Clonal Chromosomal Abnormalities Research Articles

Statistical analyses of karyotypic complexity in head and neck squamous cell carcinoma

More than 250 head and neck squamous cell carcinomas (HNSCCs) with clonal chromosomal abnormalities have been reported. Even though the pattern of aberrations is nonrandom, no specific primary or secondary karyotypic abnormalities have been identified. One explanation for the still-rudimentary understanding of the cytogenetic evolution in HNSCC could be the pronounced karyotypic complexity seen in these tumors. In an attempt to overcome this difficulty, we have applied several statistical methods such as hierarchical cluster analysis, multidimensional scaling, and k-means clustering, which allow the identification and interpretation of karyotypic pathways, as well as establishing a temporal order of chromosomal imbalances on 241 published and 70 previously unpublished HNSCC karyotypes. From the analysis of the distribution of the number of imbalances per tumor we suggest that the carcinomas evolve through three phases representing different stages of chromosomal instability. Two major cytogenetic pathways, one dominated by gains and another by losses, were identified by means of principal component analysis. These were initiated by +7 and by any of the aberrations 1p−, 3p−, or 7q−, respectively.

Clonal chromosome abnormalities in a plexiform cellular schwannoma

Cellular schwannomas are uncommon tumors of Schwann cells that can rarely have a plexiform architecture. Cellular schwannomas can be confused with low-grade malignant peripheral nerve sheath tumors (MPNST) but have been noted to have a benign clinical course. There are few published cytogenetic analyses of cellular schwannomas and, to our knowledge, there are no reports of the plexiform variant of cellular schwannoma to date. Cellular schwannomas are reported to have cytogenetic changes similar to those seen in benign schwannomas with near-diploid karyotypes having simple numerical changes often involving chromosomes 22, 7, and the sex chromosomes. MPNST are markedly different, with extensive genetic heterogeneity and complex karyotypes. We report clonal numerical changes in a cellular schwannoma with plexiform architecture: 47,XY,+17 and 48,XY,+17,+18. These findings add to the karyotypic spectrum of peripheral nerve sheath tumors.

Is trisomy 5 a distinct cytogenetic subgroup in acute lymphoblastic leukemia?

Acute lymphoblastic leukemia (ALL) is characterized by recurrent clonal chromosomal abnormalities, with numerical abnormalities being a common feature especially among children. Case reports in the literature suggest that one such recurrent numerical abnormality is the gain of chromosome 5 (trisomy 5) as the sole abnormality; due to the rarity of these cases, however, little is known about their incidence, clinical features, and prognosis. We have identified seven cases with trisomy 5 as the sole or primary chromosomal abnormality from a total of 3,400 karyotypes collected in the Leukaemia Research Fund UK Cancer Cytogenetics Group Karyotype Database. All cases had a precursor B-cell immunophenotype and there was a male predominance. Five patients were children aged between 7 and 14 years old. Four of the six patients with a reasonable follow-up period had relapsed, indicating a poor prognosis. We conclude that trisomy 5 as the sole numerical abnormality occurs predominantly in older children, may be associated with a poor outcome, and may represent a distinct, albeit rare, cytogenetic subgroup in ALL.

Chromosomal abnormalities and DNA image cytometry of haematological neoplasms in fine needle aspirates of lymph nodes.

The current diagnostics of haematological neoplasms along with morphological analysis, immunophenotyping and molecular analysis inevitably includes cytogenetic analysis. In this work the possibility of cytomorphological subclassification of haematological neoplasms from lymph node fine needle aspirates was examined without depending upon the referential histological diagnosis and cytogenetic analysis. In addition, the feasibility of cytogenetic analysis of the material obtained by lymph node fine needle aspiration (FNA) was examined. By analysing the findings of cytogenetic analysis and DNA image cytometry, it was decided to examine the possibility of comparing the findings and supplementing diagnostic possibilities of these methods. In 15 cases cytological diagnoses and cytogenetic analysis of haematological neoplasms were performed on the material obtained by lymph node FNA. In 12 of 15 cases histological diagnosis was made separately. A good cytohistological correlation was available in 9 of 12 cases (75%). Cytomorphological diagnoses in 10 of 15 cases (76%) were confirmed by the finding of a specific chromosomal translocation. In two cases cytological diagnosis did not correlate with the histological diagnosis and was confirmed only with specific chromosomal translocations. The lymphocytes obtained by lymph node FNA were adequate material for cytogenetic analysis - in 15 of 18 (83%) cases mitoses in cell cultures were obtained. In 13 of 15 (87%) cases clonal chromosomal abnormalities were detected, whereas in 2 of 15 (13%) cases a normal karyotype was found. DNA image cytometry was performed on nine samples, whereas in six samples the material was not sufficient. Although a small number of samples was analysed in the cases with identical cytomorphological diagnoses, the analysed histograms regarding the DNA index values showed heterogeneity. In conclusion, a cell culture sampled by FNA of lymph nodes is an adequate method for the chromosomal analysis. The specific cytogenetic abnormality associated with cytological diagnosis provides an opportunity to make a definitive diagnosis and provides a powerful approach when reference diagnosis on biopsy material cannot be obtained.

