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Results for “Chromosome Breakpoints”

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PubMed2001

Biased distribution of chromosomal breakpoints involving the MLL gene in infants versus children and adults with t(4;11) ALL.

Derivative chromosomes of 40 patients diagnosed with t(4;11) acute lymphoblastic leukemia (ALL) were analysed on the genomic DNA level. Chromosomal breakpoints were identified in most cases within the known breakpoint cluster regions of the involved MLL and AF4 genes. Due to our current knowledge of the primary DNA sequences of both breakpoint cluster regions, specific features were identified at the chromosomal fusion sites, including deletions, inversions and duplications of parental DNA sequences. After separation of all t(4;11) leukemia patients into two age classes (below and above 1 year of age), the analysis of chromosomal fusion sites revealed significant differences in the distribution of chromosomal breakpoints and led to the definition of two hotspot areas within the MLL breakpoint cluster region. This may point to the possibility of different age-linked mechanisms that were leading to t(4;11) chromosomal translocations.

Adult↗

PubMed1988

No statistical association between common fragile sites and nonrandom chromosome breakpoints in cancer cells.

Fragile sites and nonrandom chromosome breakpoints in cancer cells are not distributed at random within the genome, but occur mainly in the light G-bands. If this nonrandom distribution is taken into account and a statistical analysis for the association of these two phenomena within the same chromosome band is carried out, based on the 400-band karyotype, no significant association is found between the common fragile sites and cancer breakpoints although there remains an association between the rare fragile sites and cancer breakpoints. These results, along with other chromosome mapping evidence that rare fragile sites are not at the breakpoint in some cancer chromosome rearrangements, cast serious doubt on any role for fragile sites in oncogenesis.

Chromosome Banding↗

PubMed2006

Chromosome breakpoint distribution of damage induced in peripheral blood lymphocytes by densely ionizing radiation.

PURPOSE: To assess the chromosomal breakpoint distribution in human peripheral blood lymphocytes (PBL) after exposure to a low dose of high linear energy transfer (LET) alpha-particles using the technique of multiplex fluorescence in situ hybridization (m-FISH). MATERIALS AND METHODS: Separated PBL were exposed in G0 to 0.5 Gy 238Pu alpha-particles, stimulated to divide and harvested approximately 48 - 50 hours after exposure. Metaphase cells were assayed by m-FISH and chromosome breaks identified. The observed distribution of breaks were then compared with expected distributions of breaks, calculated on the assumption that the distribution of breaks is random with regard to either chromosome volume or chromosome surface area. RESULTS: More breaks than expected were observed on chromosomes 2 and 11, however no particular region of either chromosome was identified as significantly contributing to this over-representation. The identification of hot or cold chromosome regions (pter,p,cen,q,qter) varied depending on whether the data were compared according to chromosome volume or surface area. CONCLUSIONS: A deviation from randomness in chromosome breakpoint distribution was observed, and this was greatest when data were compared according to the relative surface area of each individual chromosome (or region). The identification of breaks by m-FISH (i.e., more efficient observation of interchanges than intrachanges) and importance of territorial boundaries on interchange formation are thought to contribute to these differences. The significance of the observed non-random distribution of breaks on chromosomes 2 and 11 in relation to chromatin organization is unclear.

Alpha Particles↗

PubMed1985

Cloning the chromosomal breakpoint of t(14;18) human lymphomas: clustering around JH on chromosome 14 and near a transcriptional unit on 18.

Specific chromosomal translocations found in distinct neoplasms suggest that genes that flank such breakpoints play a critical role in transformation. We have characterized the t(14;18)(q32;q21) chromosomal translocation present in over 60% of human follicular lymphomas. We exploited an unexpected rearrangement of an Ig heavy-chain gene to clone the chromosomal breakpoint. An element isolated from 18q21 mediated translocations in all four t(14;18) bearing cell lines and in six of 11 follicular lymphomas, but did not normally rearrange in other B or non-B cells. The breakpoints clustered within a small 4.3 kb region on chromosome 18. The breakpoints on chromosome 14 were focused within or immediately 5' to JH. These breakpoints retained the Ig enhancer region close to a new transcriptional unit identified on chromosome segment 18q21. Since none of the cellular oncogenes are known to map to 18q21, cloning this element provides an opportunity to characterize a potentially new transforming gene.

Cell Line↗

PubMed1998

Fluorescence in situ hybridization characterization of the chromosomal breakpoints in a case with ins(17;3)(q11.2;q21q26.3) and acute monocytic leukemia.

