Relevant bibliographies by topics / Structural breakpoint

Academic literature on the topic 'Structural breakpoint'

Author: Grafiati
Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Structural breakpoint"

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Wang, Dandan, Daixi Li, Guangrong Qin, Wen Zhang, Jian Ouyang, Menghuan Zhang, and Lu Xie. "The Structural Characterization of Tumor Fusion Genes and Proteins." Computational and Mathematical Methods in Medicine 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/912742.

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Chromosomal translocation, which generates fusion proteins in blood tumor or solid tumor, is considered as one of the major causes leading to cancer. Recent studies suggested that the disordered fragments in a fusion protein might contribute to its carcinogenicity. Here, we investigated the sequence feature near the breakpoints in the fusion partner genes, the structure features of breakpoints in fusion proteins, and the posttranslational modification preference in the fusion proteins. Results show that the breakpoints in the fusion partner genes have both sequence preference and structural preference. At the sequence level, nucleotide combination AG is preferred before the breakpoint and GG is preferred at the breakpoint. At the structural level, the breakpoints in the fusion proteins prefer to be located in the disordered regions. Further analysis suggests the phosphorylation sites at serine, threonine, and the methylation sites at arginine are enriched in disordered regions of the fusion proteins. Using EML4-ALK as an example, we further explained how the fusion protein leads to the protein disorder and contributes to its carcinogenicity. The sequence and structural features of the fusion proteins may help the scientific community to predict novel breakpoints in fusion genes and better understand the structure and function of fusion proteins.
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Still, Ivan H., Olga Chernova, David Hurd, Richard M. Stone, and John K. Cowell. "Molecular Characterization of the t(8; 13)(p11;q12) Translocation Associated With an Atypical Myeloproliferative Disorder: Evidence for Three Discrete Loci Involved in Myeloid Leukemias on 8p11." Blood 90, no. 8 (October 15, 1997): 3136–41. http://dx.doi.org/10.1182/blood.v90.8.3136.

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Abstract A reciprocal chromosome translocation between 13q12 and 8p11 is the consistent cytogenetic abnormality seen in a nonspecific myeloproliferative disorder that is associated with T-cell leukemia/lymphoma and peripheral blood eosinophilia. Detailed molecular analyses of the translocation breakpoints associated with this rearrangement have not been reported to date. We have now generated somatic cell hybrids from a newly described patient with this specific structural rearrangement and analyzed the breakpoints on the derivative chromosomes. We have shown that the breakpoint on chromosome 13 lies within a 300- to 500-kb region defined by the KIAA177 gene and D13S1123 marker. In addition, we have identified a 1.2-Mb YAC, 959A4, that crosses the translocation breakpoint on the short arm of chromosome 8 in this patient. The location of this breakpoint in 8p11 is distinct from the t(8; 16) and t(8; 22) translocations associated with M4/M5 myeloid leukemias, and suggests that three distinct loci located within 8p11 are involved in the pathogenesis of myeloid neoplasias.
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Vaandrager, Jan-Willem, Ed Schuuring, Katja Philippo, and Philip M. Kluin. "V(D)J recombinase-mediated transposition of the BCL2gene to the IGH locus in follicular lymphoma." Blood 96, no. 5 (September 1, 2000): 1947–52. http://dx.doi.org/10.1182/blood.v96.5.1947.

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Abstract Using DNA fiber fluorescence in-situ hybridization (FISH) and 3-color interphase FISH, 2 cases of follicular lymphoma were identified in which the BCL2 gene was excised from 18q21 and inserted into the immunoglobulin heavy chain (IGH) locus at 14q32. Both the insertion breakpoint at 14q32 and the deletion breakpoint at 18q21 were cloned using inverse polymerase chain reaction. Sequence analysis showed that the JH sequences were juxtaposed to the 5′-side of BCL2, and the DH sequences were juxtaposed to the 3′-side of BCL2. There were breakpoints at both the JH and DH recombination signal sequences, and N-nucleotides were present at all breakpoint junctions. At theBCL2 locus, the 3′-breakpoints in both cases were localized at exactly the same nucleotide position, 6.2 kilobase downstream of the major breakpoint region, directly adjacent to a complete cryptic recombination signal sequence (RSS) consisting of a heptamer, a nonamer, and a 23–base pair (bp) spacer. The BCL25′-breakpoints were approximately 600 bp upstream of the gene, within the CA repeats. Although less evident than for the BCL23′-breakpoints, cryptic RSSs were also identified at these breakpoints, with a 12-bp spacer. On the basis of structural characteristics of these rearrangements, a model is proposed in which the BCL2 gene is deleted from its locus by recombination activation gene-1/-2 (RAG-1/-2)–mediated excision. The gene is subsequently inserted into the recombiningIGH locus, a process involving the formation of hybrid joints between the IGH coding ends and theBCL2 signal ends.
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Vaandrager, Jan-Willem, Ed Schuuring, Katja Philippo, and Philip M. Kluin. "V(D)J recombinase-mediated transposition of the BCL2gene to the IGH locus in follicular lymphoma." Blood 96, no. 5 (September 1, 2000): 1947–52. http://dx.doi.org/10.1182/blood.v96.5.1947.h8001947_1947_1952.