Diagnostic value of detecting fusion proteins derived from chromosome translocations in acute leukaemia

Clonal chromosomal abnormalities such as balanced translocations are characteristic features of several human leukaemias and have long been detected by conventional cytogenetics on banded metaphases. The advent of molecular biology techniques, advanced karyotyping and immunohistochemistry methods has not only allowed identification of gene involvement at altered chromosome sites and better knowledge of leukaemia pathogenesis, but also contributed important improvements in diagnosis of these heterogeneous diseases. Such novel diagnostic strategies are nowadays being increasingly used to improve leukaemia classification, and in several instances, they help to establish the most appropriate therapeutic strategy in individual patients. Moreover, at least two leukaemia-associated fusion proteins derived from chromosome translocation are specifically targeted by therapeutic approaches which result in significantly increased anti-leukaemia efficacy and reduced toxicity. In this chapter, we highlight the importance of identifying these genetic lesions at diagnosis in acute leukaemia. Further, we discuss briefly the clinical utility of detecting these alterations for prognostic assessment and evaluation of response to treatment.

T(5;14)/HOX11L2-positive T-cell acute lymphoblastic leukemia. A collaborative study of the Groupe Français de Cytogénétique Hématologique (GFCH).

To accurately estimate the incidence of HOX11L2 expression, and determine the associated cytogenetic features, in T-cell acute lymphoblastic leukemia (T-ALL), the Groupe Français de Cytogénétique Hématologique (GFCH) carried out a retrospective study of both childhood and adult patients. In total, 364 patients were included (211 children </=15 years and 153 adults), and 67 (18.5%) [47 children (22.4%) and 20 adults (13.1%)] were shown to either harbor the t(5;14)q35;q32) translocation or express the HOX11L2 gene or both. Most of the common hematological parameters did not show significant differences within positive and negative populations, whereas the incidence of CD1a+/CD10+ and cytoplasmic CD3+ patients was significantly higher in positive than in negative children. Out of the 63 positive patients investigated by conventional cytogenetics, 32 exhibited normal karyotype, whereas the others 31 showed clonal chromosome abnormalities, which did not include classical T-ALL specific translocations. Involvement of the RANBP17/HOX11L2 locus was ascertained by fluorescence in situ hybridization in six variant or alternative (three-way translocation or cytogenetic partner other than 14q32) translocations out of the 223 patients. Our results also show that HOX11L2 expression essentially occurs as a result of a 5q35 rearrangement, but is not associated with another identified T-ALL specific recurrent genetic abnormality, such as SIL-TAL fusion or HOX11 expression.

Core binding factor (CBF) acute myeloid leukemia: is molecular monitoring by RT-PCR useful clinically?

