GTG Banding Research Articles

Analysis of chromosome aberrations in cell lines derived from laryngeal cancer in relation to tumor progression

Cell lines provide a good model for studies on molecular and cellular events accompanying neoplastic transformation and cancer progression. The data in recent literature suggest an occurrence of repetitive chromosome aberrations that can be linked with particular stages of cancer. Ten cell lines derived from squamous cell carcinoma of the larynx at the University of Turku were karyotyped. The studied cell lines represented a variety of primary locations of the tumors, TNM staging and histological grading. Karyotyping was done by the classical cytogenetic technique with the application of GTG, QFQ and other banding techniques; some complex aberrations were analyzed by the FISH technique. The results document several numerical and structural aberrations. Attention was focused on the monosomy of chromosomes 13, 17 and 18, frequent deletions of the Y chromosome. Structural aberrations were frequently seen at chromosomes 1, 3, 4, 7, 8, 9 and 11, mostly as deletions (usually deletions of a whole arm), translocations, isochromosomes, duplications and marker chromosomes. The study is in progress and aims to find a correlation between particular aberrations and disease staging. At present, two observations seem to be firm: the amplification of the 11q13 region appeared in tumors with a short survival. However, the primary location of the tumor should be taken into account when considering 11q13 as a prognostic marker. The same is applicable for del(9p), which indicates an early stage of disease. Besides the frequent chromosome aberrations, attention should be paid to marker chromosomes that are potentially specific for laryngeal cancer.

Cytogenetic and molecular characterization of�eight new reciprocal translocations in the pig species. Estimation of their incidence in French populations

Eight new cases of reciprocal translocation in the domestic pig are described. All the rearrangements were highlighted using GTG banding techniques. Chromosome painting experiments were also carried out to confirm the proposed hypotheses and to accurately locate the breakpoints. Three translocations, rcp(4;6)(q21;p14), rcp(2;6)(p17;q27) and rcp(5;17)(p12;q13) were found in boars siring small litters (8.3 and 7.4 piglets born alive per litter, on average, for translocations 2/6 and 5/17, respectively). The remaining five, rcp(5;8)(p12;q21), rcp(15;17)(q24;q21), rcp(7;8)(q24;p21), rcp(5;8)(p11;p23) and rcp(3;15)(q27;q13) were identified in young boars controlled before entering reproduction. A decrease in prolificacy of 22% was estimated for the 3/15 translocation after reproduction of the boar carrier. A parental origin by inheritance of the translocation was established for the (5;8)(p11;p23) translocation. The overall incidence of reciprocal translocations in the French pig populations over the 2000/2001 period was estimated (0.34%).

Establishment and characterization of human metastatic hepatocellular carcinoma cell line

Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide with a poor prognosis. Recently, we established a HCC cell line from a metastatic HCC tumor. GTG banding analysis was performed and the karyotype showed that this metastatic HCC cell line is a hypertriploid (71–78 chromosomes) with a large marker chromosome containing a long homogeneously staining region (hsr). Comparative genomic hybridization was applied to characterize the chromosomal alterations in this metastatic HCC cell line. The results showed that the hsr was composed of amplified DNA sequences from 11q13. Further characterization of the hsr may lead to the isolation of the putative amplified oncogene at 11q13.

Delineation of the dup5q phenotype by molecular cytogenetic analysis in a patient with dup5q/del 5p (cri du chat)

An infant girl presented with multiple congenital abnormalities and a distinctive mewing cry. Her karyotype was 46,XX,add5p. Chromosome analysis on the mother revealed an apparently balanced pericentric inversion of chromosome 5, with the precise position of the breakpoints not clearly discernable by GTG banding, 46,XX,inv(5)(p15.2/3?q35.1?). Fluorescence in situ hybridization (FISH) studies using a commercial cri du chat probe (D5S721,D5S23) revealed signals on both the normal and derivative chromosomes. Telomeric probes specific for 5p and 5q were used to confirm the pericentric inversion in the mother and demonstrated the loss of the terminal 5p region and a duplication of the terminal 5q region in the proband. The imbalance on chromosome 5 in the patient was further defined using comparative genomic hybridization (CGH), which revealed a loss of material from 5p15.3 --> pter and a gain of 5q34 --> qter. The presence of the cat-like cry appears to be the only specific feature that can be linked to the loss of 5p material. The remaining dysmorphic features of this infant appear to be due specifically to the duplication of the 5q sequences. The combination of FISH, CGH, and cytogenetics has confirmed that the characteristic cry of the cri du chat syndrome is due to the deletion of the most distal part of the classic del 5p region. More importantly, our investigation has defined the duplication of 5q34 --> qter as a distinct clinical phenotype.