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Using DNA fiber fluorescence in-situ hybridization (FISH) and 3-color interphase FISH, 2 cases of follicular lymphoma were identified in which the BCL2 gene was excised from 18q21 and inserted into the immunoglobulin heavy chain (IGH) locus at 14q32. Both the insertion breakpoint at 14q32 and the deletion breakpoint at 18q21 were cloned using inverse polymerase chain reaction. Sequence analysis showed that the JH sequences were juxtaposed to the 5′-side of BCL2, and the DH sequences were juxtaposed to the 3′-side of BCL2. There were breakpoints at both the JH and DH recombination signal sequences, and N-nucleotides were present at all breakpoint junctions. At theBCL2 locus, the 3′-breakpoints in both cases were localized at exactly the same nucleotide position, 6.2 kilobase downstream of the major breakpoint region, directly adjacent to a complete cryptic recombination signal sequence (RSS) consisting of a heptamer, a nonamer, and a 23–base pair (bp) spacer. The BCL25′-breakpoints were approximately 600 bp upstream of the gene, within the CA repeats. Although less evident than for the BCL23′-breakpoints, cryptic RSSs were also identified at these breakpoints, with a 12-bp spacer. On the basis of structural characteristics of these rearrangements, a model is proposed in which the BCL2 gene is deleted from its locus by recombination activation gene-1/-2 (RAG-1/-2)–mediated excision. The gene is subsequently inserted into the recombiningIGH locus, a process involving the formation of hybrid joints between the IGH coding ends and theBCL2 signal ends.
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Schnause, Anna Clara, Katalin Komlosi, Barbara Herr, Jürgen Neesen, Paul Dremsek, Thomas Schwarz, Andreas Tzschach, et al. "Marfan Syndrome Caused by Disruption of the FBN1 Gene due to A Reciprocal Chromosome Translocation." Genes 12, no. 11 (November 21, 2021): 1836. http://dx.doi.org/10.3390/genes12111836.

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Marfan syndrome (MFS) is a hereditary connective tissue disease caused by heterozygous mutations in the fibrillin-1 gene (FBN1) located on chromosome 15q21.1. A complex chromosomal rearrangement leading to MFS has only been reported in one case so far. We report on a mother and daughter with marfanoid habitus and no pathogenic variant in the FBN1 gene after next generation sequencing (NGS) analysis, both showing a cytogenetically reciprocal balanced translocation between chromosomes 2 and 15. By means of fluorescence in situ hybridization of Bacterial artificial chromosome (BAC) clones from the breakpoint area on chromosome 15 the breakpoint was narrowed down to a region of approximately 110 kb in FBN1. With the help of optical genome mapping (OGM), the translocation breakpoints were further refined on chromosomes 2 and 15. Sequencing of the regions affected by the translocation identified the breakpoint of chromosome 2 as well as the breakpoint of chromosome 15 in the FBN1 gene leading to its disruption. To our knowledge, this is the first report of patients with typical clinical features of MFS showing a cytogenetically reciprocal translocation involving the FBN1 gene. Our case highlights the importance of structural genome variants as an underlying cause of monogenic diseases and the useful clinical application of OGM in the elucidation of structural variants.
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Wareham, D. G., K. J. Hall, and D. S. Mavinic. "An ORP screening protocol for biological phosphorus removal in sequencing batch reactors." Canadian Journal of Civil Engineering 22, no. 2 (April 1, 1995): 260–69. http://dx.doi.org/10.1139/l95-035.

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This research discusses two strategies for adding acetate to sequencing batch reactors operating as biological removal (Bio-P) systems. The control (fixed-time) reactor adds the acetate at a set time of 1 h 25 min, which is an assumed time for complete denitrification. The experimental (real-time) reactor adds the acetate when a computer detects the disappearance of nitrates, as indicated by a distinctive "breakpoint" or "kink" in the oxidation-reduction potential versus time profile. This control strategy is therefore based upon a known time for complete denitrification. The time-of-occurrence of the nitrate breakpoint is utilized in the development of a screening protocol for interpreting the behaviour (in terms of nitrate reactions) for reactors operating in biological phosphorus removal mode. The protocol involves categorizing the timing of the nitrate breakpoint into two groupings. A "failure" category corresponds to acetate being added prior to the breakpoint, because, in these cases, the acetate is used partially for denitrification and partially for Bio-P carbon storage. A "success" category corresponds to breakpoints occurring prior to the addition of acetate. In such cases, acetate is used solely for carbon storage by Bio-P organisms. Key words: oxidation-reduction potential, biological phosphorus removal, sequencing batch reactor, real-time computer control.
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Lefeuvre, P., J. M. Lett, A. Varsani, and D. P. Martin. "Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses." Journal of Virology 83, no. 6 (December 30, 2008): 2697–707. http://dx.doi.org/10.1128/jvi.02152-08.

