CGH and direct diagnosis of mosaic structural chromosomal abnormalities: description of a mosaic ring chromosome 17 and review of the literature

We report the characterisation of a de novo supernumerary chromosome marker in a mosaic state (50%) by comparative genomic hybridisation (CGH) in an 8-year-old child with hypotonia, dysmorphia and mild-to-moderate mental retardation. We describe the combined use of CGH and fluorescence in situ hybridisation (FISH) to identify the origin of the additional chromosomal material. Visual analysis of 10 CGH-metaphase spreads revealed a gain of green fluorescent signal on pericentromeric region of chromosome 17. The CGH finding was confirmed by FISH analysis using a whole chromosome 17 paint, a chromosome 17 centromeric probe and the probe coding for the Smith-Magenis locus in 17p11.2. These results show that performing both CGH and FISH in combination with classical karyotyping will certainly allow the identification of imbalanced chromosome rearrangements and, by the way, allow the identification of genes involved in mental retardation and/or malformative pathology.     

Imbalances of chromosome 17 in medulloblastomas determined by comparative genomic hybridisation and fluorescence in situ hybridisation.

AIMS: To investigate the status of chromosome 17 in a series of medulloblastomas using comparative genomic hybridisation (CGH) and fluorescence in situ hybridisation (FISH). METHODS: Frozen tissue and formalin fixed, paraffin was embedded tissue from 27 medulloblastomas were analysed by CGH and FISH, respectively. CGH ratio profiles for chromosome 17 were compared with the results of FISH, for which loss or gain of 17p or 17q was assessed in two distinct ways using a combination of differentially labelled subtelomeric and centromeric probes and analysing 200 nuclei in each tumour. RESULTS: CGH revealed imbalances consistent with isochromosome 17q in eight of 27 tumours. Either loss of 17p or gain of 17q was identified in a further nine tumours, whereas 10 tumours were apparently balanced. Using control results from preparations of paraffin wax embedded tonsils, thresholds for the detection of abnormalities by FISH were established, either by determining the dominant pattern of signals in each case, or the mean ratio of subtelomeric to centromeric signals. Results by CGH and FISH were concordant in 21 of 27 tumours. In the remainder, most discrepancies related to methodological differences. CONCLUSIONS: CGH has a role in disclosing common, genome wide chromosomal gains or losses in tumours, the clinical relevance of which can then be studied in large archival series of paraffin wax embedded tumours using FISH.     

Supernumerary ring chromosome in a Bednar tumor (pigmented dermatofibrosarcoma protuberans) is composed of interspersed sequences from chromosomes 17 and 22: a fluorescence in situ hybridization and comparative genomic hybridization analysis

Cytogenetic analysis of Bednar tumor (pigmented dermatofibrosarcoma protuberans) has not been reported previously. Here, we report the identification of a supernumerary ring chromosome in a Bednar tumor by chromosome painting with fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH). Chromosome painting with FISH demonstrated that the supernumerary ring chromosome was composed of discontinuous, interwoven sequences from chromosomes 17 and 22. Amplification of chromosomes 17 and 22 sequences was confirmed by CGH. These results indicate that Bednar tumor and dermatofibrosarcoma protuberans are characterized by the same chromosomal features. To our knowledge, this is the first report that the ring chromosome in Bednar tumor is composed of amplified material from chromosomes 17 and 22.     

Comparative genomic hybridisation in mentally retarded patients with dysmorphic features and a normal karyotype

Segmental aneusomy for small chromosomal regions has been shown to be a common cause of mental retardation and multiple congenital anomalies. A screening method for such chromosome aberrations that are not detected using standard cytogenetic techniques is needed. Recent studies have focused on detection of subtle terminal chromosome aberrations using subtelomeric probes. This approach however excludes significant regions of the genome where submicroscopic rearrangements are also liable to occur. The aim of the present study was to evaluate the efficiency of comparative genomic hybridisation (CGH) for screening of submicroscopic chromosomal rearrangements. CGH was performed in a cohort of 17 patients (14 families) with mental retardation, dysmorphic features and a normal karyotype. Five subtle unbalanced rearrangements were identified in 7 patients. Subsequent FISH studies confirmed these results. Although no interstitial submicroscopic rearrangement was detected in this small series, the study emphasises the value of CGH as a screening approach to detect subtle chromosome rearrangements in mentally retarded patients with dysmorphic features and a normal karyotype.     

