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Cooper DN, Bacolla A, Férec C, Vasquez KM, Kehrer-Sawatzki H, Chen JM. On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease. Hum Mutat 2011; 32:1075-99. [PMID: 21853507 DOI: 10.1002/humu.21557] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 06/17/2011] [Indexed: 12/21/2022]
Abstract
Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher order features of the genomic architecture. The human genome is now recognized to contain "pervasive architectural flaws" in that certain DNA sequences are inherently mutation prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here, we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of noncanonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair and may serve to increase mutation frequencies in generalized fashion (i.e., both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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2
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Kurahashi H, Inagaki H, Ohye T, Kogo H, Tsutsumi M, Kato T, Tong M, Emanuel BS. The constitutional t(11;22): implications for a novel mechanism responsible for gross chromosomal rearrangements. Clin Genet 2011; 78:299-309. [PMID: 20507342 DOI: 10.1111/j.1399-0004.2010.01445.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The constitutional t(11;22)(q23;q11) is the most common recurrent non-Robertsonian translocation in humans. The breakpoint sequences of both chromosomes are characterized by several hundred base pairs of palindromic AT-rich repeats (PATRRs). Similar PATRRs have also been identified at the breakpoints of other nonrecurrent translocations, suggesting that PATRR-mediated chromosomal translocation represents one of the universal pathways for gross chromosomal rearrangement in the human genome. We propose that PATRRs have the potential to form cruciform structures through intrastrand-base pairing in single-stranded DNA, creating a source of genomic instability and leading to translocations. Indeed, de novo examples of the t(11;22) are detected at a high frequency in sperm from normal healthy males. This review synthesizes recent data illustrating a novel paradigm for an apparent spermatogenesis-specific translocation mechanism. This observation has important implications pertaining to the predominantly paternal origin of de novo gross chromosomal rearrangements in humans.
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Affiliation(s)
- H Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan.
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3
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Kurahashi H, Inagaki H, Hosoba E, Kato T, Ohye T, Kogo H, Emanuel BS. Molecular cloning of a translocation breakpoint hotspot in 22q11. Genome Res 2007; 17:461-9. [PMID: 17267815 PMCID: PMC1832093 DOI: 10.1101/gr.5769507] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
It has been well documented that 22q11 contains one of the most rearrangement-prone sites in the human genome, where the breakpoints of a number of constitutional translocations cluster. This breakage-sensitive region is located within one of the remaining unclonable gaps from the human genome project, suggestive of a specific sequence recalcitrant to cloning. In this study, we cloned a part of this gap and identified a novel 595-bp palindromic AT-rich repeat (PATRR). To date we have identified three translocation-associated PATRRs. They have common characteristics: (1) they are AT-rich nearly perfect palindromes, which are several hundred base pairs in length; (2) they possess non-AT-rich regions at both ends of the PATRR; (3) they display another nearby AT-rich region on one side of the PATRR. All of these features imply a potential for DNA secondary structure. Sequence analysis of unrelated individuals indicates no major size polymorphism, but shows minor nucleotide polymorphisms among individuals and cis-morphisms between the proximal and distal arms. Breakpoint analysis of various translocations indicates that double-strand-breakage (DSB) occurs at the center of the palindrome, often accompanied by a small symmetric deletion at the center. The breakpoints share only a small number of identical nucleotides between partner chromosomes. Taken together, these features imply that the DSBs are repaired through nonhomologous end joining or single-strand annealing rather than a homologous recombination pathway. All of these results support a previously proposed paradigm that unusual DNA secondary structure plays a role in the mechanism by which palindrome-mediated translocations occur.
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MESH Headings
- AT Rich Sequence
- Animals
- Base Sequence
- Chromosome Breakage
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 22/genetics
- Cloning, Molecular
- Cricetinae
- DNA/chemistry
- DNA/genetics
- Humans
- Hybrid Cells
- Mice
- Polymerase Chain Reaction
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, DNA
- Translocation, Genetic
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Affiliation(s)
- Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.