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ABSTRACT The combinatorial nature of genetic recombination can potentially provide organisms with immediate access to many more positions in sequence space than can be reached by mutation alone. Recombination features particularly prominently in the evolution of a diverse range of viruses. Despite rapid progress having been made in the characterization of discrete recombination events for many species, little is currently known about either gross patterns of recombination across related virus families or the underlying processes that determine genome-wide recombination breakpoint distributions observable in nature. It has been hypothesized that the networks of coevolved molecular interactions that define the epistatic architectures of virus genomes might be damaged by recombination and therefore that selection strongly influences observable recombination patterns. For recombinants to thrive in nature, it is probably important that the portions of their genomes that they have inherited from different parents work well together. Here we describe a comparative analysis of recombination breakpoint distributions within the genomes of diverse single-stranded DNA (ssDNA) virus families. We show that whereas nonrandom breakpoint distributions in ssDNA virus genomes are partially attributable to mechanistic aspects of the recombination process, there is also a significant tendency for recombination breakpoints to fall either outside or on the peripheries of genes. In particular, we found significantly fewer recombination breakpoints within structural protein genes than within other gene types. Collectively, these results imply that natural selection acting against viruses expressing recombinant proteins is a major determinant of nonrandom recombination breakpoint distributions observable in most ssDNA virus families.
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Beauchamp, N. J., M. Makris, F. E. Preston, I. R. Peake, and M. E. Daly. "Major Structural Defects in the Antithrombin Gene in Four Families with Type I Antithrombin Deficiency." Thrombosis and Haemostasis 83, no. 05 (2000): 715–21. http://dx.doi.org/10.1055/s-0037-1613898.

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SummaryThe molecular basis of quantitative antithrombin deficiency was investigated in four families predicted to have major antithrombin gene rearrangements. A 1,442 bp deletion and insertion of the sequence 5’T(n = 38-40)GAGACG was characterised in one case. Sequence surrounding the breakpoints contained two perfect, and one imperfect, inverted repeats which may have mediated formation of a stem loop structure on one strand during DNA replication potentiating the deletion. A 9,219 bp deletion spanning introns 2 to 5 was identified in a second family. The identical 6 bp sequence was upstream of each breakpoint and the 5’ breakpoint was located in a sequence of the Alu 3 repeat predicted to be susceptible to strand breakage during transcription. This may have promoted misalignment, and deletion, of one of the repeats and the intervening DNA. A novel 1.8 kb antithrombin gene fragment was present in DNA digests from affected members of the third family suggesting a partial antithrombin gene duplication event while in the remaining family, evidence supporting a complete gene deletion was obtained.
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van den Broek, Evert, Stef van Lieshout, Christian Rausch, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Remond J. A. Fijneman, and Sanne Abeln. "GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes." F1000Research 5 (September 19, 2016): 2340. http://dx.doi.org/10.12688/f1000research.9259.1.

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Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large) series of tumor samples. ‘GeneBreak’ is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH) or by (low-pass) whole genome sequencing (WGS). First, ‘GeneBreak’ collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, ‘GeneBreak’, is implemented in R (www.cran.r-project.org) and is available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/GeneBreak.html).
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van den Broek, Evert, Stef van Lieshout, Christian Rausch, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Remond J. A. Fijneman, and Sanne Abeln. "GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes." F1000Research 5 (July 6, 2017): 2340. http://dx.doi.org/10.12688/f1000research.9259.2.

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Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large) series of tumor samples. ‘GeneBreak’ is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH) or by (low-pass) whole genome sequencing (WGS). First, ‘GeneBreak’ collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, ‘GeneBreak’, is implemented in R (www.cran.r-project.org) and is available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/GeneBreak.html).
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Dissertations / Theses on the topic "Structural breakpoint"

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Zeileis, Achim, and Christian Kleiber. "Validating multiple structural change models. A case study." Institut für Statistik und Mathematik, WU Vienna University of Economics and Business, 2004. http://epub.wu.ac.at/584/1/document.pdf.

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In a recent article, Bai and Perron (2003, Journal of Applied Econometrics) present a comprehensive discussion of computational aspects of multiple structural change models along with several empirical examples. Here, we report on the results of a replication study using the R statistical software package. We are able to verify most of their findings; however, some confidence intervals associated with breakpoints cannot be reproduced. These confidence intervals require computation of the quantiles of a nonstandard distribution, the distribution of the argmax functional of a certain stochastic process. Interestingly, the difficulties appear to be due to numerical problems in GAUSS, the software package used by Bai and Perron.
Series: Research Report Series / Department of Statistics and Mathematics
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Zeileis, Achim, and Christian Kleiber. "Validating multiple structural change models. An extended case study." Institut für Statistik und Mathematik, WU Vienna University of Economics and Business, 2005. http://epub.wu.ac.at/280/1/document.pdf.

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In a recent article, Bai and Perron (2003, Journal of Applied Econometrics) present a comprehensive discussion of computational aspects of multiple structural change models along with several empirical examples. Here, we report on the results of a replication study using the R statistical software package. We are able to verify most of their findings; however, some confidence intervals associated with breakpoints cannot be reproduced. These confidence intervals require computation of the quantiles of a nonstandard distribution, the distribution of the argmax functional of a certain stochastic process. Interestingly, the difficulties appear to be due to numerical problems in GAUSS, the software package used by Bai and Perron.
Series: Research Report Series / Department of Statistics and Mathematics
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Oliveira, Mariana Angelozzi de. "Caracterização de rearranjos cromossômicos em pacientes com malformações congênitas múltiplas e/ou retardamento mental (MCA/MR)." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-08072008-110038/.