Reorganization of the X chromosome in voles of the genus Microtus

Comparative chromosomal analysis is a powerful tool in the investigation of the mechanisms of chromosomal evolution. The accuracy of the analysis depends on the availability of region-specific markers to follow the fate of the particular chromosomal region through the evolution of species. We have assigned 12 unique sequences to the euchromatic part of the vole X chromosome, which serve as reliable markers of chromosomal segments. Together with region-specific libraries and GTG banding, these markers allow us to delineate the homologous regions of the X chromosomes in five species of the genus Microtus. We found that X chromosomes of these species differ by numerous rearrangements and all rearrangements are clustered at specific breakpoints. Moreover, these breakpoints were found to colocalise with repetitive and/or duplicated DNA sequences. We suggest that clusters of repeated and/or duplicated DNA sequences have played a crucial role in the formation of rearrangement hot spots during evolution of the X chromosome in the subgenus Microtus.

Maternal insertion of 18q11.2-q12.2 in 18p11.3 of the same chromosome analysed by microdissection and multicolour banding (MCB).

Different aberrations in one chromosome 18 were prenatally detected during each of three different pregnancies of a healthy woman. Routine cytogenetic analysis revealed a morphologically altered maternal chromosome 18 as well. The purpose of the current study was to characterize these cytogenetic changes in detail and thus to clarify the reason for the recurrent appearance of morphologically altered chromosomes 18 in this family. As GTG banding did not allow resolution of the kind of aberrations present in these four cases, the following molecular cytogenetic approaches were used: microdissection combined with reverse painting and multicolour banding (MCB) analysis using a chromosome 18 specific probe set. Molecular cytogenetic approaches revealed that fetus 1 had a derivative chromosome del(18)(q11.2q12.2), fetus 2 and the mother had the identical derivative chromosomes ins(18)(pterp11.32::q12.2q11.2::p11.32q11.2::q12.3qter) and fetus 3 had a dup(11.2q12.2). Partial monosomy in fetus 1 and partial trisomy in fetus 3 can be explained by crossing over events during maternal meiosis.

GTG banding pattern on human metaphase chromosomes revealed by high resolution atomic-force microscopy.

Surface topography of human metaphase chromosomes following GTG banding was examined using high resolution atomic force microscopy (AFM). Although using a completely different imaging mechanism, which is based on the mechanical interaction of a probe tip with the chromosome, the observed banding pattern is comparable to results from light microscopy and a karyotype of the AFM imaged metaphase spread can be generated. The AFM imaging process was performed on a normal 2n = 46, XX karyotype and on a 2n = 46, XY, t(2;15)(q23;q15) karyotype as an example of a translocation of chromosomal bands.

Cytogenetics in Acute Lymphoblastic Leukemia in Mexican Children: An Institutional Experience

Background Cytogenetic studies in acute lymphoblastic leukemia (ALL) have identified numerical and structural chromosomal abnormalities related to the disease's pathophysiologic characteristics. These findings correlate with prognosis and response to treatment in ALL patients. The purpose of this study was to define the frequency of chromosomal abnormalities in a group of Mexican children with ALL and to compare these data with those reported in the literature. Methods Bone marrow chromosome studies with GTG bands were performed in 150 pediatric patients with ALL who were naive to antileukemic treatment and aged from 5 months to 16 years; the majority was diagnosed as L1. Results Among 131 patients, 30 (22.9%) karyotypes were normal and the remaining 101 (77.1%) had abnormal karyotypes with numerical and/or structural abnormalities. Among patients with numerical abnormalities, the most frequent karyotypes were hyperdiploidy with 51–65 chromosomes (30 patients) and hyperdiploidy with 47–50 chromosomes (18 patients). Among recurrent, non-random, and primary structural abnormalities, the most frequent was t(9;22), followed by t(1;19). Aberrations involving band 11q23 were not detected, and only one of two patients with L3 had the t(8;14). Of the secondary non-random abnormalities, dup(1q), del(6q), and i(7)(q10) were found. Conclusions The frequency and type of chromosomal abnormalities found was comparable to those reported in the literature with similar methodology and pediatric populations; however, the number of cases analyzed should be increased to create a database of Mexican children with ALL, and several patients require molecular analysis to identify chromosomal abnormalities not detected through conventional cytogenetic studies.

Multicolour karyotyping

A 35-year-old woman with a cystic hygroma detected on early obstetrical ultrasound underwent chorionic villus sampling. Fetal chromosome analysis by standard GTG banding revealed a male karyotype with additional chromosome material of unknown origin attached to the short arm of a chromosome 9 (panel A). Multiplex fluorescence in-situ hybridisation (M-FISH), distinguishes all 24 human chromosomes in different colours with chromosome-specific paint probes. M-FISH showed that the additional material came from chromosome 2 (panel B).

