of bone and soft tissue tumors (BSTT) have revealed that most histopathologic entities investigated in sufficient detail are characterized by acquired, clonal chromosome aberrations. Many of these rearrangements are nonrandom and several of them are strongly associated with specific histo pathologic tumor subtypes. Cytogenetic studies using chromosome banding techniques have been an important first mapping step that has guided further efforts to identify mutations at the gene level by fluorescence in situ hybridization (FISH), reverse-transcriptase polymerase chain reaction (RT-PCR) and other molecular techniques. Chromosomal comparative genomic hybridization (CGH), and more recently CGH microarray techniques, have revealed many specific ampli cons in various sarcomas. The strong association between chromosome or gene rearrangements and tumor subtype has more and more been exploited to aid the diagnostic work. Less conclusive data are available as regards the role of genetic aberrations for disease progression, but there are reports indicating that some genetic changes may provide prognostically important information. Even less is known about the origin of chromosome mutations and the relation between genetic aberrations and abnormal cellular processes associated with tumorigenesis.

Chromosomal comparative genomic hybridization abnormalities in early- and late-onset human breast cancers: correlation with disease progression and TP53 mutations

Nearly 30% of the breast cancer patients in the Taiwanese community have their diseases diagnosed before the age of 40. Their 5-year survival rate is poorer than that of their late-onset breast cancer counterparts. Genomic abnormalities between these two breast cancer age groups were compared using comparative genomic hybridization (CGH) analyses. The sample set was made up of 44 early-onset (<35 years old) and 54 late-onset cases (>63 years old). Frequent CGH changes were noted, such as gains on 8q, 1q, and 17q and losses on 16q, 17p, and 8p. These were very similar for the two age groups, as well as for Taiwanese women and other ethnic populations. In contrast, several less common lesions, such as gains on 16p and 8p and losses on 11q and 9p, were significantly different between the early- and late-onset breast tumors. In addition, more profound chromosomal changes were consistently associated with the more advanced-stage tumors, and less expression of the estrogen and the progesterone receptors, and of HER-2/neu. About 19% of the breast cancers examined carried a TP53 mutation in exons 4–9. Of these, 88% (15/17) were missense point mutations and these were distributed randomly along the tested gene fragments without apparent clustering, as has been shown in certain other ethnic or regional studies. On average, patients carrying these TP53 mutations had 9.5 CGH lesions per case, compared to only 2.8 changes in samples that had no TP53 mutation. Our results indicate that certain genomic lesions, especially 11q loss, may play a role in early-onset breast tumor formation, and that combined use of genomic patterns and molecular targets may provide a useful tool for diagnostic, therapeutic, and prognostic purposes.

Hidden gene amplifications in aggressive B-cell non-Hodgkin lymphomas detected by microarray-based comparative genomic hybridization.

DNA amplifications are important mechanisms for proto-oncogene activation. Comparative genomic hybridization (CGH) to metaphase chromosome preparations has revealed amplifications in 10-20% of B-cell lymphomas (B-NHL). We analysed a series of 16 aggressive non-Hodgkin lymphomas by the new approach termed Matrix-CGH (M-CGH) using genomic DNA microarrays as hybridization target. For M-CGH, a dedicated B-cell lymphoma chip was constructed containing 496 genomic targets covering oncogenes, tumor suppressor genes as well as chromosome regions frequently altered in B-NHL. In 10 of 16 samples a total of 15 DNA amplifications were identified. The amplicons included BCL2, REL, CCND1, CCND2, JAK2, FGF4 and MDM2. Four of the 15 amplifications remained undetected by chromosomal CGH. The respective amplicons mapped to bands 2p13, 9p13-p21 and 12q24 and, were confirmed by fluorescence in situ hybridization. Furthermore, for four genomically amplified genes real-time quantitative reverse transcription polymerase chain reaction revealed elevated mRNA expression levels. These data show the superior diagnostic sensitivity of the newly developed diagnostic tool. As only a small portion of the genome (approximately 1.5%) has been analysed by the present DNA array, it is likely that gene amplifications are much more common in aggressive lymphomas than previously assumed.