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As alterações cromossômicas estruturais associadas a fenótipos clínicos oferecem a oportunidade de identificação e localização de genes cujas mutações possam estar determinando essas patologias, tendo em vista a possibilidade de que esses genes podem ter sido alterados pelas quebras ou ter o número de cópias modificado. Um número cada vez maior de evidências aponta para a participação de certas seqüências do genoma na formação de rearranjos cromossômicos recorrentes e não recorrentes. Este trabalho compreendeu o estudo de duas translocações cromossômicas aparentemente equilibradas e uma duplicação do braço curto do cromossomo 20 em decorrência de mosaicismo materno. O objetivo foi determinar os pontos de quebra por hibridação in situ fluorescente (FISH) e identificar genes candidatos, alterados pelas quebras dos rearranjos e que pudessem explicar o quadro clínico dos portadores. A caracterização das seqüências nos pontos de quebra e a junção desses rearranjos é fundamental para a compreensão dos mecanismos de formação das alterações cromossômicas. A delimitação precisa dos segmentos deletados é necessária para a correlação com o quadro clínico.
Two apparently \"de novo\" balanced translocations and one duplication of the short arm of chromosome 20 were studied. Our aim was to determine the breakpoints by chromosomal analysis through fluorescentin situ hybridization (FISH) and identify candidate genes and how they were involved with the clinical phenotypes of the patients. Patient 1 carried a duplication of the short arm of chromosome 20 (p11.22p13), inherited from the mother that showed normal and dup(20) lymphocytes. The duplication was determined by FISH using BAC and PAC clones, and nine clones were duplicated except one (20p11.21). The patient shared many of the common characteristics of trisomy 20p including delay in motor development, hypertelorism, poor coordination, round face with prominent cheeks, vertebral and dental abnormalities and cranial asymmetry with high and large forehead. She also had learning difficulties, behavioral disorders and pubertal growth spurt at 12 years. As our patient is an example of pure trisomy 20p, the features are of particular importance to delineate the syndrome. Three genes were mapped on the segment that contain the duplication (20p11.2-13), one of these genes is the SSTR4 (Somatostatin receptor 4). The somatostatin is widely distributed throughout the body and is important regulator of endocrine and nervous system function. It is an inhibitor of growth hormone secretion. The second gene is the BMP2 that produce bone morphogenetic proteins and it has a direct function with the nervous system. The third gene is the GHRH that produce proteins connected with the growth hormone. These genes might have been over expressed and thus contributing to the patient\'s clinical features. Patient 2, carried a 46,XY,t(5;14)(q14.1;q31.3)de novo translocation. On chromosome 14 the breakpoint was mapped to a segment contained in BAC RP11-315O17 (14q31.3). On the chromosome 5 the breakpoint was mapped to a segment contained in BAC RP11-30D15 (5q14.1). Although the breakpoint, on the chromosome 14, has been mapped in 14q31.3, our patient shared many of the common characteristics of terminal 14q32 deletion: mental retardation, dolicocephaly, prominent ears, hypertelorism, strabismus, upturned palpebral fissures, highly arched palate, simian crease, severe myopia, coloboma and palpebral ptosis. As mental retardation and ocular abnormalities were the main patient\'s clinical features, we are suggesting that: 1) a region of segment 14q31.3 was deleted. 2) A gene inside this segment (14q31.3) could be responsible for ocular development and 3) a disrupted gene could interfere on the expression of other genes. On chromosome 5 eleven genes were localized and four of them are expressed in nervous system (AP3B1; SCAMP1; BHMT2 e CMYA5). One of these genes might have been disrupted and is contributing to the patient\'s clinical features. Patient 3 was the carrier of a 46,XY,t(1;15)(p13.2;q25.2)de novo translocation. The breakpoint on chromosome 15 was mapped to the segment contained in clone RP11-152F13 (15q25.2). The breakpoint on chromosome 1 was mapped to the segment contained in clone RP5-1037B23 (1p13.2). The genes mapped at the breakpoint regions of chromosome 1 and chromosome 15 are expressed in nervous system and muscles. Our patient shows few clinical features: speech delay, stutter and learning difficulties, probably because one or more of these genes, mapped at the breakpoint region, could be disrupted.
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Vieira, Luiz Carlos Zangrande. "Os mecanismos de formação e os efeitos clínicos de duas deleções cromossômicas: del(X)(p11.23) e del(8)(p23.1)." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-26102007-172006/.

