Overrepresentation Of Chromosome Research Articles

I-FISH Guided Cytogenetic Study of Non-Hodgkin Lymphomas in Children and Adolescents: Correlation with Etiology and Outcome

Introduction: Pediatric non-Hodgkin lymphomas (NHLs) comprise approximately 10% of all childhood cancers. The diagnosis requires extensive workup with multiple ancillary studies. Genetic testing using fluorescence in situ hybridization (FISH) is a cytogenetic approach that is often utilized in pediatric NHL. Patients and Methods: Our study included 146 children (113 boys-33 girls), aged 0.33-17.8 years (median 9.16 years), with NHL diagnosis based on histopathology (table 1). The histological diagnosis was based on the complete microscopic and immunohistochemical study of infiltrated tissue. Touch imprints from the diagnostic biopsy samples were further investigated with i-FISH (table 2). Results: In all BL cases MYC gene rearrangement was identified. At least one additional chromosomal aberration was also found in 47 patients. Six hyperdiploid cases were identified among 72 children (8.3%), with at least 3 chromosomes involved. Interestingly, there were no cases of refractory disease, relapse, or death among hyperdiploid patients, and their overall survival (OS) was comparable to that of MYC rearrangement subgroup, a unique finding. Among LBL patients, a high frequency of 9p21 region deficiency was found, as in Acute Lymphoblastic Leukemia (ALL). Also, the chromosomes most frequently involved in hyperdiploid B-LBL (X,17,21) were identical to chromosomes commonly overrepresented in ALL. In contrast, the absence of cases positive for ETV6/RUNX1 hybrid gene is surprising. Possibly, the incidence of the most common cytogenetic atypias is different between leukemia and lymphoma. Of note, the two patients with KMT2A rearrangement achieved complete remission after first-line therapy. Finally, we identified cases with a normal karyotype but existing cytogenetic atypia demonstrable by i-FISH exclusively in LBLs. ALK gene rearrangement was found in all ALCL patients while no MYC gene rearrangement was found. At least one additional atypia was identified in 6/12 patients. Interestingly, ALCL patients had proportionally more recurrences than any other histological category, but without a corresponding increase in mortality. Among DLBCL group we found the highest rate of hyperdiploidy (22.2%). Only two (non-hyperdiploid) patients with BCL6 gene rearrangement were found. The single patient who relapsed had an IGL gene rearrangement, suggesting activation of an oncogene in the context of reciprocal chromosomal translocation involving the 22q11 region. No MYC or BCL2 gene rearrangements were found among DLBCL cases. In hyperdiploid patients, overrepresentation of chromosome 8 was found, along with overrepresentation of chromosome 3 (and, in addition, 18 in one of the two cases). This combination of atypias apparently leads to supernumerary copies of MYC gene, simultaneously with the presence of supernumerary alleles of BCL6 (or BCL2, respectively). Regarding findings in FL, MZL and PTLD, due to the small number of patients in these subgroups, any observation is of limited value. Absence of BCL2 gene rearrangement in childhood FL was confirmed. In the study's only patient with MZL, the identification of trisomy 3 may not be accidental, since this atypia is common in the corresponding adult disease. Of particular interest is the one patient with PTLD. Although monomorphic Burkitt-type PTLD was diagnosed and B-clonality documented based on VDJ recombination of IGH gene, marrow karyotyping and thorough i-FISH screening revealed no chromosomal atypia. The phenomenon has been highlighted in the literature and indicates that PTLD's aggressive clinical course is not necessarily associated with genomic instability and damage. In our study no patient met double-hit lymphoma criteria. We might wonder whether, in our series, the hyperdiploid patients with supernumerary copies of intact MYC, BCL2 and/or BCL6 genes constitute a subgroup of the "alternative" double hit lymphomas. With a median follow-up time of 61.5 months (range 7-123 months), 20 patients succumbed, yielding: 3-year and 5-year progression free survival (PFS) in all patients 84.5% και 82.5% respectively, and 3-year and 5-year OS in all patients 86.7%. Conclusions: This extensive i-FISH investigation provides clinically meaningful information on the genetic profile of NHLs, raises new questions, and points to directions for further investigation within the field of childhood lymphoproliferation. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