Genetic profiling of colorectal cancer liver metastases by combined comparative genomic hybridization and G‐banding analysis

The majority of genetic studies of colorectal carcinogenesis have focused on changes found in primary tumors. Despite the fact that liver metastases are a leading cause of colorectal cancer deaths, the molecular genetic basis of the advanced disease stages remains poorly understood. We performed comparative genomic hybridization (CGH) on 17 liver metastases from colorectal carcinomas and compared the quantitative profile with the qualitative profile previously obtained with chromosome banding. An average of 12.6 aberrations per tumor was found by CGH. Chromosome 18 and chromosome arms 4q, 8p, and 17p were most frequently lost, whereas chromosomes 7 and 20 and chromosome arms 6p, 8q, and 13q were most frequently gained. We compared the chromosome banding and CGH data after converting the karyotypes into net copy number gains and losses. Ten tumors showed agreement between the findings of the two techniques, whereas five tumors did not (in two cases, no mitotic cells were obtained for banding analysis). All five discordant cases had a "simple" abnormal or normal karyotype, but revealed multiple changes by CGH. A likely explanation for this discrepancy is that in vitro growth before G-banding selected against the cancer cells. Interestingly, by comparing the CGH profiles of the "complex" vs. the "simple"/normal karyotype groups, deletion of 8p and gain of 16q were seen more frequently in the former group. The liver metastases had the same aberrations as seen in primary colorectal carcinomas, summarized in a literature survey. However, these aberrations were seen more frequently in liver metastases, which may be attributable to increased genetic instability.

Automated Screening for Genomic Imbalances using Matrix-Based Comparative Genomic Hybridization

Genome-wide screening for chromosomal imbalances using comparative genomic hybridization (CGH) revealed a wealth of data on previously unrecognized tumor-specific genomic alterations. CGH to microarrays of DNA, an approach termed matrix-CGH, allows detection of genomic imbalances at a much higher resolution. We show that matrix CGH is also feasible from small tissue samples requiring universal amplification of genomic DNA. Because widespread application of matrix-CGH experiments using large numbers of DNA targets demands a high degree of automation, we have developed a protocol for a fully automated procedure. The use of specialized instrumentation for the generation of DNA chips, their hybridization, scanning, and evaluation required numerous alterations and modifications of the initial protocol. We here present the elaboration and testing of automated matrix-CGH. A chip consisting of 188 different genomic DNA fragments, cloned in bacterial artificial chromosome (BAC) or P1-derived artificial chromosome (PAC) vectors and immobilized in replicas of 10, was used to assess the performance of the automated protocol in determining the gene dosage variations in tumor cell lines COLO320-HSR, HL60, and NGP. Although ratios of matrix-CGH were highly concordant with results of chromosomal CGH (85%), the dynamic range of the matrix-CGH ratios was highly superior. Investigation of the two amplicons on 8q24 in COLO320-HSR and HL60, containing the MYC gene, revealed a homogeneous amplicon in COLO320-HSR but a heterogeneous amplification pattern in HL60 cells. Although control clones for normalization of the signal ratios can be predicted in cases with defined chromosomal aberrations, in primary tumors such data are often not available, requiring alternative normalization algorithms. Testing such algorithms in a primary high-grade B-cell lymphoma, we show the feasibility of this approach. With the matrix-CGH protocol presented here, robust and reliable detection of genomic gains and losses is accomplished in an automated fashion, which provides the basis for widespread application in tumor and clinical genetics.

Bacterial comparative genomic hybridization: a method for directly identifying lateral gene transfer

Horizontally transferred DNA is largely responsible for the dissemination of virulence traits amongst bacteria. Rapid identification of acquired DNA remains difficult as whole-genome sequencing of outbreak strains is impractical, and microarray-based approaches, while powerful, are limited to genes present only in the reference strains. Here we present a novel bacterial comparative genomic hybridization method that directly compares the genomes of related strains at sub-kilobase resolution in order to identify acquired DNA. Bacterial comparative genomic hybridization utilizes the concept of metaphase chromosome comparative genomic hybridization, and exploits the resolving power of two-dimensional DNA electrophoresis. Comparison of isogenic variants of the pathogen Pseudomonas aeruginosa detected a single-copy gene insertion responsible for gentamicin resistance.

Quantitative analysis of chromosomal CGH in human breast tumors associates copy number abnormalities with p53 status and patient survival.

We present a general method for rigorously identifying correlations between variations in large-scale molecular profiles and outcomes and apply it to chromosomal comparative genomic hybridization data from a set of 52 breast tumors. We identify two loci where copy number abnormalities are correlated with poor survival outcome (gain at 8q24 and loss at 9q13). We also identify a relationship between abnormalities at two loci and the mutational status of p53. Gain at 8q24 and loss at 5q15-5q21 are linked with mutant p53. The 9q and 5q losses suggest the possibility of gene products involved in breast cancer progression. The analytical techniques are general and also are applicable to the analysis of array-based expression data.