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As alterações cromossômicas estruturais associadas a fenótipos clínicos oferecem a oportunidade de identificação de genes cujas mutações possam estar determinando essas patologias, tendo em vista a possibilidade de que esses genes podem ter sido alterados pelas quebras ou ter o número de cópias modificado. Um número cada vez maior de evidências aponta para a participação de certas seqüências do genoma na formação de rearranjos cromossômicos recorrentes e não recorrentes. Neste trabalho, estudamos duas deleções cromossômicas detectadas em indivíduos com retardo mental associado a sinais clínicos. O objetivo foi determinar que mecanismos originaram esses rearranjos e como a perda ou quebra dos segmentos cromossômicos está relacionada com o fenótipo dos portadores. A caracterização das seqüências nos pontos de quebra e junção desses rearranjos é fundamental para a compreensão dos mecanismos de formação das alterações cromossômicas. A delimitação precisa dos segmentos deletados é necessária para a correlação com o quadro clínico. Para isso, este trabalho aliou o estudo cromossômico por hibridação in situ fluorescente (FISH) à análise do DNA.
Structural chromosomal alterations related to clinical phenotypes bring the opportunity to identify gene mutations determining the pathologies, because the causative genes may have been disrupted by the breaks or may have an altered number of copies. The delimitation of the segments involved in the chromosomal rearrangements is necessary for these genotype-phenotype correlations. The characterization of breakpoint and junction sequences in these chromosome alterations enables the identification of mechanisms originating them, and evidence has been produced pointing to the participation of particular genomic sequences in their formation. In this work, we studied two chromosomal deletions in patients with syndromic mental retardation, combining chromosomal analysis by fluorescent in situ hybridization (FISH) to DNA analysis. Our aim was to determine the mechanisms that originated these aberrations and how they were involved with the clinical phenotypes.
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Thomas, Antoine. "Problèmes de réarrangement avec marqueurs génomiques dupliqués." Phd thesis, Université des Sciences et Technologie de Lille - Lille I, 2014. http://tel.archives-ouvertes.fr/tel-01067114.

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La compréhension de la dynamique des réarrangements génomiques est importante en phylogénie. La phylogénie est l'étude de l'évolution des espèces. Un but majeur est d'établir les relations d'évolution au sein d'un groupe d'espèces, pour déterminer la topologie de l'arbre d'évolution formé par ce groupe et des ancêtres communs à certains sous-ensembles. Pour ce faire, il est naturellement très utile de disposer d'un moyen d'évaluer les distances évolutionnaires relatives entre des espèces, ou encore d'être capable d'inférer à un groupe d'espèces le génome d'un ancêtre commun à celles-ci. Ce travail de thèse, dans la lignée d'autres travaux, consiste à élaborer de tels moyens, ici dans des cas particuliers où les génomes possèdent des gènes en multiples copies, ce qui complique les choses. Plusieurs hypotèses explicatives de la présence de duplications ont été considérées, des formules de distance ainsi que des algorithmes de calcul de scénarios ont été élaborés, accompagnés de preuves de complexité.
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Kayondo, Jonathan K. "Genetic structure, SNP establishment, and cloning the 2La-inversion distal breakpoint in the malaria vector Anopheles gambiae." 2006. http://etd.nd.edu/ETD-db/theses/available/etd-07062006-125643/.

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Books on the topic "Structural breakpoint"

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Makatjane, Katleho, and Roscoe van Wyk. Identifying structural changes in the exchange rates of South Africa as a regime-switching process. UNU-WIDER, 2020. http://dx.doi.org/10.35188/unu-wider/2020/919-8.

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Exchange rate volatility is said to exemplify the economic health of a country. Exchange rate break points (known as structural breaks) have a momentous impact on the macroeconomy of a country. Nonetheless, this country study makes use of both unsupervised and supervised machine learning algorithms to classify structural changes as regime shifts in real exchange rates in South Africa. Weekly data for the period January 2003–June 2020 are used. To these data we apply both non-linear principal component analysis and Markov-switching generalized autoregressive conditional heteroscedasticity. The former approach is used to reduce the dimensionality of the data using an orthogonal linear transformation by preserving the statistical variance of the data, with the proviso that a new trait is non-linearly independent, and it identifies the number of regime switches that are to be used in the Markov-switching model. The latter is used to partition the variance in each regime by allowing an estimation of multiple break transitions. The transition breakpoints estimates derived from this machine learning approach produce results that are comparable to other methods on similar system sizes. Application of these methods shows that the machine learning approach can also be employed to identify structural changes as a regime-switching process. During times of financial crisis, the growing concern over exchange rate volatility, including its adverse effects on employment and growth, broadens the debates on exchange rate policies. Our results should help the South African monetary policy committee to anticipate when exchange rates will pick up and be prepared for the effects of periods of high exchange rates.
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Strissel-Broeker, Pamela Lynn. The relationship of chromatin structure of breakpoints in translocations and deletions in human cancer: Specifically gliomas and leukemias. 1993.

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Book chapters on the topic "Structural breakpoint"

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Chong, Zechen, and Ken Chen. "Structural Variant Breakpoint Detection with novoBreak." In Methods in Molecular Biology, 129–41. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8666-8_10.

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Kiknadze, L. I., L. I. Gunderina, A. G. Istomina, V. D. Gusev, and L. A. Nemytikova. "Similarity Analysis of Inversion Banding Sequences in Chromosomes of Chironomus Species (Breakpoint Phylogeny)." In Bioinformatics of Genome Regulation and Structure, 245–53. Boston, MA: Springer US, 2004. http://dx.doi.org/10.1007/978-1-4419-7152-4_26.

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Liu, Junrong, and Zhiming Feng. "Inquiring into the Economic Structural Breakpoints and Postwar U.S. Business Cycle." In Proceedings of the Eighth International Conference on Management Science and Engineering Management, 563–70. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-55182-6_49.

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Ohtsuki, Tomohiko, Naoki Nariai, Kaname Kojima, Takahiro Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Testuo Shibuya, and Masao Nagasaki. "SVEM: A Structural Variant Estimation Method Using Multi-mapped Reads on Breakpoints." In Algorithms for Computational Biology, 208–19. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-07953-0_17.