Clonal chromosomal abnormalities are the most important prognostic indicators in acute myeloid leukemia (AML). Two of the most prevalent cytogenetic subtypes of adult primary AML, t(8;21)(q22;q22) and inv(16)(p13q22)/t(16;16)(p13;q22), are characterized by disruption of the AML1(CBFA2, RUNX1) and CBFbeta genes, respectively, which encode subunits of core binding factor (CBF), a regulator of normal hematopoiesis. At the molecular level, t(8;21) and inv(16)/t(16;16) result in the creation of novel fusion genes, AML1/ETO and CBFbeta/MYH11, respectively, which encode fusion transcripts readily detectable by the reverse transcription-polymerase chain reaction (RT-PCR). Although the detection of t(8;21) or inv(16)/t(16;16) in adult patients with primary AML represents a favorable independent prognostic indicator for achievement of cure following intensive chemotherapy or stem cell transplantation, a substantial number of these patients (i.e. 40-50%) relapse and eventually die of their disease. Therefore, timely identification and therapeutic stratification of those patients deemed at high risk for disease relapse could ultimately result in a further improvement of clinical outcome within these cytogenetic subgroups of AML. As relapse is likely to occur as the result of failure of treatment to completely eradicate leukemic blasts, the detection of the AML1/ETO and CBFbeta/MYH11 fusion transcripts using sensitive RT-PCR assays has been utilized as a surrogate marker for resistant disease and, in turn, to predict disease recurrence during remission. The purpose of this paper is to review the applicability of this strategy to the clinical management of t(8;21) and inv(16)/t(16;16) primary AML, here collectively referred to as CBF AML.

Anomalies cytogénétiques dans les leucémies aiguës lymphoblastiques

Acute lymphoblastic leukemias (ALL) represent malignant clonal proliferations of stem cells commited in lymphoid differentiation, B or T-cell ALL. Clonal chromosomal abnormalities are found in 80% children and 70% adult cases. They are associated with an independant prognostic value which modifies the therapeutic approach and therefore karyotyping at diagnosis is mandatory. Molecular techniques such as FISH and RT-PCR are very helpful too as cryptic chromosomal abnormalities have been described. In this review, numerical and structural abnormalities are described : frequency, diagnosis and prognosis value as well as genes involved in structural abnormalities.

Cytogenetic and molecular findings related to rhabdomyosarcoma. An analysis of seven cases

Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma in childhood. Histologically, it is subdivided histologically into two main subtypes: alveolar (ARMS) and embryonal (ERMS). ARMS is characterized by t(2;13)(q35;q14) or its variant t(1;13)(p36;q14), which fuse PAX3 and PAX7, respectively, with FKHR to produce chimeric genes. ERMS is frequently associated with loss of heterozygosity of 11p15.5. We investigated seven RMS (three ARMS and four ERMS) by means of cytogenetic, fluorescence in situ hybridization, and molecular analyses, including the study of the main genes implicated in the G1- to S-phase cell cycle transition, and correlated these studies with pathologic findings and clinical outcome. All tumors showed clonal, numerical, and structural chromosomal abnormalities. Two ARMS had the t(2;13)(q35;q14) and the third a PAX7/ FKHR fusion, a cryptic t(1;13)(p36;q14), undetected by cytogenetic techniques, but revealed by reverse transcriptase polymerase chain reaction. One ERMS showed a der(11)t(3;11)(p21;p15) as a sole structural anomaly. Gene amplification was seen in four tumors, as double minutes or in the form of homogeneously staining regions. Overexpression of MYCN oncogene was found in two ARMS; N-myc DNA probe detected oncogene amplification located on the double minutes of these cases. Analysis of the regulatory genes responsible for G1- to S-phase transition showed a homozygous deletion of the 9p21 locus genes in a spindle-cell ERMS.

Preponderant mitotic activity of nonleukemic cells plays an important role in failures to detect abnormal clone in childhood acute lymphoblastic leukemia.

At diagnosis, clonal chromosomal abnormalities are found in the bone marrow blasts in more than two thirds of children with acute lymphoblastic leukemia (ALL). Practically, however, failure to detect these abnormalities is frequent and usually attributed to poor marrow sampling, inadequate metaphases, and/or a preponderant mitotic activity among nonleukemic cells. The authors applied fluorescence in situ hybridization (FISH) techniques to re-examine 30 cases of karyotypically "normal" childhood ALL to explore the role of preponderant mitotic activities of nonleukemic cells in failures to detect clonal abnormalities. The FISH test were performed using TEL/AML1 fusion gene probe and the centromere probes for chromosome 8 and 10 to detect the t(12;21) translocation and/or hyperdiploidy. Half of the karyotypically "normal" ALL cases examined have been found to have abnormal clones with t(12;21) rearrangement and/or hyperdiploidy by this specially designed FISH assay. Contrary to expectation, the authors found a higher incidence (52%) of clonal abnormalities in cases where over 20 metaphases had been examined than in cases (44%) where fewer than 20 metaphases had been analyzed. These findings suggest that a preponderant mitotic activity of nonleukemic cells plays an important role in failures to detect an abnormal clone by conventional cytogenetic studies. Therefore, karyotypically "normal" childhood ALL patients should undergo FISH studies to rule out the presence of t(12;21) and/or hyperdiploid clone.