A 63-year-old patient with acute myeloid leukemia of FAB M5 subtype revealing chromosomal breakpoints in 3q21 and 3q26 is presented. Although rearrangements of 3q21 and 3q26 are relatively common in patients with myelocytic malignancies, this is the first report of ins(17;3)(q11.2;q21q26.3). We defined the chromosomal breakpoints and the extent of the insertion by fluorescence in situ hybridization (FISH) with yeast artificial chromosomes (YACs).

Chromosome Aberrations↗

PubMed1991

Patterns of chromosomal breakpoint locations in Burkitt's lymphoma: relevance to geography and Epstein-Barr virus association.

We have examined, by Southern blotting, the patterns of chromosomal breakpoint locations in 55 cases of Burkitt's lymphoma (BL) with respect to geography and Epstein-Barr virus (EBV) association. We have confirmed the association between chromosome 8 breakpoint and geography: 74% of endemic (eBL) but only 9% of sporadic BL (sBL) had breakpoints outside the HindIII fragment encompassing the c-myc gene (P2 less than .00001). Conversely, not only did 91% of sBL manifest a rearranged HindIII fragment, but at least 56% of these cases, in contrast to 17% of eBL cases, had a breakpoint within the first exon or intron of c-myc (P2 less than .004). Breakpoints outside the switch mu (S mu) region (ie, the HindIII fragment encompassing S mu) on chromosome 14 were twice as common overall (73%) as those within S mu (27%), but in the 15 tumors with S mu breakpoints, 13 (87%) had a rearranged c-myc gene. Breakpoints outside the HindIII fragment encompassing c-myc on chromosome 8 were predominantly associated with non-S mu breakpoints on chromosome 14 (85%) and this was the combination most frequently associated with eBL (65%; 6% of sBL, P2 less than .00001). In sBL, the most frequent breakpoint combination was a rearranged c-myc gene with a non-S mu breakpoint (63%; 13% of eBL). Twenty-eight percent of sBL and 13% of eBL had breakpoints both within c-myc and within S mu. EBV DNA was present in 19 of 20 tumors with breakpoints outside c-myc, in none of 7 with a breakpoint in the immediate 5' region of c-myc, in 4 of 5 tumors with breakpoints in the first exon, and in 7 of 12 tumors with breakpoints in the first intron. These data suggest that the pathogeneses of eBL and sBL differ with regard to the mechanism of c-myc deregulation, and probably also with regard to the state of differentiation of the target cell for malignant transformation. We have formulated a testable hypothesis regarding the potential role of EBV in pathogenesis: that it is required to contribute to the deregulation of c-myc in the presence of some, but not all, types of c-myc damage arising from the chromosomal translocations.

Blotting, Southern↗

PubMed2001

Improved definition of chromosomal breakpoints using high-resolution multicolour banding.

Characterisation of chromosome rearrangements using conventional banding techniques often fails to determine the localisation of breakpoints precisely. In order to improve the definition of chromosomal breakpoints, the high-resolution multicolour banding (MCB) technique was applied to identify human chromosome 5 breakpoints from 40 clinical cases previously assessed by conventional banding techniques. In 30 cases (75%), at least one breakpoint was redefined, indicating that MCB markedly improves chromosomal breakpoint localisation. The MCB pattern is highly reproducible and, in contrast to conventional banding pattern, is consistent in both short and elongated chromosomes. This might be of fundamental interest for the detection of chromosomal abnormalities, especially in tumour cells. Moreover, MCB even allows the detection of abnormalities that remain cryptic in GTG-banding analysis.

Chromosome Aberrations↗

PubMed1990

Distribution of X-ray-induced chromosome breakpoints in Down syndrome lymphocytes.

Down syndrome (DS) individuals are known to be predisposed to develop leukemia and their lymphocytes are highly sensitive to the induction of chromosome aberrations by X-rays. A study was conducted to identify the chromosome breakpoints and to evaluate whether site specificity for chromosome breakage and rearrangement may exist which may explain the predisposition phenomenon. DS lymphocytes at the G1 phase of the cell cycle were irradiated with 300, 450, and 600 rad of X-rays. Cells were harvested after 3 days in culture and 193 G-banded karyotypes were analyzed to identify the induced chromosome abnormalities. Out of 273 breakpoints identified, 122 were involved in the formation of stable chromosome rearrangements and 151 in the formation of unstable abnormalities. The Poisson analysis of these breakpoints demonstrated that 16 chromosome bands located in chromosomes 1, 3, 7, 12, 17, 19 and X were preferentially involved in breakage and rearrangement (P less than 0.05). These 16 bands are also found to be locations of "cancer breakpoints," oncogenes, or fragile sites. Many abnormal cells were observed to carry stable chromosome rearrangements only. Therefore, these cells are presumed to be compatible with survival and to be "initiated" in the transformation process. We propose that similar stable and site-specific chromosome rearrangements may exist in proliferating cells in DS individuals after exposure to clastogens and that this abnormality predisposes them to develop leukemia.