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Meschede, Dieter. "Structural chromosome abnormalities." In Oxford Textbook of Endocrinology and Diabetes, 1404–8. Oxford University Press, 2011. http://dx.doi.org/10.1093/med/9780199235292.003.9084.

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The term ‘structural chromosome abnormalities’ encompasses pathological alterations of chromosome structure that are detectable through microscopic examination of banded metaphase preparations (Chapter 9.3.5). It excludes smaller lesions diagnosable only with molecular genetic methods. Medium-sized genomic alterations, e.g. microdeletions demonstrable through molecular-cytogenetic methods such as fluorescence in situ hybridization (FISH), may also be classified as structural chromosome abnormalities. Some structural rearrangements, such as Robertsonian translocations and marker chromosomes, imply a change in chromosome number. By convention, they are regarded as structural and not numerical chromosome abnormalities. Reciprocal and Robertsonian translocations, inversions, marker chromosomes, X and Y isochromosomes, and Y-chromosomal deletions are of practical importance in male endocrinology (Fig. 9.4.6.1) (1–4). Other classes of structural chromosome abnormalities such as rings, insertions, duplications, three-way and other complex translocations, fragile sites, and chromosome breakage syndromes (5) play no appreciable role in clinical andrology and are not further considered here. The distinction between balanced and unbalanced structural aberrations is pivotal. The former are characterized by a deviation from normal chromosome structure without accompanying net loss or gain of genetic material. In contrast, the genome of a carrier of an unbalanced aberration is not fully diploid, but nullisomic, monosomic, trisomic, or higher aneuploid for an entire chromosome or parts of it. If no important gene is disrupted at the breakpoints, balanced structural aberrations exert no negative effect on general health. They are of clinical importance through their potential to adversely affect fertility, and to give rise to unbalanced karyotypes in the carrier’s offspring (5).
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Rivero, R., and G. David. "Modeling structural breakpoints in volatility of Philippine Peso-US Dollar currency exchange rate." In Empowering Science and Mathematics for Global Competitiveness, 413–17. CRC Press, 2019. http://dx.doi.org/10.1201/9780429461903-59.

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Habacivch, Olivia A., Ryan A. Redilla, and James J. Jozefowicz. "The Convergence Behind the Curtain." In Applied Econometric Analysis, 89–120. IGI Global, 2020. http://dx.doi.org/10.4018/978-1-7998-1093-3.ch005.

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This chapter extends applications of unconditional and conditional β-convergence and unconditional σ-convergence analysis to Part I crime rates in a panel data sample of Pennsylvania counties during the period 1990-2015. Temporal structural breaks at specific points in the business cycle during the time frame and spatial breakpoints between rural and urban counties in Pennsylvania are acknowledged in the analysis in order to avoid spurious inferences regarding convergence behavior. Unit-root testing is performed on measures of dispersion as well as directly on the underlying crime-rate series via panel-data tests for non-stationarity. The findings support the existence of both unconditional and conditional β-convergence in the pooled, urban, and rural samples during 1990-2015. Visual and statistical evidence reveals the presence of σ-convergence in the three samples across the time span as well. The comprehensive convergence analysis of appropriately disaggregated data performed in this study offers strong support for the predictions of modernization theory.
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"The Ecology of Juvenile Salmon in the Northeast Pacific Ocean: Regional Comparisons." In The Ecology of Juvenile Salmon in the Northeast Pacific Ocean: Regional Comparisons, edited by Joseph A. Orsi, Jeffrey A. Harding, Suzan S. Pool, Richard D. Brodeur, Lewis J. Haldorson, James M. Murphy, Jamal H. Moss, et al. American Fisheries Society, 2007. http://dx.doi.org/10.47886/9781888569957.ch5.

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Abstract.—We compared epipelagic fish assemblages associated with juvenile (ocean-age 0) Pacific salmon <em>Oncorhynchus </em>spp. from neritic waters of the California Current and Alaska Current regions in the spring–summer and summer–fall periods of 2000–2004. Catches originated from rope trawl surveys conducted between latitudes 37°N and 60°N and spanned more than 1,100 km in the coastal and inshore habitats of each region. Catch data were used from the epipelagic sampling of waters from near surface to depths of about 18 m, primarily over the continental shelf. Catch composition, frequency of occurrence, and density were evaluated between regions and habitats for day sampling. Diel (night and day) catch comparisons were also made at a few localities in each region. In day catches from both regions, a total of 1.69 million fish and squid representing 52 fish families and 118 fish species were sampled from 2,390 trawl hauls. Ninety-seven percent of the daytime catch was composed of 11 fish families and squid in coastal and inshore habitats of each region: clupeids dominated catches in the California Current (72% and 76% of catch, respectively), and salmonids dominated catches in the Alaska Current (46% and 62% of catch, respectively). Juveniles comprised 81–99% of salmon sampled in both coastal and inshore habitats of each region. Frequencies of occurrence were highest for juvenile salmon in both regions, but average densities were highest for Pacific herring <em>Clupea pallasii </em>and Pacific sardine <em>Sardinops sagax </em>in the California Current region. Cluster analyses revealed distinct geographic breakpoints in coastal species assemblages off central Vancouver Island and in inshore species assemblages in southeastern Alaska. Species were found to cluster into six groups from coastal localities and four groups from inshore localities. Indicator species analysis and nonmetric multidimensional scaling revealed that most species of juvenile salmonids were located in northern localities. Although juvenile salmon had the most uniform distribution of any species group, their densities relative to associated species were dramatically lower in the California Current, suggesting a higher degree of interactions between juvenile salmon and other species in this region. Diel comparisons in both regions indicated substantially higher catches at night, particularly of clupeids, osmerids, and gadids. Salmonids were a relatively minor component of the night catch in both regions due to dramatic diel shifts in community structure. Additional study of diel interactions of juvenile salmon and associated species is needed to quantify habitat utilization dynamics in marine ecosystems.
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Conference papers on the topic "Structural breakpoint"