PS921 INACTIVATION OF SH2B3 THROUGH CN‐LOH 12Q IS UNIQUELY ASSOCIATED WITH B‐CELL PRECURSOR ALL WITH IAMP21 OR OTHER CHROMOSOME 21 GAIN

Background:In more than 30% of childhood B‐cell precursor acute lymphoblastic leukaemia (B‐ALL), chromosome 21 sequence is overrepresented through constitutional or acquired aneuploidy or structural rearrangements, exemplified by intrachromosomal amplification of chromosome 21 (iAMP21). How these abnormalities promote B‐ALL remains obscure but a mechanistic link is suggested by the existence of shared co‐occurring abnormalities.Aims:We aimed to identify and characterise acquired genetic abnormalities that cooperate with amplification or aneuploidy of chromosome 21 to promote B‐ALL.Methods:Regions of copy neutral loss of heterozygosity and deletion were defined by analysis of SNP6.0 arrays, methylation arrays were used to assess loss of imprinting. The mutational status of SH2B3 was determined by amplicon sequencing and a homology model based on the resolved structure of the Sh2 domain of Sh2b1 was used to assess the impact of an acquired in‐frame substitution. STAT activation status was determined by flow cytometric immunophenotyping.Results:Analysis of B‐ALL patients with iAMP21, other structural amplifications of chromosome 21 or constitutional or acquired additional whole copies of chromosome 21 (n = 99), revealed recurrent CN‐LOH of 6p, 9p and 12q. In patients without overrepresentation of chromosome 21, CN‐LOH 6p and 9p were also recurrent but intriguingly, CN‐LOH 12q was absent, among our own (n = 203) or published cases (n = 974). Further analysis demonstrated CN‐LOH 12q was not associated with loss of imprinting but with homozygous mutations or deletions of the adaptor protein, SH2B3. In patients without CN‐LOH 12q, bi‐allelic abnormalities of SH2B3 occurred, but only in iAMP21‐ALL, giving an overall incidence of 18% in this sub‐type. Taking into account our own cohort, analysis of archival array data and review of published cases, we conclude that in B‐ALL, SH2B3 abnormalities are invariably bi‐allelic, frequent in iAMP21‐ALL, recurrent but less common in association with acquired aneuploidy 21 but extremely rare in the absence of overrepresentation of chromosome 21. Importantly, as iAMP21 patients are now uniformly treated as high risk, preliminary analysis of 26 patients treated on UKALL97/99 (n = 5) or UKALL2003 (n = 21), linked 12q abnormalities to poor outcome in iAMP21‐ALL (p = 0.03). Homology modelling of an iAMP21‐ALL associated R392W mutation in the SH2 domain of SH2B3 demonstrated loss of critical interactions required for binding and suppression of activated JAK. Further implicating the JAK/STAT pathway as one target for SH2B3 tumour suppressor activity, stimulation with IL7 of iAMP21‐ALL patient derived xenograft cells, with but not without SH2B3 inactivation, resulted in activation of STAT5 though not other STATs.Summary/Conclusion:Although chromosome 21 copy number profiles are highly heterogeneous in iAMP21‐ALL a limited number of candidate oncogenes are consistently amplified, overexpressed and spared from disruption by structural rearrangements. From our data we infer that in iAMP21‐ALL, high expression of one or more of these candidate genes creates strong pressure for loss of SH2B3 function while lower but still elevated expression of the same gene/s, resulting from gain of one or two copies of whole chromosome 21, produces a similar though weaker selective environment. Since JAK/STAT activation is common in B‐ALL without gain of chromosome 21 and given the near‐exclusive association we observed, we are currently exploring the possibility that SH2B3 also interacts with other pathways specifically activated by increased doses of chromosome 21 genes.