Hybridization to oligonucleotide arrays for the assessment of gene copy number

Array-based comparative genomic hybridization (CGH) provides a higher-resolution and more quantitative alternative to chromosome CGH for the assessment of abnormalities in genomic copy number. In array-based CGH analyses published to date, array elements have been composed of cloned DNA sequences (such as P1s, BACs or complementary DNAs), and thus copy number abnormalities can be mapped from data on the genomic mapping of such clones. These advanced methods are limited by difficulties in the production of cloned DNAs and distortions in the data arising from elements in the arrays that are present at multiple copies in the normal genome. To overcome some of these limitations, we have produced a low-complexity probe based on the polymerase chain reaction (PCR). In oligonucleotide array CGH, probes are prepared by multiplex PCR amplification using 10−50 primer pairs. Two 50-base oligonucleotides that map between the primer pairs serve as array elements. Because the linearity of this method apparently depends on primer complexity during PCR, we substituted adapter sequences (which make up the 5' end of our PCR primers). We compared the performances of T7 and R24 adapters in a 24-plex PCR with one another and with previously obtained copy number data on several chromosome 20 loci in MCF7 cells obtained from fluorescence in situ hybridization. We found that use of the T7 adapters improved the amplitude of test-to-reference ratios 2.3-fold, suggesting less-dampened ratios and increased linearity in our assessment of copy number by this method. We will demonstrate the large-scale application of oligonucleotide array CGH to ovarian and breast cancer samples.

Matrix-based comparative genomic hybridization: Biochips to screen for genomic imbalances

Comparative genomic hybridization (CGH) to metaphase chromosomes has been widely used for the genome-wide screening of genomic imbalances in tumor cells. Substitution of the chromosome targets by a matrix consisting of an ordered set of defined nucleic acid target sequences would greatly enhance the resolution and simplify the analysis procedure, both of which are prerequisites for a broad application of CGH as a diagnostic tool. However, hybridization of whole genomic human DNA to immobilized single-copy DNA fragments with complexities below the megabase pair level has been hampered by the low probability of specific binding because of the high probe complexity. We developed a protocol that allows CGH to chips consisting of glass slides with immobilized target DNAs arrayed in small spots. High-copy-number amplifications contained in tumor cells were rapidly scored by use of target DNAs as small as a cosmid. Low-copy-number gains and losses were identified reliably by their ratios by use of chromosome-specific DNA libraries or genomic fragments as small as 75 kb cloned in PI or PAC vectors as targets, thus greatly improving the resolution achievable by chromosomal CGH. The ratios obtained for the same chromosomal imbalance by matrix CGH and by chromosomal CGH corresponded very well. The new matrix CGH protocol provides a basis for the development of automated diagnostic procedures with biochips designed to meet clinical needs.

Comparative genomic hybridization and molecular cytogenetic characterization of two prostate cancer xenografts

Conventional cytogenetic analysis of two prostate tumor xenografts, LuCaP 23.1 and RP22090, was unsatisfactory for comprehensive genetic evaluation of the cell lines. Fluorescence in situ hybridization (FISH) for chromosome enumeration and comparative genomic hybridization (CGH) for numerical imbalance detection were performed and resulted in a more complete molecular cytogenetic characterization of these lines. Both xenografts were hypertriploid and had significant numerical imbalances. For example, LuCaP 23.1 had gain of all or part of chromosomes 3, 5, 6, 7, 8, 11, and 12 and the X chromosome and loss of all or part of chromosomes 2, 3 6, 8, 9, 10, 17, and 18. In RP22090, gain of all or part of chromosomes 5, 7, 8, 9, 10, 12, 14, and 15 was seen, whereas loss was seen for all or part of chromosomes 4, 6, 8, 15, 16, 17, 19, 20, and 22. Both xenografts reflect the high frequency of chromosomal changes seen in some late-stage prostate cancers, including many novel changes and some changes such as the loss of 8p and gain of 8q, which have been reported previously in primary and metastatic prostate cancers. Consistent changes in both lines, such as loss of chromosomes 6 and chromosome arm 8p and gain of chromosome 7 and chromosome arm 8q, may represent genetic events specific for prostate cancer development, but imbalances on other chromosomes such as 3, 9, 19, and 20, not frequently reported in prostate cancers, may reflect potentially important changes that should also be examined.