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Broek, E. van den, O. Krijgsman, D. Sie, JC Haan, M. Komor, J. Traets, DAM Heideman, et al. "Abstract 4285: Structural variant breakpoint detection in advanced colorectal cancer." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-4285.

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Oduro-Gyimah, Francis Kwabena, and Kwame Osei Boateng. "Investigating the influence of seasonality and structural breakpoint on telecommunication network traffic prediction." In 2018 IEEE 7th International Conference on Adaptive Science & Technology (ICAST). IEEE, 2018. http://dx.doi.org/10.1109/icastech.2018.8507112.

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Broek, Evert van den, Maurits J. J. Dijkstra, Quirinus J. M. Voorham, Beatriz Carvalho, Mark A. van de Wiel, Sanne Abeln, Gerrit A. Meijer, and Remond J. A. Fijneman. "Abstract A07: Detection of structural variants and recurrent breakpoint genes in colorectal adenoma-to-carcinoma progression." In Abstracts: AACR Special Conference: Colorectal Cancer: From Initiation to Outcomes; September 17-20, 2016; Tampa, FL. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.crc16-a07.

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Rybina, Natalia Vladimirovna, Alexey Viktorovich Alpatov, Nikolai Borisovich Rybin, and Alexei Alekseevich Maslov. "Determination of Surface Structural Complexity of Solid-State Materials." In 32nd International Conference on Computer Graphics and Vision. Keldysh Institute of Applied Mathematics, 2022. http://dx.doi.org/10.20948/graphicon-2022-1012-1019.

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In this paper we analyzed methods of investigating structure features in solid-state materials and developed a new algorithm for determining the surface structural complexity of these materials based on the two-dimensional detrended fluctuation analysis and the scale-space analysis. It is proposed to evaluate the surface structural complexity by calculating tangent of the angle of the fluctuation – spatial scale function and number of breakpoints on the fluctuation – spatial scale function. The developed algorithm was tested on the surface image of the Si layer implanted by Ag<sup>+<?sup> ions, subjected to the pulsed laser annealing. We found that investigated surface belongs to the type of surfaces with a high structural complexity. It was also shown that the scaling index – smoothing coefficient (scale) dependence can be used to study the dynamics of changes in the correlation properties of the surface. Knowledge about surface structural complexity of solid-state materials can be used to determine the material functional purpose in different fields of science.
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Schultz, Nicole, Elizabeth Aston, Jane Metrik, and Jason Ramirez. "Validation of the Marijuana Purchase Task Among Adolescent Marijuana Users." In 2021 Virtual Scientific Meeting of the Research Society on Marijuana. Research Society on Marijuana, 2022. http://dx.doi.org/10.26828/cannabis.2022.01.000.43.

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Marijuana is the most commonly used illicit substance, with daily use rising among 8th and 10th graders. Adolescents view marijuana use as carrying minimal risk despite a host of associated psychosocial consequences. Within the behavioral economic framework, the Marijuana Purchase Task (MPT) has been used to understand demand (i.e., relative value) for marijuana. The MPT is a hypothetical purchase task that produces five demand indices reflective of the relative reinforcing value of marijuana and include intensity (i.e., amount consumed at zero cost), Omax (i.e., maximum expenditure), Pmax (i.e., price at maximum expenditure), breakpoint (i.e., cost at which consumption is suppressed to zero), and elasticity (i.e., rate at which consumption decreases as price increases). To date, the MPT has only been validated with adult samples; thus, the current study aimed to validate the MPT with a late adolescent sample who presumably have less experience in purchasing and using marijuana relative to adult users. Convergent validity was established via correlations between demand indices and marijuana outcomes (i.e., marijuana use, consequences, craving, and recent marijuana expenditures). Divergent validity was established via t-tests to examine group differences between hazardous and non-hazardous users as differentiated by the Cannabis Use Disorders Identification Test-Revised (CUDIT-R; scores of 8 or greater indicate hazardous use). Participants were 115 adolescents (Mage = 16.94, SDage = 0.88; 52% female; 64% high school student) between the ages of 15-18 who reported lifetime marijuana use and current marijuana demand. As expected, results showed that as price increased, hypothetical marijuana use decreased. Convergent validity was established via significant associations between demand indices and marijuana outcomes. Omax, breakpoint, and elasticity were significantly correlated with marijuana use outcomes in predicted directions such that greater demand was associated with more use, consequences, craving, and recent expenditures (ps <.05). Intensity was positively correlated with craving and expenditures (ps < .05). Pmax was not significantly correlated with any marijuana use outcome. Divergent validity was also established; compared to non-hazardous users (n = 39), hazardous users (n = 76) exhibited significantly higher Omax (t = 3.11, p <.01), Pmax (t = 2.08, p <.05), breakpoint (t = 3.71, p < .001), and elasticity (t = 3.11, p <.01). There was no difference in intensity across user types. Findings from the current study are unique in several ways. First, in contrast with previous literature, intensity was less consistently associated with marijuana outcomes. However, indices related to price sensitivity are important metrics in this age group, as evidenced by significant associations between Omax, breakpoint, and elasticity and marijuana outcomes. These findings are further evidenced by the ability of Omax, Pmax, breakpoint, and elasticity to differentiate non-hazardous versus hazardous users. Together, these findings suggest that the MPT is a valid measure for assessing the reinforcing value of marijuana among adolescents. Future research should replicate these findings, as well as examine the factor structure of the MPT among adolescents.
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Horrell, Jeremy C., Aileen M. Aldrich, and Heidi J. Gill Super. "Abstract 2990: Analysis of chromatin structure in the Myeloid-Lymphoid Leukemia gene translocation breakpoint cluster region." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-2990.