SH2B3 inactivation through CN-LOH 12q is uniquely associated with B-cell precursor ALL with iAMP21 or other chromosome 21 gain

In more than 30% of B-cell precursor acute lymphoblastic leukaemia (B-ALL), chromosome 21 sequence is overrepresented through aneuploidy or structural rearrangements, exemplified by intrachromosomal amplification of chromosome 21 (iAMP21). Although frequent, the mechanisms by which these abnormalities promote B-ALL remain obscure. Intriguingly, we found copy number neutral loss of heterozygosity (CN-LOH) of 12q was recurrent in iAMP21-ALL, but never observed in B-ALL without some form of chromosome 21 gain. As a consequence of CN-LOH 12q, mutations or deletions of the adaptor protein, SH2B3, were converted to homozygosity. In patients without CN-LOH 12q, bi-allelic abnormalities of SH2B3 occurred, but only in iAMP21-ALL, giving an overall incidence of 18% in this sub-type. Review of published data confirmed a tight association between overrepresentation of chromosome 21 and both CN-LOH 12q and SH2B3 abnormalities in B-ALL. Despite relatively small patient numbers, preliminary analysis linked 12q abnormalities to poor outcome in iAMP21-ALL (p = 0.03). Homology modelling of a leukaemia-associated SH2 domain mutation and in vitro analysis of patient-derived xenograft cells implicated the JAK/STAT pathway as one likely target for SH2B3 tumour suppressor activity in iAMP21-ALL.

Rapid Prenatal Testing Using Semiconductor Sequencing?

Recent developments in sequencing technology have had a large impact in several areas of human genetics. One area in which the implementation of this new technology is closest to clinical use is prenatal testing. One tube of blood drawn from a pregnant woman is sufficient for testing the unborn child for Down syndrome with high diagnostic sensitivity and specificity. Approximately 10% of the DNA in maternal plasma is of fetal origin (1). Next-generation sequencing (NGS)2 allows the parallel determination of the chromosomal origin for millions of plasma DNA molecules. This capability allows the detection of an overrepresentation of chromosome 21 in the case of a fetus with Down syndrome, although the majority of the sequenced molecules are derived from the healthy mother. This noninvasive testing will replace invasive tests, which come with a small risk of miscarriage. Several NGS platforms have proved the feasibility of the detection of fetal trisomies (2–5 …

Chromosomal imbalances, 11q21 rearrangement and MECT1-MAML2 fusion transcript in mucoepidermoid carcinomas of the salivary gland

The aim of this study was to determine genetic alterations in mucoepidermoid carcinomas of the salivary gland in association with clinical and histopathological parameters. Nineteen formalin-fixed, paraffin-embedded tumors were analysed by using comparative genomic hybridization (CGH), fluorescence in situ hybridization (FISH) on interphase nuclei and reverse transcriptase-polymerase chain reaction (RT-PCR) for detection of MECT1-MAML2 fusion transcript. The CGH analysis showed an overrepresentation of chromosome X and losses of entire chromosomes or regions on chromosome 1, 2, and 15 as the most frequent copy number changes. In 37% of the analysed tumors a MAML2-rearrangement by interphase FISH was detected, whereas 58% of the samples showed expression of MECT1-MAML2 fusion transcript. We conclude that the presence of MAML2-rearrangement as well as of MECT1-MAML2 fusion transcript may reflect a more favourable prognosis and may be a useful marker for clinical prediction of the biological behavior of these tumors as previously reported.

Genomic copy number and expression patterns in testicular germ cell tumours

Testicular germ cell tumours of adults and adolescents (TGCT) include seminomas (SE) and nonseminomas (NS), with spermatocytic seminomas (SSE) representing a distinct entity in older men. SE and NS have gain of 12p material in all cases, whereas SSE are associated with overrepresentation of chromosome 9. Here, we compare at the chromosomal level, copy number imbalances with global expression changes, identified by comparative expressed sequence hybridisation analyses, in seven SE, one combined tumour, seven NS and seven cell lines. Positive correlations were found consistent with copy number as a main driver of expression change, despite reported differences in methylation status in SE and NS. Analysis of chromosomal copy number and expression data could not distinguish between SE and NS, in-keeping with a similar genetic pathogenesis. However, increased expression from 4q22, 5q23.2 and 9p21 distinguished SSE from SE and NS and decreased copy number and expression from 2q36–q37 and 6q24 was a specific feature of NS-derived cell lines. Our analysis also highlights 19 regions with both copy number and expression imbalances in greater than 40% of cases. Mining available expression array data identified genes from these regions as candidates for involvement in TGCT development. Supplementary data is available at http://www.crukdmf.icr.ac.uk/array/array.html.