Applications of comparative genomic hybridisation in constitutional chromosome studies

G band cytogenetic analysis often leads to the discovery of unbalanced karyotypes that require further characterisation by molecular cytogenetic studies. In particular, G band analysis usually does not show the chromosomal origin of small marker chromosomes or of a small amount of extra material detected on otherwise normal chromosomes. Comparative genomic hybridisation (CGH) is one of several molecular approaches that can be applied to ascertain the origin of extra chromosomal material. CGH is also capable of detecting loss of material and thus is also applicable to confirming or further characterising subtle deletions. We have used comparative genomic hybridisation to analyse 19 constitutional chromosome abnormalities detected by G band analysis, including seven deletions, five supernumerary marker chromosomes, two interstitial duplications, and five chromosomes presenting with abnormal terminal banding patterns. CGH was successful in elucidating the origin of extra chromosomal material in 10 out of 11 non-mosaic cases, and permitted further characterisation of all of the deletions that could be detected by GTG banding. CGH appears to be a useful adjunct tool for either confirming deletions or defining their breakpoints and for determining the origin of extra chromosomal material, even in cases where abnormalities are judged to be subtle. We discuss internal quality control measures, such as the mismatching of test and reference DNA in order to assess the quality of the competitive hybridisation effect on the X chromosome.     

A new strategy for cryptic telomeric translocation screening in patients with idiopathic mental retardation.

Cryptic unbalanced chromosome rearrangements in the telomeric bands of human chromosomes constitute a significant cause of "idiopathic" mental retardation. Here, we have described a new strategy based upon comparative genomic hybridisation (CGH) to screen for these abnormalities. A modified CGH analysis showed three unbalanced cryptic rearrangements in five patients from three families. These chromosome abnormalities and their balanced forms in the relatives were then confirmed by fluorescence in situ hybridisation (FISH). This study describes a new approach to the diagnosis of cryptic translocations between the G band negative ends of chromosomes and confirms the significant contribution of cryptic telomeric rearrangements to idiopathic mental retardation.     

A familial inverted duplication 2q33-q34 identified and delineated by multiple cytogenetic techniques

We describe a unique family with two children having a delay in psychomotor development. In both children we identified an interstitial duplication dup(2)(q34q33) using multiple, complementary molecular cytogenetic techniques. Comparative genomic hybridisation (CGH) and array-CGH were used to determine the size and the location of the duplicated region, the orientation of the duplicated region was identified with fluorescence in situ hybridisation (FISH). Both parents demonstrated a normal karyotype and normal CGH and array-CGH-profiles. However, FISH on peripheral blood cells from the mother showed the inv dup(2) in 9% of metaphases and 19% of interphase nuclei. To our knowledge this is the first report of a mosaic carrier of duplication in the long arm of chromosome 2. The finding of chromosomal mosaicism of at least 19% in the mother increases the recurrence risk. The exact characterisation of the inv dup(2) with FISH probes enabled us to offer a reliable prenatal FISH test. Comparison of the clinical features of the two children with those of previously described cases supports the hypothesis that the characteristic facial phenotype is linked to the distal part of the 2q33-q37 region. This report illustrates that in case of two sibs with an identical structural chromosomal abnormality the possibility of parental chromosomal mosaicism must be thoroughly investigated.     

Delineation of a supernumerary marker chromosome utilizing a multimodal approach of G-banding, fluorescent in situ hybridization, confirmatory P1 artificial chromosome fluorescent in situ hybridization, and high-resolution comparative genomic hybridization

We describe the structure of a supernumerary marker in a child who presented with a right atretic ear and multiple congenital anomalies. Using G-banding, fluorescent in situ hybridization (FISH), P1 artificial chromosome FISH and high-resolution comparative genomic hybridization (CGH), the marker was demonstrated to be a derivative chromosome resulting from malsegregation of a paternal 8;22 translocation: 47,XY, +der(22)t(8;22)(q24.1; q11.2). This case is noteworthy because the marker, while sharing similarities to der(22) in the Cat Eye syndrome (CES), also contains chromosome 8q material. This partial 8q trisomy confounds the diagnosis of CES associated with pure trisomy or pure tetrasomy 22q. The paternal translocation is noted with prolonged infertility and oligospermia, which again highlights the utility and necessity of chromosome analysis in this setting.     