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4
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Vorstman J, Jalali G, Rappaport E, Hacker A, Scott C, Emanuel B. MLPA: a rapid, reliable, and sensitive method for detection and analysis of abnormalities of 22q. Hum Mutat 2006; 27:814-21. [PMID: 16791841 PMCID: PMC2814414 DOI: 10.1002/humu.20330] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In this study, essential test characteristics of the recently described multiplex ligation-dependent probe amplification (MLPA) method are presented, using chromosome 22 as a model. This novel method allows the relative quantification of approximately 40-45 different target DNA sequences in a single reaction. For the purpose of this study, MLPA was performed in a blinded manner on a training set containing over 50 samples, including typical 22q11.2 deletions, various atypical deletions, duplications (trisomy and tetrasomy), and unbalanced translocations. All samples in the training set have been previously characterized by fluorescence in situ hybridization (FISH) with cosmid or BAC clones and/or cytogenetic studies. MLPA findings were consistent with cytogenetic and FISH studies, no rearrangement went undetected and repeated tests gave consistent results. At a relative change in comparative signal strength of 30% or more, sensitivity and specificity values were 0.95 and 0.99, respectively. Given that MLPA is likely to be used as an initial screening method, a higher sensitivity, at the cost of a lower specificity, was deemed more appropriate. A receiver operator characteristic (ROC) curve analysis was performed to calculate the most optimal threshold range, with associated sensitivity and specificity values of 0.99 and 0.97, respectively. Finally, performance of each individual probe was analyzed, providing further useful information for the interpretation of MLPA results. In conclusion, MLPA has proven to be a highly sensitive and accurate tool for detecting copy number changes in the 22q11.2 region, making it a fast and economic alternative to currently used methods. The current study provides valuable and detailed information on the characteristics of this novel method.
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Affiliation(s)
- J.A.S. Vorstman
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Rudolf Magnus Institute of Neurosciences, Utrecht, The Netherlands
| | - G.R. Jalali
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - E.F. Rappaport
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - A.M. Hacker
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - C. Scott
- Department of Biostatistics and Data Management Core, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - B.S. Emanuel
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
- Correspondence to: Division of Human Genetics, The Children’s Hospital of Philadelphia, Abramson Research Center, Room 1002, 3615 Civic Center Blvd. Philadelphia, PA 19104-4318.
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5
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Ashley T, Gaeth AP, Inagaki H, Seftel A, Cohen MM, Anderson LK, Kurahashi H, Emanuel BS. Meiotic recombination and spatial proximity in the etiology of the recurrent t(11;22). Am J Hum Genet 2006; 79:524-38. [PMID: 16909390 PMCID: PMC1559541 DOI: 10.1086/507652] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Accepted: 07/10/2006] [Indexed: 01/27/2023] Open
Abstract
Although balanced translocations are among the most common human chromosomal aberrations, the constitutional t(11;22)(q23;q11) is the only known recurrent non-Robertsonian translocation. Evidence indicates that de novo formation of the t(11;22) occurs during meiosis. To test the hypothesis that spatial proximity of chromosomes 11 and 22 in meiotic prophase oocytes and spermatocytes plays a role in the rearrangement, the positions of the 11q23 and 22q11 translocation breakpoints were examined. Fluorescence in situ hybridization with use of DNA probes for these sites demonstrates that 11q23 is closer to 22q11 in meiosis than to a control at 6q26. Although chromosome 21p11, another control, often lies as close to 11q23 as does 22q11 during meiosis, chromosome 21 rarely rearranges with 11q23, and the DNA sequence of chromosome 21 appears to be less susceptible than 22q11 to double-strand breaks (DSBs). It has been suggested that the rearrangement recurs as a result of the palindromic AT-rich repeats at both 11q23 and 22q11, which extrude hairpin structures that are susceptible to DSBs. To determine whether the DSBs at these sites coincide with normal hotspots of meiotic recombination, immunocytochemical mapping of MLH1, a protein involved in crossing over, was employed. The results indicate that the translocation breakpoints do not coincide with recombination hotspots and therefore are unlikely to be the result of meiotic programmed DSBs, although MRE11 is likely to be involved. Previous analysis indicated that the DSBs appear to be repaired by a mechanism similar to nonhomologous end joining (NHEJ), although NHEJ is normally suppressed during meiosis. Taken together, these studies support the hypothesis that physical proximity between 11q23 and 22q11--but not typical meiotic recombinational activity in meiotic prophase--plays an important role in the generation of the constitutional t(11;22) rearrangement.