Cytogenetic abnormalities in childhood acute myeloid leukaemia: a Nordic series comprising all children enrolled in the NOPHO‐93‐AML trial between 1993 and 2001

Between 1993 and 2001, 318 children were diagnosed with acute myeloid leukaemia (AML) in the Nordic countries. The patient group comprised 237 children < 15 years of age with de novo AML, 42 children < 15 years with Down syndrome (DS) and de novo AML, 18 adolescents 15-18 years of age with de novo AML, and 21 children < 15 years with treatment-related AML (t-AML). The first group was all-inclusive, yielding an annual childhood de novo AML incidence of 0.7/100 000. Cytogenetic analyses were successful in 288 cases (91%), and clonal chromosomal abnormalities were detected in 211 (73%). The distribution of ploidy levels were pseudodiploidy (55%), hyperdiploidy (34%) and hypodiploidy (11%). The most common aberrations (> 2%) were + 8 (23%) (as a sole change in 6.2%), 11q23-translocations, including cryptic MLL rearrangements (22%) [t(9;11)(p21-22;q23) in 11%], t(8;21)(q22;q22) (9.0%), inv(16)(p13q22) (6.2%), -7/7q- (5.2%), and t(15;17)(q22;q12) (3.8%). Except for +8, these abnormalities were rare in group 2; only one DS patient had a t(8;21) and none had 11q23-translocations, t(15;17) or inv(16). In the t-AML group, three cases displayed 11q23-rearrangements, all t(9;11); and there were no t(8;21), t(15;17) or inv(16). Overall, the observed frequencies of t(8;21) and t(15;17) were lower, and frequencies of trisomy 8 and 11q23-translocations higher, than in previous studies. Furthermore, seven abnormalities that were previously reported as only single AML cases were also seen, meaning that der(4)t(4;11)(q26-27;q23), der(6)t(1;6)(q24-25;q27), der(7)t(7;11)(p22;q13), inv(8)(p23q11-12), t(11;17)(p15;q21), der(16)t(10;16)(q22;p13) and der(22)t(1;22)(q21;q13) are now classified as recurrent abnormalities in AML. In addition, 37 novel aberrations were observed, 11 of which were sole anomalies.

Studies on the Molecular Pathogenesis of Extraskeletal Myxoid Chondrosarcoma—Cytogenetic, Molecular Genetic, and cDNA Microarray Analyses

Extraskeletal myxoid chondrosarcomas (EMCs) are characterized by recurrent chromosome translocations resulting in fusions of the nuclear receptor TEC to various NH(2)-terminal partners. Here we describe the phenotypic, cytogenetic, and molecular genetic characteristics of a series of 10 EMCs. Using spectral karyotyping and fluorescence in situ hybridization, clonal chromosome abnormalities were detected in all but one tumor. A t(9;22)(q22;q12) translocation was found in three cases; a del(22)(q12-13)in one case; and variant translocations, including t(9;17)(q22;q11-12), t(7;9;17)(q32;q22;q11), and t(9;15)(q22;q21), were detected in one case each. Recurrent, secondary abnormalities, including trisomy 1q, 7, 8, 12, and 19, were found in seven tumors. All tumors contained translocation-generated or cryptic gene fusions, including EWS-TEC (five cases, of which one was a novel fusion), TAF2N-TEC (four cases), and TCF12-TEC (one case). cDNA microarray analysis of the gene expression patterns of two EMCs and a myxoid liposarcoma reference tumor revealed a remarkably distinct and uniform expression profile in both EMCs despite the fact that they had different histologies and expressed different fusion transcripts. The most differentially expressed gene in both tumors was CHI3L1, which encodes a secreted glycoprotein (YKL-40) previously implicated in various pathological conditions of extracellular matrix degradation as well as in cancer. Our findings suggests that EMC exhibits a tumor-specific gene expression profile, including overexpression of several cancer-related genes as well as genes implicated in chondrogenesis and neural-neuroendocrine differentiation, thus distinguishing it from other soft tissue sarcomas.