Identification and characterization of a de novo partial trisomy 10p by comparative genomic hybridization (CGH)

We report the characterization of a de novo unbalanced chromosome rearrangement by comparative genomic hybridization (CGH) in a 15-day-old child with hypotonia and dysmorphia. We describe the combined use of CGH and fluorescence in situ hybridization (FISH) to identify the origin of the additional chromosomal material on the short arm of chromosome 6. Investigation with FISH revealed that the excess material was not derived from chromosome 6. Identification of unknown unbalanced aberrations that could not be identified by traditional cytogenetics procedures is possible by CGH analysis. Visual analysis of digital images from CGH-metaphase spreads revealed a predominantly green signal on the telomeric region of chromosome 10p. After quantitative digital ratio imaging of 10 CGH-metaphase spreads, a region of gain was found in the chromosome band 10p14-pter. The CGH finding was confirmed by FISH analysis, using a whole chromosome 10 paint probe. These results show the usefulness of CGH for a rapid characterization of de novo unbalanced translocation, unidentifiable by karyotype alone.     

Liver metastatic ability of human melanoma cell line is associated with losses of chromosomes 4, 9p21-pter and 10p

Genetic changes underlying the aggressive progression of human cutaneous melanoma are not completely understood. In order to characterise genetic alterations associated with the metastatic behaviour of this neoplasm we used comparative genomic hybridisation (CGH) in combination with fluorescence in situ hybridisation (FISH) on an experimental metastatic model of three related human melanoma cell lines. Tumour lines were selected based on their various metastatic capacity to liver in immunosuppressed mice. The parental cell line (A2058) was a human amelanotic melanoma cell line, adaptation of this line to in vivo growth as xenograft the HT168 tumour and its cell line was established. After intrasplenic transplantation of HT168 cells into immunosuppressed mice, a highly metastatic variant (HT168-M1) was selected. Several chromosomal aberrations common to all three lines indicating common clonal origin, as well as additional non-shared chromosomal changes were found. The original cell line (A2058) exhibited the highest number of genetic changes. Chromosomal alterations present only in the highly metastatic line (HT168-M1) involved losses on chromosome 4, 9p21.3-pter and 10p. Chromosome copy number patterns and the nature of chromosome 4 loss were further investigated by FISH using different centromeric probes and a chromosome 4 painting probe. According to our CGH and FISH results we assume that alterations present only in the aggressive metastatic subline are associated with the increased – metastatic potential. Our observations further support the hypothesis, based on some recently published data, that certain (so far unidentified) suppressor genes having an important role in tumour progression are located on these chromosomes. This revised version was published online in July 2006 with corrections to the Cover Date.     

Comparative genomic hybridization as a tool to define two distinct chromosome 12-derived amplification units in well-differentiated liposarcomas

Well-differentiated liposarcomas (WDLPS) are frequently characterized by a near-diploid karyotype with supernumerary ring and/or giant rod-shaped marker chromosomes. We have shown, using fluorescence in situ hybridization (FISH) and molecular strategies, that these markers contain chromosome 12-derived sequences. Here we report the analysis of six WDLPS for the presence of amplified DNA segments by means of the recently developed comparative genomic hybridization (CGH) strategy. Two distinct chromosome 12-derived amplification units could be identified in all tumors examined, one located in the q 14-q 15 region as expected, the second unexpectedly mapping to q21.3-q22. Our results indicate that the concerted amplification of these two distinct regions on the long arm of chromosome 12 may be a consistent characteristic of WDLPS. These amplifications are most likely directly related to the presence of supernumerary ring and/or giant marker chromosomes in this group of soft tissue tumors. Genes Chrom Cancer 9:292-295 (1994). © 1994 Wiley-Liss, Inc.     

联合应用多种细胞及分子细胞遗传学技术确诊额外标记染色体

目的应用比较基因组杂交技术（comparative genomic hybridization，CGH）、荧光原位杂交（fluorescence in situ hybridization，FISH）和传统细胞遗传学技术分析1例额外标记染色体（supernumerary marker chromosome，SMC），探讨这些技术的联合使用在识别新发生的标记染色体方面的临床应用。方法1例智力低下患儿，通过常规G显带技术分析其染色体核型。针对发现的SMC，通过CGH分析其起源，通过FISH技术证实。同时应用N带和C带技术分析SMC的随体组成和着丝粒组成。结合已有的文献报道，分析该SMC的表型效应。结果染色体G带分析显示患者为携带SMC的嵌合体，核型描述为mos．47，XX，＋may[31]／48，XX，＋2mar[29]。CGH分析显示患儿基因组中有15q11→q14片段重复，以15q探针与患者中期分裂相进行FISH检测证实SMC来源于15号染色体。应用检测缺失型Prader-wiUi综合征／Angelman综合征的UBE3A探针与患者中期分裂相检测显示SMC有两个UBE3A杂交信号，对照的PML位点没有信号。N带显示SMC携带双随体，c带分析SMC为双着丝粒。综合上述结果，患者核型为：mos．47，xx，＋der（15）（pter＋q14：：q14→pter）[31]／48，XX，＋2der（15）（pter→q14：：q14→pter）[29]．ish der（15）（WCPl5＋，UBE3A＋＋，PML-）。结论CGH对于检测出不平衡染色体结构重排具有提示作用，结合FISH和传统的细胞遗传学技术，为确定SMC的结构组成提供了可信的技术平台，为分析这类异常核型个体的表型、预后和复发风险提供了依据。     

Duplication of 8p23.1: a cytogenetic anomaly with no established clinical significance.