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Affiliation(s)
- Terry Ashley
- Genetics Department, School of Medicine, Yale University, New Haven, USA
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Kurahashi H, Inagaki H, Ohye T, Kogo H, Kato T, Emanuel BS. Palindrome-mediated chromosomal translocations in humans. DNA Repair (Amst) 2006; 5:1136-45. [PMID: 16829213 PMCID: PMC2824556 DOI: 10.1016/j.dnarep.2006.05.035] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Recently, it has emerged that palindrome-mediated genomic instability contributes to a diverse group of genomic rearrangements including translocations, deletions, and amplifications. One of the best studied examples is the recurrent t(11;22) constitutional translocation in humans that has been well documented to be mediated by palindromic AT-rich repeats (PATRRs) on chromosomes 11q23 and 22q11. De novo examples of the translocation are detected at a high frequency in sperm samples from normal healthy males, but not in lymphoblasts or fibroblasts. Cloned breakpoint sequences preferentially form a cruciform configuration in vitro. Analysis of the junction fragments implicates frequent double-strand-breaks (DSBs) at the center of both palindromic regions, followed by repair through the non-homologous end joining (NHEJ) pathway. We propose that the PATRR adopts a cruciform structure in male meiotic cells, creating genomic instability that leads to the recurrent translocation.
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Affiliation(s)
- Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.
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Arcand SL, Mes-Masson AM, Provencher D, Hudson TJ, Tonin PN. Gene expression microarray analysis and genome databases facilitate the characterization of a chromosome 22 derived homogeneously staining region. Mol Carcinog 2004; 41:17-38. [PMID: 15352123 DOI: 10.1002/mc.20038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Karyotype and fluorescence in situ hybridization (FISH) analyses previously identified a homogeneously staining region (HSR) derived from chromosome 22 in OV90, an epithelial ovarian cancer (EOC) cell line. Affymetrix expression microarrays in combination with the UniGene and Human Genome Browser databases were used to identify the candidate genes comprising the amplicon of the HSR, based on comparison of expression profiles of OV90, EOC cell lines lacking HSRs and primary cultures of normal ovarian surface epithelial (NOSE) cells. A group of probe sets displaying a minimum 3-fold overexpression with a high reliability score (P-call) in OV90 were identified which represented genes that mapped within a 1-2 Mb interval on chromosome 22. A large number of probe sets, some of which represent the same genes, displayed no evidence of overexpression and/or low reliability scores (A-call). An investigation of the probe set sequences with the Affymetrix and Sanger Institute Chromosome 22 Group databases revealed that some of the probe sets displaying discordant results for the same gene were complementary to intronic sequences and/or the antisense strand. Microarray results were validated by RT-PCR. Genomic analysis suggests that the HSR was derived from the amplification of a 1.1 Mb interval defined by the chromosomal map positions of ZNF74 and Hs.372662, at 22q11.21. The deduced amplicon is derived from a complex region of chromosome 22 that harbors low-copy repeats (LCRs). The amplicon contains 18 genes as likely targets for gene amplification. This study illustrates that large-scale expression microarray analysis in combination with genome databases is sufficient for deducing target genes associated with amplicons and stresses the importance of investigating probe set design before engaging in validation studies.
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Affiliation(s)
- Suzanna L Arcand
- Department of Human Genetics, McGill University, Montreal, Canada
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Kurahashi H, Inagaki H, Yamada K, Ohye T, Taniguchi M, Emanuel BS, Toda T. Cruciform DNA structure underlies the etiology for palindrome-mediated human chromosomal translocations. J Biol Chem 2004; 279:35377-83. [PMID: 15208332 PMCID: PMC2810964 DOI: 10.1074/jbc.m400354200] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
There is accumulating evidence to suggest that palindromic AT-rich repeats (PATRRs) represent hot spots of double-strand breakage that lead to recurrent chromosomal translocations in humans. As a mechanism for such rearrangements, we proposed that the PATRR forms a cruciform structure that is the source of genomic instability. To test this hypothesis, we have investigated the tertiary structure of a cloned PATRR. We have observed that a plasmid containing this PATRR undergoes a conformational change, causing temperature-dependent mobility changes upon agarose gel electrophoresis. The mobility shift is observed in physiologic salt concentrations and is most prominent when the plasmid DNA is incubated at room temperature prior to electrophoresis. Analysis using two-dimensional gel electrophoresis indicates that the mobility shift results from the formation of a cruciform structure. S1 nuclease and T7 endonuclease both cut the plasmid into a linear form, also suggesting cruciform formation. Furthermore, anti-cruciform DNA antibody reduces the electrophoretic mobility of the PATRR-containing fragment. Finally, we have directly visualized cruciform extrusions from the plasmid DNA with the size expected of hairpin arms using atomic force microscopy. Our data imply that for human chromosomes, translocation susceptibility is mediated by PATRRs and likely results from their unstable conformation.