Over-representation of specific regions of chromosome 22 in cells from human glioma correlate with resistance to 1,3-bis(2-chloroethyl)-1-nitrosourea

BackgroundGlioblastoma multiforme is the most malignant form of brain tumor. Despite treatment including surgical resection, adjuvant chemotherapy, and radiation, these tumors typically recur. The recurrent tumor is often resistant to further therapy with the same agent, suggesting that the surviving cells that repopulate the tumor mass have an intrinsic genetic advantage. We previously demonstrated that cells selected for resistance to 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) are near-diploid, with over-representation of part or all of chromosomes 7 and 22. While cells from untreated gliomas often have over-representation of chromosome 7, chromosome 22 is typically under-represented.MethodsWe have analyzed cells from primary and recurrent tumors from the same patient before and after in vitro selection for resistance to clinically relevant doses of BCNU. Karyotypic analyses were done to demonstrate the genetic makeup of these cells, and fluorescent in situ hybridization analyses have defined the region(s) of chromosome 22 retained in these BCNU-resistant cells.ResultsKaryotypic analyses demonstrated that cells selected for BCNU resistance were near-diploid with over-representation of chromosomes 7 and 22. In cells where whole copies of chromosome 22 were not identified, numerous fragments of this chromosome were retained and inserted into several marker and derivative chromosomes. Fluorescent in situ hybridization analyses using whole chromosome paints confirmed this finding. Additional FISH analysis using bacterial artificial chromosome probes spanning the length of chromosome 22 have allowed us to map the over-represented region to 22q12.3–13.32.ConclusionCells selected for BCNU resistance either in vivo or in vitro retain sequences mapped to chromosome 22. The specific over-representation of sequences mapped to 22q12.3–13.32 suggest the presence of a DNA sequence important to BCNU survival and/or resistance located in this region of chromosome 22.

Amplification and overexpression of CKS1B at chromosome band 1q21 is associated with reduced levels of p27 Kip1 and an aggressive clinical course in multiple myeloma

The molecular basis for aggressive transformation of multiple myeloma (MM) and other cancers is not completely understood. Global gene expression profiling on highly purified malignant plasma cells from 351 newly diagnosed patients with MM treated with autologous stem cell transplantation revealed a statistically significant over-representation of chromosome 1 genes in a group of 70 genes whose expression was linked to poor outcome. In particular, over-expression of CKS1B , which maps to an amplicon at 1q21 in myeloma and regulates SCF Skp2 -mediated ubquitination and proteolysis of the cyclin dependent kinase inhibitor p27 Kip1 was significantly over-expressed in patients with poor survival. Interphase fluorescence in-situ hybridization revealed that CKS1B expression was strongly correlated with DNA copy number in a subset of 197 cases ( P

Interphase chromosomal abnormalities and mitotic missegregation of hypomethylated sequences in ICF syndrome cells

The immunodeficiency, centromeric region instability, facial anomalies (ICF) syndrome is a rare autosomal recessive disease. Usually, it is caused by mutations in the DNA methyltransferase 3B gene, which result in decreased methylation of satellite DNA in the juxtacentromeric heterochromatin at 1qh, 16qh, and 9qh. Satellite II-rich 1qh and 16qh display high frequencies of abnormalities in mitogen-stimulated ICF lymphocytes without these cells being prone to aneuploidy. Here we show that in lymphoblastoid cell lines from four ICF patients, there was increased colocalization of the hypomethylated 1qh and 16qh sequences in interphase, abnormal looping of pericentromeric DNA sequences at metaphase, formation of bridges at anaphase, chromosome 1 and 16 fragmentation at the telophase-interphase transition, and, in apoptotic cells, micronuclei with overrepresentation of chromosome 1 and 16 material. Another source of anaphase bridging in the ICF cells was random telomeric associations between chromosomes. Our results elucidate the mechanism of formation of ICF chromosome anomalies and suggest that 1qh-16qh associations in interphase can lead to disturbances of mitotic segregation, resulting in micronucleus formation and sometimes apoptosis. This can help explain why specific types of 1qh and 16qh rearrangements are not present at high frequencies in ICF lymphoid cells despite diverse 1qh and 16qh aberrations continuously being generated.