Comparative genomic hybridization-aided unraveling of complex karyotypes in human hematopoietic neoplasias

The information obtained by conventional cytogenetics (CC) in human leukemias is sometimes limited, in particular by complex karyotypes with many marker chromosomes. While CC is restricted to metaphases with a good quality, interphase fluorescence in situ hybridization (I-FISH) is also capable of analyzing specific anomalies in the interphase nuclei. Comparative genomic hybridization (CGH) gives additional information about the imbalanced karyotype changes in the whole genome. The aim of this study was to assess the contribution of CGH to the unraveling of complex GTG karyotypes, which are difficult to evaluate by banding analysis, and to compare these results with those by CC and FISH. Thirteen bone marrow samples and one sample obtained from peripheral blood of 13 leukemia patients were examined by CC, FISH and CGH. The GTG banding analysis showed complex karyotypes with many marker chromosomes. The most frequent abnormalities were numerical and structural aberrations on chromosomes 5 and 7. In 12 of the 14 samples, the CGH analysis was able to detect chromosomal imbalances with losses of material on chromosome 5 and 7 as the most frequent aberrations. In all 14 samples, additional FISH analyses were performed. For most of the studied neoplasias, a close correlation between CC, FISH and CGH data was observed. CGH was considerably helpful in adding additional information to classical karyotyping, if the low quality or number of metaphases was insufficient for a reliable CC analysis. Even in cases where whole chromosome painting could be applied, it added information on the breakpoints of the observed rearrangements. In only 2 of the studied 14 samples, neither CGH nor I-FISH could improve the result of karyotyping. CGH, nevertheless, can be regarded as a powerful additional technique in leukemias with unsuccessful CC, incomplete, or complex karyotypes with many marker chromosomes. A systematic analysis by three techniques such as CC, FISH and CGH guarantees an optimal genetic characterization of the neoplasias.

Unbalanced translocation t(15;22) in ‘severe’ Prader–Willi syndrome

A 13-year-old girl with an unbalanced karyotype 45,XX,-15,der(22)t(15;22)(q13;q13.3) de novo had Prader–Willi syndrome (PWS), (score 13.5), but with features of mental and physical retardation more severe than usually seen in PWS. The clinical diagnosis of PWS was confirmed by methylation analysis that showed absence of the paternal band. With GTG banding, the cytogenetic breakpoint on chromosome 15q13, with 15q14 intact, encompassed the PWS region, while the breakpoint on 22q was terminal. Investigations with FISH utilised ten different probes/combinations, namely SNRPN/PML, TUPLE1/22q13.3, TUPLE/ARSA, GABRB3, three YAC clones and one cosmid for specific regions within chromosome 15q, painting probes for the long arm of chromosomes 15 and 22 and a pantelomere probe. Deletion of SNRPN,TYAC 9 (at 15q11-12), TYAC19 (at 15q13) and GABRB3 (within the PWS locus), was evident on the derivative (22) chromosome, while TYAC10 (at 15q22), cos15-5 (at 15q22) and PML (15q22) were not deleted. On the der(22), 22q13.3 and ARSA were not deleted, but the most distal non specific pantelomeric probe was deleted. Thus, the severe phenotype could be attributable to deletion on chromosome 15q extending beyond q13 to q14, (further than the usual chromosome 15q deletion (q11-13) in PWS), or be related to loss of the very terminal 22q region (from ARSA to the pantelomere) or be due to genetic factors elsewhere in the genome.

Chromosomal investigations in patients with mental retardation and/or congenital malformations

We investigated the chromosomal constitution of patients with mental retardation and/or congenital malformations in order to determine genetic causes for such disturbances. The GTG and CBG banding patterns were studied using phytohemagglutinin M-stimulated lymphocytes cultured from peripheral blood. Among 98 individuals with mental retardation and/or congenital malformations who were analyzed there were 12 cases of Down's syndrome, two of Edward's syndrome, one of Patau's syndrome, five of Turner's syndrome, two of Klinefelter's syndrome, one of "cri-du-chat" syndrome, one case of a balanced translocation between chromosomes 13 and 14, one case of a derivative chromosome and one of a marker chromosome. We found abnormal chromosomes in 26% of the patients, 82% of which were numerical abnormalities, with the remaining 18% being structural variants. We conclude that patients with mental retardation and/or congenital malformations should be routinely karyotyped.