Cells, Cultured↗

PubMed1994

Subtelomeric chromosome instability in Plasmodium falciparum: short telomere-like sequence motifs found frequently at healed chromosome breakpoints.

The stability of chromosome ends of the human malaria parasite P. falciparum was analysed using a polymerase chain reaction (PCR) assay that detects potential chromosome breaks that have been healed by the addition of telomere repeats. The data show that the Pf332 and Pf87 genes located in subtelomeric positions of chromosomes 3 and 11, respectively, represent fragile sites. Breakpoints were observed in different regions of these genes. In the broken genes, the DNA sequences preceding the telomere addition sites generally have complementarity to the predicted RNA template of a P. falciparum telomerase ribonucleoprotein enzyme complex. We propose a model for the creation of new telomeres in P. falciparum adjacent to broken ends containing short telomere-like sequence motifs.

Animals↗

PubMed1978

A specific chromosome breakpoint associated with mouse plasmacytomas.

The chromosomes of uncultured cells of the near-diploid mouse plasmacytoma MOPC-31C were studied. The modal number of chromosomes was 44. The tumor lacked two marker chromosomes, reciprocal translocation [rcp t(12; 15)], that in previous studies were found to be common to 3 other uncultured myelomas and 1 cultured mouse myeloma. Through the formation of two markers, rcp t(6; 15), unique to this tumor, however, the tumor shared with other tumors and their specific markers a common breakpoint in chromosome "15 at band D3/E. This breakpoint has been found in all mouse plasmacytomas examined with banding thus far and is considered of possible importance in the development of this tumor.

Animals↗

PubMedDate not supplied

Identification of a clustering of chromosomal breakpoints in the analysis of 203 human primary solid tumor non specific karyotypic rearrangements.

The distribution of 271 chromosomal breakpoints involved in 203 clonal structural non "specific" rearrangements identified in 82 human primary solid tumors of various histologies has been analyzed. According to the "mean + 1 SD" criterion the normalized breakpoint frequency was significantly higher for chromosomes 1p, 3p, 3q, 4q, 6q, 7q, and 11p. Clusters of 3 or more breakpoints were assigned to only 24 of the 329 bands (7%) of the standard karyotype, and 9 high density breakpoint segments have been identified. These results indicate that a nonrandom pattern of chromosomal rearrangements can be extracted from the complex karyotypic changes observed in solid tumors, which suggest that the involved regions play a general role in tumorigenesis.

Chromosome Aberrations↗

PubMed1998

Localization of chromosome breakpoints: implication of the chromatin structure and nuclear architecture.

Restriction endonucleases and ionizing radiations have been extensively used to study the origin of chromosomal aberrations. Although a non-random distribution of chromosome breakpoints induced by these agents has been claimed by several authors, the significance of the chromatin structure and nuclear architecture in the localization of breakpoints is still not well understood. Breakpoint patterns produced by endonucleases targeted to specific genome sequences or by ionizing radiations could provide additional evidence to clarify this point. Results obtained from the localization of breakpoints induced by AluI, BamHI or DNase I as well as by neutrons or gamma-rays in G-banded Chinese hamster ovary (CHO) chromosomes are presented. AluI and BamHI were electroporated into CHO cells either during the G1 or S-phase of the cell cycle. A co-localization of breakpoints was found with a preferential occurrence in G-light bands independent of the cell cycle stage in which aberration production took place. Since AluI and BamHI recognition sequences are partitioned in the housekeeping and tissue-specific subgenomes respectively, we postulated that nuclease sensitive sites in active chromatin could be the main targets for the induction of breakpoints by these endonucleases. This assumption is supported by the finding that DNase I-induced breakpoint patterns in CHO cells are similar to those produced by AluI and BamHI. Digestion of fixed CHO chromosomes with these endonucleases induced G-banding suggesting a higher sensitivity of G-light chromatin. For comparison purposes, CHO cells were irradiated with neutrons or gamma-rays and breakpoints localized in G-banded chromosome aberrations. A higher occurrence of breakpoints in G-light bands was also observed. We detected seven breakage-prone G-light bands that were preferentially damaged by the three endonucleases and by both types of radiation. These results emphasize the possible implication of the chromatin structure and the nuclear architecture in the localization of chromosome breakpoints induced by endonucleases, neutrons and gamma-rays.