Molecular genetic studies on ganglioglioma

To study the genetic alterations of ganglioglioma through the entire genome, and to investigate the pathogenesis of this neoplasm. Comparative genomic hybridization was used to provide an overview of genetic abnormalities in gangliogliomas. Five cases of gangliogliomas, including 3 males and 2 females, were studied genetically. Loss of genetic materials on the short arm of chromosome 9(9p) was a common genetic alteration found in 3 of 5 cases. Overrepresentation of chromosome 7 was another recurrent chromosomal imbalance, which was further confirmed by fluorescence in situ hybridization. Immunohistochemical analysis was performed on epidermal growth factor receptor (EGFR), which was located on 7p11-p13. All five cases revealed no abnormal expression of EGFR. On the other hand, genetic imbalances were also involved in multiple chromosomes including 2q33-q34, 8q12-q22, 14q21-qter, 15q26-qter and Y. Loss of genetic materials on chromosome 9p and gain on chromosome 7 may be associated with the pathogenesis of this neoplasm.

Investigation of MYCN status in neuroblastoma by fluorescence in situ hybridization

Neuroblastoma, a form of neuroblastic tumor, is one of the most common neoplasms seen in early childhood. The diverse clinical behavior of this tumor is most probably explainable by the heterogeneity in the associated genetic changes. We investigated 12 neuroblastoma patients for MYCN amplification and chromosome 2 aneusomy by fluorescence in situ hybridization (FISH) and results were correlated with conventional cytogenetics. Samples from both primary tumor tissue and bone marrow metastasis were available in two cases. The copy number of MYCN oncogene paralleled that of chromosome 2 in 10 cases, whereas two cases (16.7%) showed numerous distinct signals within the nuclei of the tumor cells, consistent with MYCN amplification as double minute (dmin). The morphology of dmin in one case was of an extremely small type and might potentially be missed by conventional chromosome analysis. Discordant cytogenetics and FISH results was observed between primary tumor and metastasis disease in one case, with loss of chromosome 2 tetrasomic and pentasomic cells as well as over-representation of chromosome 2 disomic cells harboring MYCN amplification in bone marrow deposits. Our study reaffirmed the need for MYCN status to be determined in light of chromosome 2 copy number, as recommended by published guidelines. We also showed that genetic heterogeneity might occur between primary tumor and bone marrow metastasis. Finally, atypical dmin morphology when encountered would need confirmation by FISH study.

Detection of genetic alterations in primary bladder carcinoma with dual-color and multiplex fluorescence in situ hybridization

Cytogenetic studies of bladder cancer have shown several nonrandom aberrations. Numerical aberrations of both sex chromosomes were investigated in 32 primary bladder tumors with bicolor fluorescence in situ hybridization (FISH). Loss of chromosome Y and overrepresentation of chromosome X were observed in subgroups of male patients. Chromosome X was represented normally in female patients. Two of the above primary bladder tumors, a transitional cell carcinoma (TCC) and an adenocarcinoma, were further analyzed with both multiplex FISH (24-color M-FISH) and G-banding. Both cases exhibited 1) common breakpoints on 5q11∼q12 and 15q24; 2) involvement of the pericentromeric area of chromosome 13; 3) structural abnormalities of chromosomes 8 and 17, with loss of material on the short arm; 4) structural abnormalities involving chromosome 11; and 5) loss of chromosome Y. The TCC case also exhibited structural abnormalities of chromosome 9, resulting in loss of 9q. The combined G-banding and M-FISH findings could help reveal regions potentially involved in bladder tumorigenesis.