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Affiliation(s)
- Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
- Division of Functional Genomics, Department of Post-Genomics and Diseases, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
- To whom correspondence should be addressed: Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan. Tel.: 81-562-93-9391; Fax: 81-562-93-8831;
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Kouji Yamada
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Tamae Ohye
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Mariko Taniguchi
- Division of Functional Genomics, Department of Post-Genomics and Diseases, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Beverly S. Emanuel
- Division of Human Genetics and Molecular Biology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Tatsushi Toda
- Division of Functional Genomics, Department of Post-Genomics and Diseases, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
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Gotter AL, Shaikh TH, Budarf ML, Rhodes CH, Emanuel BS. A palindrome-mediated mechanism distinguishes translocations involving LCR-B of chromosome 22q11.2. Hum Mol Genet 2003; 13:103-15. [PMID: 14613967 PMCID: PMC2818528 DOI: 10.1093/hmg/ddh004] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Two known recurrent constitutional translocations, t(11;22) and t(17;22), as well as a non-recurrent t(4;22), display derivative chromosomes that have joined to a common site within the low copy repeat B (LCR-B) region of 22q11.2. This breakpoint is located between two AT-rich inverted repeats that form a nearly perfect palindrome. Breakpoints within the 11q23, 17q11 and 4q35 partner chromosomes also fall near the center of palindromic sequences. In the present work the breakpoints of a fourth translocation involving LCR-B, a balanced ependymoma-associated t(1;22), were characterized not only to localize this junction relative to known genes, but also to further understand the mechanism underlying these rearrangements. FISH mapping was used to localize the 22q11.2 breakpoint to LCR-B and the 1p21 breakpoint to single BAC clones. STS mapping narrowed the 1p21.2 breakpoint to a 1990 bp AT-rich region, and junction fragments were amplified by nested PCR. Junction fragment-derived sequence indicates that the 1p21.2 breakpoint splits a 278 nt palindrome capable of forming stem-loop secondary structure. In contrast, the 1p21.2 reference genomic sequence from clones in the database does not exhibit this configuration, suggesting a predisposition for regional genomic instability perhaps etiologic for this rearrangement. Given its similarity to known chromosomal fragile site (FRA) sequences, this polymorphic 1p21.2 sequence may represent one of the FRA1 loci. Comparative analysis of the secondary structure of sequences surrounding translocation breakpoints that involve LCR-B with those not involving this region indicate a unique ability of the former to form stem-loop structures. The relative likelihood of forming these configurations appears to be related to the rate of translocation occurrence. Further analysis suggests that constitutional translocations in general occur between sequences of similar melting temperature and propensity for secondary structure.
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Affiliation(s)
- Anthony L. Gotter
- Division of Human Genetics and Molecular Biology, Children’s Hospital of Philadelphia, 3615 Civic Center Boulevard, ARC 1002, Philadelphia, PA 19104, USA
| | - Tamim H. Shaikh
- Division of Human Genetics and Molecular Biology, Children’s Hospital of Philadelphia, 3615 Civic Center Boulevard, ARC 1002, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Marcia L. Budarf
- Division of Human Genetics and Molecular Biology, Children’s Hospital of Philadelphia, 3615 Civic Center Boulevard, ARC 1002, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - C. Harker Rhodes
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Beverly S. Emanuel
- Division of Human Genetics and Molecular Biology, Children’s Hospital of Philadelphia, 3615 Civic Center Boulevard, ARC 1002, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- To whom correspondence should be addressed. Tel: +1 2155903856; Fax: +1 2155903764;
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10
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Spiteri E, Babcock M, Kashork CD, Wakui K, Gogineni S, Lewis DA, Williams KM, Minoshima S, Sasaki T, Shimizu N, Potocki L, Pulijaal V, Shanske A, Shaffer LG, Morrow BE. Frequent translocations occur between low copy repeats on chromosome 22q11.2 (LCR22s) and telomeric bands of partner chromosomes. Hum Mol Genet 2003; 12:1823-37. [PMID: 12874103 DOI: 10.1093/hmg/ddg203] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The chromosome 22q11.2 region is susceptible to rearrangements, mediated by low copy repeats (LCR22s). Deletions and duplications are mediated by homologous recombination events between LCR22s. The recurrent balanced constitutional translocation t(11;22)(q23;q11) breakpoint occurs in an LCR22 and is mediated by double strand breaks in AT-rich palindromes on both chromosomes 11 and 22. Recently, two cases of a t(17;22)(q11;q11) were reported, mediated by a similar mechanism (21). Except for these constitutional translocations, the molecular basis for non-recurrent, reciprocal 22q11.2 translocations is not known. To determine whether there are specific mechanisms that could mediate translocations, we analyzed cell lines derived from 14 different individuals by genotyping and FISH mapping. Somatic cell hybrid analysis was carried out for four cell lines. In five cell lines, the translocation breakpoints occurred in the same LCR22 as for the t(11;22) translocation, suggesting that similar molecular mechanisms are responsible. An additional three occurred in other LCR22s, and six were in non-LCR22 regions, mostly in the proximal half of the 22q11.2 region. The translocation breakpoints on the partner chromosomes were all located in the telomeric bands, proximal to the most telomeric unique sequence probe, in eight cell lines and distal to those loci in six. Therefore, several of the breakpoints were found to occur in the vicinity of highly dynamic regions of the genome, 22q11.2 and telomeric bands. We hypothesize that these regions are more susceptible to breakage and repair, resulting in translocations.