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Matthews, R. J., D. S. Anson, I. R. Peake, and A. L. Bloom. "GENE DELETIONS IN THE FACTOR IX LOCUS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643871.

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Previous studies have indicated that the majority of haemophilia B patients who produce anti-factor IX inhibitors (antibodies) have some kind of deletion of the factor IX gene. We have analysed DNA from nine haemophilia B inhibitor patients using the Southern blotting method and hybridisation with (i) factor IX cDNA and intragenomic probes (ii) probes originating from flanking sequences up to 60kb 5' and 170kb 3' to the factor IX gene that have been isolated by gene walking experiments (D.S.Anson and G.G.Brownlee, unpublished observations).Two patients who are brothers (haemophilia B (Chicago I)) were shown to have a presumably identical complex rearrangement of the factor IX gene involving two separate deletions. The first deletion is approx. 5.0kb and removes exon e. The second deletion is between 9 and 29kb and removes exons g and h but leaves exon f intact. An abnormal TaqI fragment at one end of the deletions junctions acted as a marker for the inheritance of haemophilia B in the patients' family. Furthermore, an abnormal llkb Bglll fragment (detected with an intragenomic probe containing exon f) in DNA from both patients and their mother acted as a marker for the presence of both deletions. Since the patients' grandmother only showed the normal 12kb Bgl II fragment then both deletions appear to have arisen at the same time. We believe that haemophilia B (Chicago 1) is the first observation of a natural gene rearrangement involving two separate deletions within the same gene.Patient haemophilia B (Jersey 1) was revealed to have a deletion of at least 170kb including the entire factor IX gene and > 60kb of 5' flanking sequence. The 3' breakpoint of this deletion was mapped to between 80 and 140kb 3' to the factor IX gene. One further patient, haemophilia B (Boston I) was shown to have a deletion of > 230kb including the factor IX gene, > 60kb of 5' flanking sequence and >140kb of 3' flanking sequence. Five other inhibitor patients had a structurally intact gene as detected by this method.Although all nine haemophilia B inhibitor patients studied did not have a detectable plasma factor IX only in four of them is this absence due to a large deletion of the factor IX gene.
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Hamed, Ashraf M., Paramsothy Jayakumar, Michael D. Letherwood, David J. Gorsich, Antonio M. Recuero, and Ahmed A. Shabana. "Ideal Compliant Joints and Integration of Computer Aided Design and Analysis." In ASME 2014 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/detc2014-34423.

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This paper discusses fundamental issues related to the integration of computer aided design and analysis (I-CAD-A) by introducing a new class of ideal compliant joints that account for the distributed inertia and elasticity. The absolute nodal coordinate formulation (ANCF) degrees of freedom are used in order to capture modes of deformation that cannot be captured using existing formulations. The ideal compliant joints developed can be formulated, for the most part, using linear algebraic equations, allowing for the elimination of the dependent variables at a preprocessing stage, thereby significantly reducing the problem dimension and array storage needed. Furthermore, the constraint equations are automatically satisfied at the position, velocity, and acceleration levels. When using the proposed approach to model large scale chain systems, differences in computational efficiency between the augmented formulation and the recursive methods are eliminated, and the CPU times resulting from the use of the two formulations become similar regardless of the complexity of the system. The elimination of the joint constraint equations and the associated dependent variables also contribute to the solution of a fundamental singularity problem encountered in the analysis of closed loop chains and mechanisms by eliminating the need to repeatedly change the chain or mechanism independent coordinates. It is shown that the concept of the knot multiplicity used in computational geometry methods, such as B-spline and NURBS (Non-Uniform Rational B-Spline), to control the degree of continuity at the breakpoints is not suited for the formulation of many ideal compliant joints. As explained in this paper, this issue is closely related to the inability of B-spline and NURBS to model structural discontinuities. Another contribution of this paper is demonstrating that large deformation ANCF finite elements can be effective, in some MBS application, in solving small deformation problems. This is demonstrated using a heavily constrained tracked vehicle with flexible link chains. Without using the proposed approach, modeling such a complex system with flexible links can be very challenging. The analysis presented in this paper also demonstrates that adding significant model details does not necessarily imply increasing the complexity of the MBS algorithm.
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