Transient leukaemia--a benign form of leukaemia in newborn infants with trisomy 21.

Transient leukaemia--a benign form of leukaemia in newborn infants with trisomy 21.

Translocation (X;20)(q13.1;q13.3) as a primary chromosomal finding in two patients with myelocytic disorders

Reports of X chromosome translocations, as primary chromosomal changes associated with hematologic disorders, remain relatively uncommon. Herein, we report the detection, by conventional cytogenetic methods, of a cytogenetically identical t(X;20) in two different patients with hematologic disorders (probable myelodysplasia and polycythemia vera/acute myelocytic leukemia). In both cases, this translocation appeared as the primary clonal chromosome abnormality, with breakpoints occurring in the long arms of both the X chromosome and chromosome 20 (Xq13.1 and 20q13.3, respectively). Further characterization and comparison of the translocation chromosome products of these two cases by use of fluorescence in situ hybridization techniques is also described. Similar previously reported cytogenetically cases and the potential that this specific rearrangement may represent a nonrandom chromosomal finding are discussed.

Chromosomal abnormalities in relation to clinical disease in patients with cutaneous T-cell lymphoma: a 5-year follow-up study.

Patients with cutaneous T-cell lymphoma (CTCL) show chromosomal aberrations in skin and blood lymphocytes. To evaluate the significance of peripheral blood clonal or non-clonal chromosomal abnormalities in comparison with the clinical course of cutaneous T-cell lymphoma patients. Five patients with large-plaque parapsoriasis (LPP) or with follicular mucinosis, eight with mycosis fungoides and two with Sézary syndrome were followed for an average of 54 months. G-banding and enzyme-detected in situ hybridization (EDISH) were used to identify aberrations in chromosomes 1, 6, 8, 9, 11, 13/21, 15 or 17, that had previously showed frequent aberrations. The aberration rates of all chromosomes studied differed between patients with active disease and healthy or photochemotherapy-treated controls by EDISH or G-banding (P < 0.01 to P < 0.05). Patients in complete remission differed from healthy controls for aberrations of chromosomes 1, 6 and 11, and from patients with active, progressing disease for chromosomes 1, 6, 8, 11 and 17 (P < 0.01 to P < 0.05, EDISH or G-banding). All 11 samples representing active, progressing disease showed elevated levels of chromosome 8 aberrations in EDISH. The change in chromosomal aberration rate and clinical condition between two consecutive samples agreed for chromosomes 1, 8, 9 and 15 (G-banding) and for chromosome 17 (G-banding and EDISH; kappa > 0.5-0.6). Six of seven patients (five CTCL, one LPP patient) with clonal chromosomal aberrations by G-banding showed continuously active disease and four of them, but none of the other patients, died within 30 months of the detection of the clone. The rate of chromosomal aberrations associates with the activity of CTCL, and has prognostic significance. Aberrations of chromosomes 1, 6 and 11, although increasing with activity of the disease, seem to be a hallmark of existing disease, detectable even in remission. Aberrations of chromosomes 8 and 17 especially associate with active or progressive disease.

Metaphase Harvest and Cytogenetic Analysis of Malignant Hematological Specimens

Cytogenetic analysis of malignant hematological disease is an important methodology used by clinicians and researchers, as observations of clonal chromosomal abnormalities have been shown to have both diagnostic and prognostic significance. The Basic Protocol describes the culture, harvest, and preparation of chromosome spreads from bone marrow aspirates. Five alternate protocols describe adaptations of the Basic Protocol for preparation of specimens from chronic lymphocytic leukemia (CLL) bone marrow, leukemic peripheral blood, CLL peripheral blood, post-bone marrow transplant (post-BMT) peripheral blood, and aplastic anemia bone marrow and peripheral blood. The modifications involve slightly different culture and harvest methods that are necessary to assure optimal results.

Does isochromosome 7q mandate bone marrow transplant in children with Shwachman-Diamond syndrome?