We present seven families with a cytogenetic duplication of the short arm of chromosome 8 at band 8p23.1. The duplication has been transmitted from parents to offspring in four of the seven families. In three families, the source of the extra material and its euchromatic origin were established using FISH with a YAC which was mapped to 8p23.1 and a whole chromosome paint for chromosome 8. FISH signals from this YAC were significantly larger on the duplicated chromosome compared with the normal chromosome in all six family members tested. Comparative genomic hybridisation (CGH) on a representative subject was consistent with these results. The families were ascertained for a variety of mostly incidental reasons including prenatal diagnosis for advanced maternal age. The transmission of this duplication by multiple phenotypically normal family members with no history of reproductive loss suggests the existence of a novel class of 8p23.1 duplications, which can be regarded as euchromatic variants or duplications with no phenotypic effect.     

Triplication of 15q11-q13 with inv dup(15) in a female with developmental delay.

A 4 year old female referred with developmental delay was found to have two de novo abnormal derivatives of chromosome 15, a supernumerary inverted duplicated marker chromosome (inv dup(15)) and an interstitial triplication of proximal 15q11-q13 or 14 in one of the two 15 homologues (trip(15)). Fluorescence in situ hybridisation (FISH) using probes within and flanking the Prader-Willi/Angelman syndrome critical region (PWASCR) confirmed the triplication in the abnormal 15 homologue. The inv dup(15) was dicentric, positive for IR39d which maps proximal to the PWASCR, but was negative for all the PWASCR FISH probes used. Results using polymorphic microsatellite repeats confirmed that the additional material in the trip(15) was maternal in origin and included several PWASCR loci. The presence of two de novo abnormalities involving the proximal region of 15q suggests a linked mechanism of origin.     

Partial tetrasomy 12pter-12p12.3 in a girl with Pallister-Killian syndrome: extraordinary finding of an analphoid, inverted duplicated marker

Cytogenetic analysis in a girl with multiple congenital anomalies indicating Pallister-Killian syndrome (PKS) showed a supernumerary marker chromosome in 1/76 lymphocytes and 34/75 fibroblast metaphases. GTG-banding pattern was consistent with the chromosomal region 12pter-12q11. While fluorescence-in-situ hybridisation (FISH) with a whole chromosome 12 painting probe confirmed the origin of the marker, a chromosome 12 specific alpha-satellite probe did not hybridise to it. FISH analysis with a specific subtelomeric probe 12p showed hybridisation to both ends of the marker chromosome. High-resolution multicolour-banding (MCB) studies revealed the marker to be a der(12)(pter-->p12.3::p12.3-->pter). Summarising the FISH information, we defined the marker as an inverted duplication of 12pter-12p12.3 leading to partial tetrasomy of chromosome 12p. In skin fibroblasts, cultured at the patient's age of 1 year and 9 years, the marker chromosome was found in similar frequencies, even after several culture passages. Therefore, we consider the marker to have a functional centromere although it lacks detectable centromeric alpha-satellite sequences. To the best of our knowledge, this is the first proven analphoid marker of chromosome 12. Molecular genetic studies indicated that this marker is of paternal origin. The finding of partial tetrasomy 12pter-12p12.3 in our PKS patient allows to narrow down the critical region for PKS.     

Analysis of selected oncogenes (AKT1, FOS, BCL2L2, TGFbeta) on chromosome 14 in granulosa cell tumors (GCTs): a comprehensive study on 30 GCTs combining comparative genomic hybridization (CGH) and fluorescence-in situ-hybridization (FISH)