Identification of two new translocations that disrupt the AML1 gene

The AML1 gene, located at chromosome 21q22, encodes a component (CBFα2) of a heterodimeric transcription factor complex termed core binding factor (CBF), which binds to DNA and activates gene expression. Chromosomal rearrangements may lead to disruption of this gene and development of acute leukemia. Twelve AML1 translocations have been identified to date, and include sites on chromosomes 1, 2, 3, 5, 8, 12, 14, 15, 16, 17, 18, and 19. Here we report two new translocations involving AML1 in acute myeloid leukemia, in which the disruption of the AML1 gene was documented by GTG banding cytogenetic studies and metaphase and interphase FISH analysis. These chromosomal breakpoints identified as harboring new fusion partners for AML1 are at 2p11.2 and 20q13.1. The two patients in who these translocation were identified were elderly males with newly diagnosed AML. These patients shared the same poor outcomes reported for other rare AML1 translocations.

Enhanced Detection of Chromosomal Abnormalities with the Use of RxFISH Multicolor Banding Technique

Hematological disorders often have complex karyotypes with multiple markers. Proper assignment of chromosome number or aberration or both can be difficult. Specific identification of chromosomal abnormalities aids in the diagnosis and selection of treatment of patients. Fluorescence in situ hybridization (FISH) has been applied to the identification of translocations, markers, and other chromosomal abnormalities in clinical cytogenetics. However, the standard FISH technique is unable to detect the entire genome in a single experiment. This report presents the use of a cross-species comparative genomic hybridization color-banding technique (RxFISH) that permits examination of an entire karyotype at one time. Specimens from two patients, one with acute lymphocytic leukemia (ALL) and the other with multiple myeloma (MM), were studied. Metaphases were prepared by standard culture techniques. Conventional cytogenetic analysis (GTG banding) showed multiple clones in each of the cases. These clones were hyperdiploid metaphases with complex chromosomal abnormalities and multiple markers. The slides were then hybridized with FITC-, Cy-3-, and Cy-5-labeled RxFISH probes; the results were analyzed by a digital imaging system. The RxFISH color banding confirmed the hyperdiploid metaphases and identified multiple chromosomal abnormalities. In the specimen from the patient with ALL, several chromosomes, which had been classified as markers by G-banding, were found to be specific chromosomes. This study suggests that RxFISH can provide more accurate and specific identification of complex chromosomal abnormalities. RxFISH is a useful complement to the clinical cytogenetic laboratory armamentarium.

COMPARATIVE GENOMIC HYBRIDIZATION IN PEDIATRIC ACUTE LYMPHOBLASTIC LEUKEMIA

Comparative genomic hybridization (CGH) was used to clarify the chromosomal status of 15 patients diagnosed with childhood acute lymphoblastic leukemia (ALL). Bone marrow samples from 10 of the 15 patients were selected because no metaphases were obtained for cytogenetic analysis. Three patients with normal trypsin and giemsa banding (GTG) karyotypes were also studied by CGH to determine whether significant abnormalities might have been missed by banding analysis, and samples from an additional 2 patients with hyperdiploidy were also included. Seven of the 10 patients with failed GTG banding analysis were found to be chromosomally abnormal by CGH; 2 out of 3 patients with normal GTG band karyotypes were abnormal, indicating that the metaphases available for karyotyping were not malignant cells, and that CGH analysis of hyperdiploid samples provided more accurate resolution than karyotyping alone. The prognostic value of chromosomal aberrations detected by CGH and the efficiency of the technique suggest a central role for CGH in routine clinical cytogenetics.

Cytogenetic findings in 250 schizophrenics: evidence confirming an excess of the X chromosome aneuploidies and pericentric inversion of chromosome 9

Chromosomal abnormalities may be of help in identifying disease genes. To search for susceptibility loci for schizophrenia, we have performed chromosomal examinations by using the GTG banding technique for 250 schizophrenics. We found five cases with an aneuploidy of the X chromosome and ten cases with pericentric inversion of chromosome 9 [inv (9)]. These results confirmed an excess of the X chromosome aneuploidies in schizophrenia, indicating a possible involvement of the X chromosome in the pathogenesis of the illness. The observed incidence (4.0%) of inv (9) in our schizophrenic sample was significantly higher ( p=0.013) than that reported in the general population in Japan (1.7%). Although inv (9) has been considered to be a normal variant, our observation implies a possible association between inv (9) and schizophrenia, suggesting that a susceptibility locus for the disease may be located at a breakpoint of the inversion on chromosome 9.

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...