Novel chromosome findings in bladder cancer cell lines detected with multiplex fluorescence in situ hybridization

Bladder cancer is a common neoplasm worldwide, consisting mainly of transitional cell carcinomas, while squamous, adenocarcinoma, and sarcomatoid bladder cancers account for the remaining cases. In the present study, multiplex fluorescence in situ hybridization (M-FISH) has been used to characterize chromosome rearrangements in eight transitional and one squamous cell carcinoma cell line, RT112, of UMUC-3, 5637, CAT(wil), FGEN, EJ28, J82, 253J, and SCaBER. Alterations of chromosome 9 are the most frequent cytogenetic and molecular findings in transitional cell carcinomas of all grades and stages, while changes of chromosomes 3, 4, 8, 9, 11, 14, and 17 are also frequently observed. In the present study, alterations previously described, including del(8)(p10), del(9)(p10), del(17)(p10), and overrepresentation of chromosome 20, as well as several novel findings, were observed. These novel findings were a del(15)(q15) and isochromosome 14q, both occurring in three of nine cell lines examined. These abnormalities may reflect changes in bladder tumor biology. M-FISH represents an effective preliminary screening tool for the characterization of complex tumor karyotypes.

Chromosomal gains and losses are uncommon in hairy cell leukemia: a study based on comparative genomic hybridization and interphase fluorescence in situ hybridization

In contrast to other subtypes of lymphoproliferative malignancies, the genetic mechanisms underlying the pathogenesis of hairy cell leukemia (HCL) are unknown. We studied densely infiltrated splenic tissue of 14 cases of HCL for the presence of chromosomal gains and losses by comparative genomic hybridization (CGH). Chromosomal imbalances were detected in only four of the 14 cases. Chromosomal gains involved the regions 5q13–q31 (two cases) and 1p32–p36.2 (one case). A loss of the region 11q14–q22 was found in one additional patient. The imbalances affecting the regions 5q and 11q were confirmed by interphase fluorescence in situ hybridization (FISH) using PAC clone 144G9 (5q31) and YAC clones 755B11 (11q22.3–q23.1) and 801E11 (11q22.3–q23.1 spanning the ATM gene) and occurred in 61% to 75% of analyzed nuclei. The latter DNA probes and probes hybridizing to chromosomal regions, which are frequently deleted in other subtypes of non-Hodgkin lymphomas (NHL), namely 9p21/ P16 INK4A, 13q14/D13S25, and 17p13/ P53 were subsequently applied to all 14 cases of HCL, but no additional abnormalities were found. We conclude that overrepresentation of chromosome 5 represents a recurrent aberration in HCL and that the commonly overrepresented region resides in 5q13–q31. Chromosomal imbalances including deletions of the tumor suppressor gene loci 9p21/ P16 INK4A, 13q14/D13S25, and 17p13/ P53 rarely occur in HCL in contrast to some other subtypes of B-cell NHL. The pathogenetic role of 11q/ ATM alterations in HCL remains to be determined.

Genetic abnormalities detected by comparative genomic hybridization in a human endometriosis-derived cell line.

Comparative genomic hybridization (CGH) was used in parallel with fluorescence in-situ hybridization (FISH) and conventional karyotyping to perform a genome-wide survey of DNA gains and losses in the endometriosis-derived permanent cell line, FbEM-1. The cytogenetic analysis showed a complex karyotype with numerical changes and multiple chromosome aberrations, including the der(1) complement marker exhibiting a large homogenous staining region (HSR). The chromosomal rearrangement interpreted as der(5) t(5;6)(q34;p11) was found in the majority of the metaphases indicating a clonal abnormality. Repeated CGH experiments demonstrated over-representation of chromosomes 1, 2, 3, 5, 6p, 7, 16, 17q, 20, 21q and 22q, while chromosomes 6q, 9, 11p, 12, 13q, 18 and X were under-represented. Using DNA from the original endometriotic tissues, including a peritoneal implant and ovarian endometrioma, CGH analysis revealed loss of DNA copy number on 1p, 22q and chromosome X, while gain was found on chromosomal arms 6p and 17q. FISH analysis confirmed that the gain at 17q includes amplification of the proto-oncogene HER-2/neu in 16% of the FbEM-1 nuclei and in 12% of cells from the primary ovarian endometrioma tissue. These findings demonstrate that FbEM-1 cells share certain molecular cytogenetic features with the original tissue and suggest that chromosomal instability is important in the development of endometriosis.