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Affiliation(s)
- Elizabeth Spiteri
- Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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11
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Stankiewicz P, Shaw CJ, Dapper JD, Wakui K, Shaffer LG, Withers M, Elizondo L, Park SS, Lupski JR. Genome architecture catalyzes nonrecurrent chromosomal rearrangements. Am J Hum Genet 2003; 72:1101-16. [PMID: 12649807 PMCID: PMC1180264 DOI: 10.1086/374385] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2002] [Accepted: 01/16/2003] [Indexed: 11/03/2022] Open
Abstract
To investigate the potential involvement of genome architecture in nonrecurrent chromosome rearrangements, we analyzed the breakpoints of eight translocations and 18 unusual-sized deletions involving human proximal 17p. Surprisingly, we found that many deletion breakpoints occurred in low-copy repeats (LCRs); 13 were associated with novel large LCR17p structures, and 2 mapped within an LCR sequence (middle SMS-REP) within the Smith-Magenis syndrome (SMS) common deletion. Three translocation breakpoints involving 17p11 were found to be located within the centromeric alpha-satellite sequence D17Z1, three within a pericentromeric segment, and one at the distal SMS-REP. Remarkably, our analysis reveals that LCRs constitute >23% of the analyzed genome sequence in proximal 17p--an experimental observation two- to fourfold higher than predictions based on virtual analysis of the genome. Our data demonstrate that higher-order genomic architecture involving LCRs plays a significant role not only in recurrent chromosome rearrangements but also in translocations and unusual-sized deletions involving 17p.
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Affiliation(s)
- Paweł Stankiewicz
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Christine J. Shaw
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Jason D. Dapper
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Keiko Wakui
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Lisa G. Shaffer
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Marjorie Withers
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Leah Elizondo
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - Sung-Sup Park
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
| | - James R. Lupski
- Departments of Molecular and Human Genetics and Pediatrics and Interdepartmental Program in Cell and Molecular Biology, Baylor College of Medicine, and Texas Children's Hospital, Houston
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12
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Debeer P, Mols R, Huysmans C, Devriendt K, Van de Ven WJM, Fryns JP. Involvement of a palindromic chromosome 22-specific low-copy repeat in a constitutional t(X; 22)(q27;q11). Clin Genet 2002; 62:410-4. [PMID: 12431258 DOI: 10.1034/j.1399-0004.2002.620510.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Segmental duplications or low-copy repeats (LCRs) on chromosome 22q11 have been implicated in several chromosomal rearrangements. The presence of AT-rich regions in these duplications may lead to the formation of hairpin structures, which facilitate chromosomal rearrangement. Here we report the involvement of such a low-copy repeat in a t(X;22) associated with a neural tube defect. Molecular analysis of the chromosomal breakpoints revealed that the chromosome 22 breakpoint maps in the palindromic non-AT-rich NF1-like region of low-copy repeat B (LCR-B). No palindromic region was encountered near the breakpoint on chromosome X. Our findings confirm that there is no single mechanism leading to translocations with chromosome 22q11 involvement. Because LCR-B does not contain genes involved in neural tube development, we believe that the gene responsible for the observed phenotype is most likely localized on chromosome X.