Animals↗

PubMed1997

Molecular analysis of the t(8;14)(q24;q11) chromosomal breakpoint junctions in the T-cell leukemia line MOLT-16.

The MOLT-16 cell line was established from the leukemic cells of a patient with T-cell acute lymphoblastic leukemia and contains a t(8;14)(q24;q11) resulting in juxtaposition of sequences downstream of the MYC gene on chromosome 8 and the J region of the T-cell receptor alpha chain gene (TCRA) on chromosome 14. The reciprocal translocation involved a complex rearrangement with two chromosome breakpoints within the TCRAJ region on chromosome 14, resulting in inversion of a 1.4 kb DNA fragment between the two breakpoints. The 5' border of the inversion joints with another segment of chromosome 14, whereas the 3' border joins with a region of chromosome 8 located at least 257 kb downstream of MYC. Extensive deletions have occurred on both chromosomes 8 and 14 in conjunction with the translocation. To investigate the possible involvement of the V(D)J recombinase in this translocation, we analyzed the nucleotide sequences surrounding the translocation breakpoints. The breakpoint on chromosome 14 occurs between a segment coding for a TCRAJ sequence and its hepatamer-nonamer signal. Heptamer-nonamer consensus sequences are also identified on chromosome 8 adjacent to the breakpoint. Inserted N and P nucleotides are observed at the breakpoint junctions.

Amino Acid Sequence↗

PubMed2006

Linksets of tumor chromosome breakpoints related to survival in ovarian adenocarcinoma.

Biological processes are often accompanied by occurrences of multiple events, such as activation of certain cell types, change in prevalence of cell subpopulations (such as T cells), changes in concentration of proteins or peptides, or breaks in chromosomes. Some co-occurrences of these events are by chance, but others may have meaningful relations to the underlying biological process. The methodology of linksets is designed to detect the presence of potentially meaningful co-occurrences. Due to the complex ways in which linksets can determine the observed occurrences of multiple events, some moderately powerful computational methods are necessary for statistical estimation. Here, linkset models are fitted to data on chromosome breakpoints in ovarian adenocarcinomas, in order to answer the question motivating the project that collected them--whether there are nonrandom co-occurrences of breakpoints in particular chromosome regions, and whether these might be of prognostic significance. The results identify breakpoints in 1p1 as associated with early mortality when they occur in linksets of breakpoints in 1p3 and any one of 11q1, 11q2, or 6q2. Conversely, breakpoints in 6p2, 1q3, and 7p1 occur in linksets associated with late mortality. This is, to our knowledge, the first demonstration of a new method for analyzing patterns of event occurrence in biological data.

Adenocarcinoma↗

PubMed2001

Restricted chromosome breakpoint sites on 11q22-q23.1 and 11q25 in various hematological malignancies without MLL/ALL-1 gene rearrangement.

We analyzed 32 patients with various hematological malignancies including acute myelocytic leukemia and non-Hodgkin lymphoma with a breakpoint at 11q22-q25 of chromosome 11, but who did not have rearrangements of the MLL/ALL-1 gene. The breakpoint in each patient was identified by fluorescence in situ hybridization using 21 cosmid probes and 2 YAC probes. Breakpoints for each "rearrangement" involving translocations such as t(1;11), t(2;11), inv(11), t(11;15), and t(10;11) found in 5 of the 11 patients had breakpoints in a small region from Ccl11-430 to Ccl11-526 at 11q22-q23.1. Furthermore, breakpoints for chromosome deletions at 11q21-q23 in 10 patients were located in the same region as that of translocations. A commonly deleted region among 8 patients was identified from Ccl11-526 to Ccl11-555 at 11q23.1. Fluorescence in situ hybridization analysis revealed that breakpoints for additive chromosome [add(11)] aberrations, which had additional material of unknown origin at 11q23 to 11q25 in 11 patients, were not located at 11q23 but rather at the more telomeric site of Ccl11-503 to VIJ(2)2072 at 11q25. These results indicated that the patients had several restricted breakpoint sites, which means that these chromosomal regions have recurrent oncogenes and tumor suppressor genes for pathogenesis for leukemia and lymphoma.