In previous studies, we have demonstrated a number of cytogenetic alterations in granulosa cell tumors (GCTs), especially on chromosomes X, 12, 14, and 22. However, little is known about specific loci on 14q, which could play an important role in tumor pathology. Therefore, we assessed four important genes in 30 GCTs using fluorescence-in situ-hybridization (FISH). Comparative genomic hybridization (CGH) was performed on paraffin-embedded material. Then, we applied FISH with gene-specific DNA probes for AKT1 (14q32.32), FOS (14q24.3), BCL2L2 (14q11.2-q12), and TGFbeta3 (14q24), and tried to find a correlation between CGH, FISH, tumor stage, and survival. In CGH, 7 of 30 cases (23.3%) showed complete gains on chromosome 14. FISH of the four loci revealed gains of hybridization signals in 8 of 30 cases (26.6%), indicating trisomy of the whole chromosome arm. The same aberration was detected by FISH in 2 of 30 cases (6.6%), which were negative using CGH. One case (1 of 30; 3.3%) was found to have a gain on chromosome 14 by CGH, which could not be confirmed by FISH. A correlation with tumor stage or survival could not be established. Our results suggest that GCTs may be characterized by trisomy of chromosome 14. A specific oncogene that could play a particular role in the tumorigenesis of GCTs was not identified on chromosome 14.     

Tetrasomy 12pter-12p13.31 in a girl with partial Pallister-Killian syndrome phenotype

A dysmorphic patient was shown to carry a small supernumerary marker chromosome. Multicolor, centromere-multicolor and regular FISH experiments proved the marker to be an analphoid 12pter derived isochromosome. Microdissection of the marker followed by reverse painting and array CGH analysis showed that the isochromosome contains approximately 6 Mb of 12pter-12p13.31 derived sequence. This is only the second report of a marker with a neocentromere 12pter and the molecular fine mapping of the duplicated region further refines the 12p region defining the Pallister-Killian syndrome phenotype. In addition, we show the feasibility of using microdissected chromosomes or chromosomal fragments to molecularly map the chromosomal breakpoints on array CGH. This technology may aid in the identification of chromosomal translocation breakpoints.     

Supernumerary ring chromosome 8: clinical and molecular cytogenetic characterization in a case report

We report on a 3-year-old male with developmental delay, autistic behavior, and minor abnormalities consistent with trisomy 8 syndrome whose cytogenetic analysis revealed mosaicism for a supernumerary ring chromosome (SRC). Fluorescence in situ hybridization (FISH) studies, using centromeric and yeast artificial chromosome (YAC) probes, were performed to characterize further the supernumerary chromosome. The ring origin has been detected from the short arm of chromosome 8, resulting in r(8)(p10p23.1). Moreover, uniparental disomy (UPD) using microsatellite analysis was excluded. To our knowledge a total of 25 cases, confirmed by FISH, have been reported with either supernumerary marker or ring chromosome 8. We present a detailed clinical and molecular cytogenetic characterization of this additional case in order to better define the genotype-phenotype correlation.     

Consistent copy number gain in chromosome 12 in primary diffuse large cell lymphomas of the stomach.

Fifteen cases of high grade primary gastric non-Hodgkin's lymphomas were studied using comparative genomic hybridization (CGH) and/or fluorescence in situ hybridization (FISH) techniques. A total of 10 cases of diffuse large cell lymphoma (DLCL) with no histologically identifiable or previous history of low grade mucosa-associated lymphoid tissue (MALT) lymphoma components were examined, four by CGH and validated by FISH, and the remaining six by FISH alone. All 10 tumors showed gains in chromosome 12. Other recurring CGH findings in DLCL included copy number gains of 1q and deletions of 6q. Five cases of high grade tumors with low grade MALT components (HGM) were also examined, three by CGH and validated by FISH and two by FISH only. Only one in five HGM showed gains of chromosome 12. Other recurring CGH findings in HGM included +7q and +11q. We conclude that high grade gastric lymphomas of DLCL type were associated with gains in chromosome 12. The change was much less frequent (P < 0.01) in the HGM type, which had a percentage similar to that observed in previously reported cytogenetics/FISH studies on low grade MALT lymphomas. Our findings suggested that many DLCL were not derived from transformation of low grade MALT lymphomas.     

Strategies to identify supernumerary chromosomal markers in constitutional cytogenetics

Supernumerary marker chromosomes (SMCs) are defined as extrastructurally abnormal chromosomes which origin and composition cannot be determined by conventional cytogenetics. SMCs are an heterogeneous group of abnormalities concerning all chromosomes with variable structure and size and are associated with phenotypic heterogeneity. The characterisation of SMCs is of utmost importance for genetic counselling. Different molecular techniques are used to identify chromosomal material present in markers such as 24-colour FISH (MFISH, SKY), centromere specific multicolour FISH (cenMFISH) and derivatives (acroMFISH, subcenMFISH), comparative genomic hybridisation (CGH), arrayCGH, and targeted FISH techniques (banding techniques, whole chromosome painting...). Based on the morphology of SMC with conventional cytogenetic and clinical data, we tried to set up different molecular strategies with all available techniques.