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Affiliation(s)
- P Debeer
- Laboratory for Molecular Oncology and Center for Human Genetics, Herestraat 49, B-3000 Leuven, Belgium
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13
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Abstract
An increasing number of human diseases are recognized to result from recurrent DNA rearrangements involving unstable genomic regions. These are termed genomic disorders, in which the clinical phenotype is a consequence of abnormal dosage of gene(s) located within the rearranged genomic fragments. Both inter- and intrachromosomal rearrangements are facilitated by the presence of region-specific low-copy repeats (LCRs) and result from nonallelic homologous recombination (NAHR) between paralogous genomic segments. LCRs usually span approximately 10-400 kb of genomic DNA, share >or= 97% sequence identity, and provide the substrates for homologous recombination, thus predisposing the region to rearrangements. Moreover, it has been suggested that higher order genomic architecture involving LCRs plays a significant role in karyotypic evolution accompanying primate speciation.
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Affiliation(s)
- Paweł Stankiewicz
- Dept Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3498, USA
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Emanuel BS, Shaikh TH. Segmental duplications: an 'expanding' role in genomic instability and disease. Nat Rev Genet 2001; 2:791-800. [PMID: 11584295 DOI: 10.1038/35093500] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The knowledge that specific genetic diseases are caused by recurrent chromosomal aberrations has indicated that genomic instability might be directly related to the structure of the regions involved. The sequencing of the human genome has directed significant attention towards understanding the molecular basis of such recombination 'hot spots'. Segmental duplications have emerged as a significant factor in the aetiology of disorders that are caused by abnormal gene dosage. These observations bring us closer to understanding the mechanisms and consequences of genomic rearrangement.
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Affiliation(s)
- B S Emanuel
- Division of Human Genetics and Molecular Biology, 1002 Abramson Research Center, The Children's Hospital of Philadelphia, 3516 Civic Center Blvd, Philadelphia, Pennsylvania 19104, USA.
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Lamszus K, Lachenmayer L, Heinemann U, Kluwe L, Finckh U, Höppner W, Stavrou D, Fillbrandt R, Westphal M. Molecular genetic alterations on chromosomes 11 and 22 in ependymomas. Int J Cancer 2001; 91:803-8. [PMID: 11275983 DOI: 10.1002/1097-0215(200002)9999:9999<::aid-ijc1134>3.0.co;2-p] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ependymomas arise from the ependymal cells at different locations throughout the brain and spinal cord. These tumors have a broad age distribution with a range from less than 1 year to more than 80 years. In some intramedullary spinal ependymomas, mutations in the neurofibromatosis 2 (NF2) gene and loss of heterozygosity (LOH) on chromosome arm 22q have been described. Cytogenetic studies have also identified alterations involving chromosome arm 11q, including rearrangements at 11q13, in ependymomas. We analyzed 21 intramedullary spinal, 14 ventricular, 11 filum terminale and 6 intracerebral ependymomas for mutations in the MEN1 gene, which is located at 11q13, and mutations in the NF2 gene, which is located at 22q12, as well as for LOH on 11q and 22q. NF2 mutations were found in 6 tumors, all of which were intramedullary spinal and all of which displayed LOH 22q. Allelic loss on 22q was found in 20 cases and was significantly more frequent in intramedullary spinal ependymomas than in tumors in other locations. LOH 11q was found in 7 patients and exhibited a highly significant inverse association with LOH 22q (p<0.001). A hemizygous MEN1 mutation was identified in 3 tumors, all of which were recurrences from the same patient. Interestingly, the initial tumor corresponded to WHO grade II and displayed LOH 11q but not yet a MEN1 mutation. In 2 subsequent recurrences, the tumor had progressed to anaplastic ependymoma (WHO grade III) and exhibited a nonsense mutation in exon 10 of MEN1 (W471X) in conjunction with LOH 11q. This suggests that loss of wild-type MEN1 may be involved in the malignant progression of a subset of ependymomas. To conclude, our findings provide evidence for different genetic pathways involved in ependymoma formation and progression, which may allow to define genetically and clinically distinct tumor entities.
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Affiliation(s)
- K Lamszus
- Department of Neuropathology, University Hospital Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany.