Acute Disease↗

PubMed1996

Chromosome breakpoint at 17q11.2 and insertion of DNA from three different chromosomes in a glioblastoma with exceptional glial fibrillary acidic protein expression.

A glioblastoma that retained glial fibrillary acidic protein (GFAP) in culture has a break in the long arm of chromosome 17 at band 17q11.2. DNA inserted at this breakpoint came from chromosome bands 3p21, 3q23, 16q11.2, and 22q11.2. These chromosome fragments were inserted in band 17q11.2 proximal to the neurofibromatosis-1 (NF-1) gene and neu (HER2; erbB2) oncogene loci. The glioblastoma also contained a reciprocal translocation between 16p12 and 20p12. These structural abnormalities, previously undescribed in gliomas, were demonstrated by high-resolution chromosome banding, microdissection, and fluorescence in situ hybridization (FISH). Numerical changes typical of glioblastoma were present: gain of chromosome 7 and losses of chromosomes 10, 13, and 22. The complex chromosome origin of DNA inserted in this glioma chromosome is described. The association of two infrequent events in this single glioblastoma line, this complex insertion and retention of GFAP expression, is not likely to be a chance occurrence. It raises the possibility of an association between the two events.

Cells, Cultured↗

PubMed2005

Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH.

Understanding the genes and genetic pathways targeted by recurrent chromosomal imbalances in malignancy, along with the molecular mechanisms that generate the imbalances, are important problems in cancer biology. In this report, we demonstrate that oligonucleotide array CGH (oaCGH) analysis can routinely map chromosomal imbalance breakpoints at exon-level resolution, including imbalances that are single copy number genomic alterations. Different tiling-path array designs were used in this study: a whole-genome array with a 6-kb median probe spacing and fine-tiling arrays for selected genomic regions with either 50- or 140-bp median probe spacing. In both array formats, oligonucleotide probes were of isothermal design and were tiled through genic and inter-genic regions. Whole-genome oaCGH analysis of two neuroblastoma cell lines and three primary tumors led to the identification of 58 chromosomal breakpoints that generated 45 large-scale partial chromosomal imbalances (> 2 Mb). An unexpectedly high proportion (34%) of these breakpoint intervals mapped to regions containing segmental duplications. In addition, 88 smaller-sized regions (< 2 Mb) of imbalance were detected, the majority of which mapped to segmentally duplicated regions and may reflect constitutional copy number polymorphisms. The chromosomal breakpoints for 12 recurrent abnormalities exhibited in neuroblastoma tumors and cell lines, including MYCN amplicon boundaries, loss of 3p, loss of 11q, and gain of 17q, could be mapped to intervals ranging from 50 bp to 10 kb in size using high-density fine-tiling oligonucleotide microarrays. Fine-tiling oaCGH analysis provides an unprecedented level of resolution, allowing detailed mapping of recurrent unbalanced chromosomal abnormalities. Supplementary material for this article can be found on the Genes, Chromosomes, and Cancer website at http://www.interscience.wiley.com/jpages/1045-2257/suppmat/index.html.

Chromosome Breakage↗

PubMed1992

Relationship between chemical-induced fragile sites and chromosomal breakpoints in malignant cells in children.

Many fragile sites in the human genome occur at or near chromosomal breakpoints reportedly involved in translocations of DNA material in neoplastic cells. This fact has led some investigators to postulate that fragile sites have a pathogenic role in human neoplasia. To learn whether caffeine-induced fragile sites relate to breakpoints found in the neoplastic cells of an individual patient, we studied lymphocytes from the peripheral blood of 32 patients in remission from malignant disease. Lymphocytes were cultured in medium containing either 5-Fluoro-2'-deoxyuridine (FdU) or FdU plus caffeine, and G-banded metaphases were examined for nonrandom breaks. Analyses of completely G-banded malignant cell chromosomes from 31 of the 32 patients were available for comparison. In only once case, a 5-year-old child with acute lymphoblastic leukemia, did a caffeine-induced fragile site (1q44) coincide with a breakpoint in the neoplastic cells [dup(1)(q21-->q44)]. Our findings suggest that chromosomal abnormalities in childhood malignancies cannot generally be explained by the presence of FdU- or FdU plus caffeine-induced fragile sites.

Adolescent↗