Cytogenetics of hepatoblastoma: further characterization of 1q rearrangements by fluorescence in situ hybridization: an international collaborative study.

Hepatoblastoma (HBT) is the most common hepatic neoplasm in children. This notwithstanding, little is known about pathogenetic factors, such as genetic abnormalities, of importance for the development and progression of this tumor type. To date, only 33 cytogenetically abnormal HBT have been published, and trisomies for chromosomes 2 and 20 have been shown to be the most frequent aberrations. Recently, unbalanced translocations involving proximal 1q have been described in several HBT, suggesting that a pathogenetically important gene maps to 1q. Six primary and one recurrent HBT were cytogenetically analyzed after short-term tissue culture. In addition, fluorescence in situ hybridization (FISH) studies, using locus-specific probes, were performed on three of these pediatric HBT as well as on one previously reported adult HBT. Total or partial trisomy 8, gain of chromosome 20, and structural rearrangements of chromosome 1 were detected in three HBT, and overrepresentation of chromosome 2 material was found in two HBT. The adjacent chromosome bands 1q12 and 1q21 were involved in three translocations, t(1;2), t(1;4), and t(1;11), which were all unbalanced and resulted in gain of 1q material. The previously reported adult HBT displayed 1q deletions with breakpoints at 1q12-21. FISH analyses of the 1q rearrangements revealed that all breakpoints were within the heterochromatic region. These findings provide further support for the importance of trisomies 2, 8, and 20 and rearrangements of 1q in the development of HBT. Furthermore, the consistent localization of breakpoints within the heterochromatic segment of chromosome 1 suggests that the important pathogenetic consequence of 1q abnormalities is the resulting genomic imbalance rather than a specific gene rearrangement.

Analysis by FISH of the spectrum of chromosome aberrations induced by X-rays in G0 human lymphocytes and their fate through mitotic divisions in culture.

The induction, distribution, and persistence of chromosome aberrations in human lymphocytes exposed to X-rays in G0 were analyzed in 48-, 70-, and 94-hr cultures by conventional metaphase analysis and painting of chromosomes 1, 2, and 4 by FISH. All cells that had been scored by FISH were relocated to determine by differential staining of chromatids whether they had passed through 1, 2, or > or =3 divisions. FISH revealed a dose-dependent induction of stable and unstable aberrations, while chromatid labeling showed mitotic lag caused by irradiation in G0. Relative to their DNA contents, there was a small but significant overrepresentation of chromosome 4 and underrepresentation of chromosome 2 among the aberrations involving chromosomes 1, 2, and 4. FISH slightly underestimated the genomic frequency of unstable aberrations measured by conventional metaphase analysis. There was a slight excess of translocations relative to dicentrics, but the data are compatible with the 1:1 ratio expected from cytogenetic theory. Many of the translocations were apparently incomplete (i.e., nonreciprocal). Incomplete translocations were more frequent at higher X-ray dose and in first division, suggesting that they may be associated with complex damage and are more apt to be lost in mitosis than complete translocations. Among the incomplete translocations, t(Ab) outnumbered t(Ba) -- a difference ascribable to the FISH technique. Aberration frequencies declined as the cells divided in culture. The overall decline in the frequency of aberrant cells (approximately 29% per cell generation) reflects a rapid decline in dicentrics and fragments (approximately 60% per cell generation) and the relative stability of translocations. The frequency of translocation-bearing cells underwent a modest decline in culture (approximately 13% per cell generation).

Chromosome alterations in breast carcinomas: frequent involvement of DNA losses including chromosomes 4q and 21q.