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Shaikh TH, Kurahashi H, Emanuel BS. Evolutionarily conserved low copy repeats (LCRs) in 22q11 mediate deletions, duplications, translocations, and genomic instability: an update and literature review. Genet Med 2001; 3:6-13. [PMID: 11339380 DOI: 10.1097/00125817-200101000-00003] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Several constitutional rearrangements, including deletions, duplications, and translocations, are associated with 22q11.2. These rearrangements give rise to a variety of genomic disorders, including DiGeorge, velocardiofacial, and conotruncal anomaly face syndromes (DGS/VCFS/CAFS), cat eye syndrome (CES), and the supernumerary der(22)t(11;22) syndrome associated with the recurrent t(11;22). Chromosome 22-specific duplications or low copy repeats (LCRs) have been directly implicated in the chromosomal rearrangements associated with 22q11.2. Extensive sequence analysis of the different copies of 22q11 LCRs suggests a complex organization. Examination of their evolutionary origin suggests that the duplications in 22q11.2 may predate the divergence of New World monkeys 40 million years ago. Based on the current data, a number of models are proposed to explain the LCR-mediated constitutional rearrangements of 22q11.2.
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Affiliation(s)
- T H Shaikh
- Division of Human Genetics and Molecular Biology, The Children's Hospital of Philadelphia, Pennsylvania 19104, USA
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Rousseau-Merck M, Versteege I, Zattara-Cannoni H, Figarella D, Lena G, Aurias A, Vagner-Capodano AM. Fluorescence in situ hybridization determination of 22q12-q13 deletion in two intracerebral ependymomas. CANCER GENETICS AND CYTOGENETICS 2000; 121:223-7. [PMID: 11063814 DOI: 10.1016/s0165-4608(00)00262-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The sole cytogenetic abnormalities encountered in two childhood anaplastic intracerebral ependymomas were an isodicentric chromosome 22 in one case and an unbalanced chromosome 22 translocation associated with a partial deletion in the other. Fluorescence in situ hybridization analysis showed that the common 22q arm loss did not involve the rhabdoid region but included the EWS and NF2 loci. These results, in conjunction with data in the literature, suggest that the most frequently recurrent genomic loss in ependymomas does not involve the proximal 22q11.2 chromosome region but is localized distally to the hSNF5/INI1 locus. A tumor-suppressor gene, independent of the NF2 gene, which seems to be exclusively involved in intramedullary spinal cord ependymomas, might be implicated in the genesis of these intracranial tumors.
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Hulsebos TJ, Oskam NT, Bijleveld EH, Westerveld A, Hermsen MA, van den Ouweland AM, Hamel BC, Tijssen CC. Evidence for an ependymoma tumour suppressor gene in chromosome region 22pter-22q11.2. Br J Cancer 1999; 81:1150-4. [PMID: 10584875 PMCID: PMC2374323 DOI: 10.1038/sj.bjc.6690822] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Ependymomas are glial tumours of the brain and spinal cord. The most frequent genetic change in sporadic ependymoma is monosomy 22, suggesting the presence of an ependymoma tumour suppressor gene on that chromosome. Clustering of ependymomas has been reported to occur in some families. From an earlier study in a family in which four cousins developed an ependymoma, we concluded that an ependymoma-susceptibility gene, which is not the NF2 gene in 22q12, might be located on chromosome 22. To localize that gene, we performed a segregation analysis with chromosome 22 markers in this family. This analysis revealed that the susceptibility gene may be located proximal to marker D22S941 in 22pter-22q11.2. Comparative genomic hybridization showed that monosomy 22 was the sole detectable genetic aberration in the tumour of one of the patients. Loss of heterozygosity studies in that tumour revealed that, in accordance to Knudson's two-hit theory of tumorigenesis, the lost chromosome 22 originated from the parent presumed to have contributed the wild-type allele of the susceptibility gene. Thus, our segregation and tumour studies collectively indicate that an ependymoma tumour suppressor gene may be present in region 22pter-22q11.2.