Trisomy 21 is a recurrent secondary aberration in childhood acute lymphoblastic leukemia withTEL/AML1 gene fusion

TEL/AML1 gene fusion is the most frequent genetic lesion in pediatric acute lymphoblastic leukemia (ALL). It occurs as a consequence of the cryptic chromosomal translocation t(12;21)(p13;q22). In a cohort of 50 RT-PCR-positive TEL/AML1 patients, karyotype examination by GTG banding and fluorescence in situ hybridization (FISH) allowed us to identify chromosome anomalies in addition to the already existing t(12;21). Secondary aberrations were found in 29 out of 41 patients (71%) at initial diagnosis and in all 9 patients with relapse. Structural rearrangements affected chromosome arms 2p, 2q, 5q, 9p, 12p (n = 2), 6q, 11p (n = 3), and 21q (n = 4). An extra chromosome 21 was found to be the most frequent anomaly. It was detected in 6 out of 41 patients at initial diagnosis (15%) and in 7 out of the 9 patients at relapse. No karyotype with trisomy 21 exceeded 47 chromosomes. Gain of chromosome 21 was the sole anomaly in GTG-banding analysis in 2/41 patients at initial diagnosis and in 4/9 at relapse. Notably, chromosome painting analysis performed in 11 out of the 13 patients with an extra chromosome 21 revealed duplication of the normal chromosome 21 in 8, and duplication of der(21)t(12;21) in 3 patients. Furthermore, gain of der(21)t(12;21) chromosome was confined exclusively to the relapse patients.

Single cell chromosome rearrangements in indivuduals with reproductive failure

Single cell chromosome rearrangements (SCCR) are incidental findings in cell cultures. Nevertheless, some authors have implicated them in habitual abortion. Ninety individuals classified in four groups were prospectively studied: A) individuals with spontaneous abortions, malformed children or molar pregnancies (N = 36); B) azoospermic males (N = 14); C) individuals with one or more children with either de novo or inherited, constitutional, chromosome abnormalities (N = 26), and D) individuals with healthy children and no reproductive failure (control group, N = 14). Lymphocyte chromosome preparations were stained for GTG bands, and 50-100 metaphases were scored per individual. The rearrangements observed were translocations, deletions, duplications, isochromosomes, rings, fragments and markers. Thirty-four individuals (21 males, 13 females) had a range of 1-5 SCCR. Four had rearrangements only of chromosomes 7 and 14. SCCR frequency (with the exception of rearrangements involving chromosomes 7 and 14) was 0.0063, while that of rearrangements between chromosomes 7 and 14 was 0.0010. Statistical intergroup comparisons (<FONT FACE="Symbol">c</font>2 with Yates correction) did not show significant differences. Hence, the occurrence of SCCR in our sample was found to be independent of ascertainment mode and sex.

Discordant detection of monosomy 7 by GTG banding and FISH in a patient with Schwachman-Diamond syndrome

Schwachman-Diamond Syndrome (SDS) is an inherited illness characterized by exocrine pancreatic insufficiency and by congenital neutropenia. Patients with SDS are at increased risk of developing myelodysplastic syndrome (MDS) and acute myelogenous leukemia (AML). Bone marrow aspiration and biopsy can be used to detect MDS in a presymptomatic state. Monosomy 7 is a poor prognostic sign in MDS and AML, and therefore establishing its presence is important. However, different methods of detection may lead to different results in some patients.A three month old girl was referred to Rhode Island Hospital in 1988 with failure to thrive. White blood cell count was mildly depressed at 4 × 109 cells/L and pancreatic insufficiency was demonstrated. The diagnosis of SDS was made. In February of 1998, surveillance bone marrow cytogenetic analysis of a suboptimal specimen demonstrated the following karyotype by GTG banding: 45,XX,-C[3]/46,XX[45]/47,XX+C[1]. Fluorescent in Situ Hybridization (FISH) was performed with a chromosome 7 specific alpha-satellite probe (D7Z1). 373 of 376 cells exhibited only one chromosome 7 signal. A further marrow aspiration in August of 1998 showed an essentially normal karyotype by GTG-banding. FISH with the same chromosome 7 probe showed 230 of 250 cells to be monosomic for chromosome 7. A whole chromosome 7 painting probe demonstrated disomy for chromosome 7 in 90 out of 90 cells, but subtle heteromorphism in the centromeric regions of the two copies of chromosome 7 was noted in some cells.This case demonstrates that FISH can give results discordant with those of other methodologies and should not be used as a stand-alone cytogenetic test. The chromosome 7 variant detected in this patient may or may not be related to MDS. The relationship of the patient's karyotype to SDS is also not known. Thus, further investigation with repeated bone marrow examination in this patient and further characterization of the abnormalities in other SDS patients are warranted.