Comparative genomic hybridization was applied to map DNA gains and losses in 39 invasive ductal breast carcinomas. Frequent abnormalities included gains on chromosomal regions 1q, 8q, 11q12-13, 16p, 19, 20q and X as well as frequent losses on 1p, 5q, 6q, 9p, 11q, 13q and 16q. Furthermore, frequent losses on 4q (20 cases) and 21q (14 cases) were found for the first time in this tumour type. High copy number amplifications were observed at 8q12-24, 11q11-13 and 20q13-ter. Highly differentiated tumours were associated with gains on 1q and 11q12-13 along with losses on 1p21-22, 4q, 13q, 11q21-ter. Undifferentiated breast carcinomas were characterized by additional DNA imbalances, i.e. deletions of 5q13-23, all of chromosome 9, the centromeric part of chromosome 13 including band 13q14 and the overrepresentation of chromosome X. We speculate that these changes are associated with tumour progression of invasive ductal breast cancer.

An Increased Frequency of Numerical Chromosomal Abnormalities and 1p36 Deletions in Isolated Cells from Paraffin Sections of Malignant Melanomas by Means of Interphase Cytogenetics

At present, little information is available on tumor and stage-specific chromosomal aberrations in malignant melanoma. Therefore, we applied fluorescence in situ hybridization on isolated interphase cells from paraffin sections of 25 cases of malignant melanomas, comprising 17 primary tumors (PTs) and 8 metastases (MTs) in various anatomical sites. We used centromeric probes for chromosomes 1, 7, 9, 10, 11, 12, 15, 17, 18, X, and Y and a midisatellite probe localized in 1p36. Four of the PTs and 5 of the MTs showed polyploidy for all applied probes. The most frequent type of numerical aberration was an overrepresentation of chromosomes 1 (3 PTs, 5 MTs) and 7 (3 PTs, 1 MT), and an underrepresentation of chromosomes 9 (3 PTs) and 10 (6 PTs, 5 MTs). The Y chromosome was lost in all male tumors. In addition, we observed monosomy 11, 12, 15, 17 or 18, and trisomy 12 or 17. Only 1 PT showed no aberrations for any applied DNA probe. A deletion in the near-telomeric region of 1p36 was found surprisingly often (9 PTs, 7 MTs). Our results suggest that the loss of gene(s) in this region is an important event in the pathogenesis of malignant melanoma of the skin.

Cytogenetic aberrations and DNA ploidy in soft tissue sarcoma: A southwest oncology group study

We performed cytogenetic analysis and determined DNA content by flow cytometry (FCM) on freshly disaggregated tumor biopsies from 45 patients with soft tissue sarcomas (STG). Cytogenetically aberrant clones characterized 30 (67%) tumors, with the remaining 15 yielding normal karyotypes with or without nonclonal aberrations. No tumors with multiple unrelated clones were observed. Among the 30 tumors with clonally abnormal karyotypes, 21 (70%) had near-diploid stemlines, six were near-triploid and three were near-tetraploid. Ten of the clonally aberrant tumors contained nonramdom chromosomal translocations characteristic of histologic subtypes. Overrepresentation of chromosomes 7 and 8 were common numerical aberrations. Structural aberrations most often involved chromosomes 1, 7, 9, 12, and 14. Clustering of breaks in 9p resulting in partial loss of the short arm was frequent. Unstable aberrations including rings, dicentrics, large markers, small numbers of double minutes, and telomeric associations were seen in nine tumors. With FCM, 27 (60%) tumors had aneuploid DNA content and 18 (40%) were DNA diploid. Of those 18 DNA diploid tumors, 11 showed clonal karyotypic aberrations. In addition, apparent discrepancies between the results of the cytogenetics and FCM with respect to ploidy pattern were seen in 13 samples; 11 had DNA content in the peritriploid to peritetraploid range but the corresponding karyotype was normal or near-diploid. When the findings of the cytogenetics and DNA content analyses were combined, an abnormal cell population by one or both methods was detected in 38 (84%) tumors. The concurrent application of standard cytogenetics and DNA ploidy by FCM provide complementary information confirming a high incidence of genetic alterations in STS.