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Affiliation(s)
- T J Hulsebos
- Department of Human Genetics, University of Amsterdam, The Netherlands
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Shaikh TH, Budarf ML, Celle L, Zackai EH, Emanuel BS. Clustered 11q23 and 22q11 breakpoints and 3:1 meiotic malsegregation in multiple unrelated t(11;22) families. Am J Hum Genet 1999; 65:1595-607. [PMID: 10577913 PMCID: PMC1288370 DOI: 10.1086/302666] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The t(11;22) is the only known recurrent, non-Robertsonian constitutional translocation. We have analyzed t(11;22) balanced-translocation carriers from multiple unrelated families by FISH, to localize the t(11;22) breakpoints on both chromosome 11 and chromosome 22. In 23 unrelated balanced-translocation carriers, the breakpoint was localized within a 400-kb interval between D22S788 (N41) and ZNF74, on 22q11. Also, 13 of these 23 carriers were tested with probes from chromosome 11, and, in each, the breakpoint was localized between D11S1340 and APOA1, on 11q23, to a region </=185 kb. Thus, the breakpoints on both chromosome 11 and chromosome 22 are clustered in multiple unrelated families. Supernumerary-der(22)t(11;22) syndrome can occur in the progeny of balanced-t(11;22) carriers, because of malsegregation of the der(22). There has been speculation regarding the mechanism by which the malsegregation occurs. To elucidate this mechanism, we have analyzed 16 of the t(11;22) families, using short tandem-repeat-polymorphism markers on both chromosome 11 and chromosome 22. In all informative cases the proband received two of three alleles, for markers above the breakpoint on chromosome 22 and below the breakpoint on chromosome 11, from the t(11;22)-carrier parent. These data strongly suggest that 3:1 meiosis I malsegregation in the t(11;22) balanced-translocation-carrier parent is the mechanism in all 16 families. Taken together, these results establish that the majority of t(11;22) translocations occur within the same genomic intervals and that the majority of supernumerary-der(22) offspring result from a 3:1 meiosis I malsegregation in the balanced-translocation carrier.
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Affiliation(s)
- Tamim H. Shaikh
- Division of
Human Genetics and Molecular Biology, The Children's Hospital
of Philadelphia, and Department of Pediatrics, University
of Pennsylvania School of Medicine, Philadelphia
| | - Marcia L. Budarf
- Division of
Human Genetics and Molecular Biology, The Children's Hospital
of Philadelphia, and Department of Pediatrics, University
of Pennsylvania School of Medicine, Philadelphia
| | - Livija Celle
- Division of
Human Genetics and Molecular Biology, The Children's Hospital
of Philadelphia, and Department of Pediatrics, University
of Pennsylvania School of Medicine, Philadelphia
| | - Elaine H. Zackai
- Division of
Human Genetics and Molecular Biology, The Children's Hospital
of Philadelphia, and Department of Pediatrics, University
of Pennsylvania School of Medicine, Philadelphia
| | - Beverly S. Emanuel
- Division of
Human Genetics and Molecular Biology, The Children's Hospital
of Philadelphia, and Department of Pediatrics, University
of Pennsylvania School of Medicine, Philadelphia
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Gräler MH, Bernhardt G, Lipp M. A lymphoid tissue-specific receptor, EDG6, with potential immune modulatory functions mediated by extracellular lysophospholipids. Curr Top Microbiol Immunol 1999; 246:131-6; discussion 137. [PMID: 10396049 DOI: 10.1007/978-3-642-60162-0_17] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Affiliation(s)
- M H Gräler
- Max-Delbrück-Center for Molecular Medicine, Department of Tumor- and Immunogenetics, Berlin, Germany
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Tomarev SI, Nakaya N. In-vitro study of the activity of ciprofloxacin alone and in combination against strains of Pseudomonas aeruginosa with multiple antibiotic resistance. J Antimicrob Chemother 1986; 40:122-38. [PMID: 19554483 DOI: 10.1007/s12035-009-8076-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 06/14/2009] [Indexed: 01/25/2023] Open
Abstract
Ciprofloxacin appears to have useful activity against Pseudomonas aeruginosa. We have studied its in-vitro activity against ten strains of Ps. aeruginosa with multiple antibiotic resistance. We have confirmed that ciprofloxacin is very active against Ps. aeruginosa with minimal inhibitory concentrations ranging from 0.07 to 0.7 mg/l. Killing curves show ciprofloxacin to be rapidly bactericidal with no regrowth after 24 h. Checkerboard studies with ciprofloxacin in combination with gentamicin, azlocillin and ceftazidime show no consistent interaction. These studies suggest that ciprofloxacin should prove a useful antibiotic in treating infections caused by multiresistant Ps. aeruginosa.
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Affiliation(s)
- Stanislav I Tomarev
- Section of Molecular Mechanisms of Glaucoma, Laboratory of Molecular and Developmental Biology, National Eye Institute, NIH, 5635 Fishers Lane, Room 1124, Bethesda, MD, 20892, USA.
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