We report on nine children with Shwachman-Diamond syndrome (SDS), eight of whom had clonal abnormalities of chromosome 7. Seven children had an isochromosome 7 [i(7)(q10)] and one a derivative chromosome 7, all with an apparently identical (centromeric) breakpoint. Children with SDS are predisposed to myelodysplasia (MDS) and acute myeloid leukaemia (AML) often with chromosome 7 abnormalities. Allogeneic transplants have been used to treat these children, however, they are a high-risk transplant group and require careful evaluation. Three of the children were transplanted but only one survived, who to our knowledge remains the longest surviving SDS transplant patient (4.5 years +). The six non-transplanted children are well. In classic MDS, chromosome 7 abnormalities are associated with rapid progression to acute leukaemia; however, we present evidence to suggest that isochromosome 7q may represent a separate disease entity in SDS children. This is a particularly interesting finding given that the SDS gene has recently been mapped to the centromeric region of chromosome 7. Our studies indicate that i(7)(q10) is a relatively benign rearrangement and that it is not advisable to offer allogeneic transplants to SDS children with i(7)(q10) alone in the absence of other clinical signs of disease progression.

Acute lymphoblastic leukaemia: diagnosis and classification

Acute lymphoblastic leukaemia (ALL) is a heterogeneous disease with distinct biological and prognostic groupings. Diagnosis relies on traditional cytomorphological and immunohistochemical evaluation of the leukaemic blasts. Subsequently, cytogenetic analysis identifies clonal numeric and/or structural chromosomal abnormalities that may be present, thus confirming the subtype classification and providing important prognostic information for treatment planning. The major chromosomal abnormalities in ALL are t(9;22)(q34;q11), t(12;21)(p13;q22), t(4;11)(q21;q23), t(1;19)(q23;p13), 8q24 translocations and hyperdiploidy. Generally, hyperdiploidy, occurring most frequently in paediatric cases, is associated with a good prognosis, while hypodiploidy confers a poor prognosis. Among structural chromosomal abnormalities, the t(9;22)(q34;q11) resulting in the BCR/ABL fusion protein, and rearrangements of the MLL gene, confer a poor prognosis in both children and adults, while t(12;21)(p13;q22), resulting in the TEL/AML1 fusion protein, and del (12p) confer a good prognosis. More recently, additional diagnostic and prognostic information has been gained from fluorescence in situ hybridization (FISH) and DNA microarray techniques.

Clonal rearrangement of 15p11.2, 16p11.2, and 16p13.3 in a case of nodular fasciitis: additional evidence favoring nodular fasciitis as a benign neoplasm and not a reactive tumefaction

This article describes a case of nodular fasciitis with the karyotype 47,XY,+4 [3]/46,XY,add(15)(p11.2), t(16;16)(p13.3;p11.2) [2]. The presence of clonal chromosomal abnormalities in this case, as well as in three previously reported cases, indicates that nodular fasciitis is a benign neoplasm and not a reactive lesion.

Exploring polycythaemia vera with fluorescence in situ hybridization: additional cryptic 9p is the most frequent abnormality detected.

Between 1986 and 2001, 220 patients with polycythaemia vera (PV) were studied using conventional cytogenetics. Of 204 evaluable patients, 52 (25.4%) had clonal abnormalities. The recurrent chromosomal rearrangements were those of chromosome 9 (21.1%), del(20q) (19.2%), trisomy 8 (19.2%), rearrangements of 13q (13.4%), abnormalities of 1q (11.5%), and of chromosomes 5 and 7 (9.6%). Subsequent analysis of 32 patients, performed at follow-up of up to 14.8 years, revealed new clonal abnormalities in five patients and the disappearance of an abnormal clone in four. Eleven patients remained normal up to 11.5 years and seven patients maintained an abnormality for over 10 years. Fifty-three patients were studied retrospectively using interphase fluorescence in situ hybridization (I-FISH), utilizing probes for centromere enumeration of chromosomes 8 and 9, and for 13q14 and 20q12 loci. Conventional cytogenetics demonstrated clonal chromosome abnormalities in 23% of these 53 patients. The addition of I-FISH increased the detection of abnormalities to 29% and permitted clarification of chromosome 9 rearrangements in an additional 5.6% of patients. FISH uncovered rearrangements of chromosome 9 in 53% of patients with an abnormal FISH pattern, which represented the most frequent genomic alteration in this series.