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Chromothripsis

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https://www.readbyqxmd.com/read/29753700/spectrum-and-prevalence-of-genetic-predisposition-in-medulloblastoma-a-retrospective-genetic-study-and-prospective-validation-in-a-clinical-trial-cohort
#1
Sebastian M Waszak, Paul A Northcott, Ivo Buchhalter, Giles W Robinson, Christian Sutter, Susanne Groebner, Kerstin B Grund, Laurence Brugières, David T W Jones, Kristian W Pajtler, A Sorana Morrissy, Marcel Kool, Dominik Sturm, Lukas Chavez, Aurelie Ernst, Sebastian Brabetz, Michael Hain, Thomas Zichner, Maia Segura-Wang, Joachim Weischenfeldt, Tobias Rausch, Balca R Mardin, Xin Zhou, Cristina Baciu, Christian Lawerenz, Jennifer A Chan, Pascale Varlet, Lea Guerrini-Rousseau, Daniel W Fults, Wiesława Grajkowska, Peter Hauser, Nada Jabado, Young-Shin Ra, Karel Zitterbart, Suyash S Shringarpure, Francisco M De La Vega, Carlos D Bustamante, Ho-Keung Ng, Arie Perry, Tobey J MacDonald, Pablo Hernáiz Driever, Anne E Bendel, Daniel C Bowers, Geoffrey McCowage, Murali M Chintagumpala, Richard Cohn, Timothy Hassall, Gudrun Fleischhack, Tone Eggen, Finn Wesenberg, Maria Feychting, Birgitta Lannering, Joachim Schüz, Christoffer Johansen, Tina V Andersen, Martin Röösli, Claudia E Kuehni, Michael Grotzer, Kristina Kjaerheim, Camelia M Monoranu, Tenley C Archer, Elizabeth Duke, Scott L Pomeroy, Redmond Shelagh, Stephan Frank, David Sumerauer, Wolfram Scheurlen, Marina V Ryzhova, Till Milde, Christian P Kratz, David Samuel, Jinghui Zhang, David A Solomon, Marco Marra, Roland Eils, Claus R Bartram, Katja von Hoff, Stefan Rutkowski, Vijay Ramaswamy, Richard J Gilbertson, Andrey Korshunov, Michael D Taylor, Peter Lichter, David Malkin, Amar Gajjar, Jan O Korbel, Stefan M Pfister
BACKGROUND: Medulloblastoma is associated with rare hereditary cancer predisposition syndromes; however, consensus medulloblastoma predisposition genes have not been defined and screening guidelines for genetic counselling and testing for paediatric patients are not available. We aimed to assess and define these genes to provide evidence for future screening guidelines. METHODS: In this international, multicentre study, we analysed patients with medulloblastoma from retrospective cohorts (International Cancer Genome Consortium [ICGC] PedBrain, Medulloblastoma Advanced Genomics International Consortium [MAGIC], and the CEFALO series) and from prospective cohorts from four clinical studies (SJMB03, SJMB12, SJYC07, and I-HIT-MED)...
May 9, 2018: Lancet Oncology
https://www.readbyqxmd.com/read/29726589/chromosomal-rearrangements-in-uveal-melanoma-chromothripsis
#2
Natasha M van Poppelen, Serdar Yavuzyigitoglu, Kyra N Smit, Jolanda Vaarwater, Bert Eussen, Tom Brands, Dion Paridaens, Emine Kiliç, Annelies de Klein
Uveal melanoma (UM) is the most common primary intraocular malignancy in the Western world. Recurrent mutations in GNAQ, GNA11, CYSLTR2, PLCB4, BAP1, EIF1AX and SF3B1 are described as well as non-random chromosomal aberrations. Chromothripsis is a rare event in which chromosomes are shattered and rearranged and has been reported in a variety of cancers including UM. SNP arrays of 249 UM from patients who underwent enucleation, biopsy or endoresection were reviewed for the presence of chromothripsis. Chromothripsis was defined as ten or more breakpoints per chromosome involved...
May 4, 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29684357/genome-wide-somatic-copy-number-alterations-and-mutations-in-high-grade-pancreatic-intraepithelial-neoplasia
#3
Tatsuo Hata, Masaya Suenaga, Luigi Marchionni, Anne Macgregor-Das, Jun Yu, Koji Shindo, Koji Tamura, Ralph H Hruban, Michael Goggins
To obtain a better understanding of the genetic alterations of high-grade pancreatic intraepithelial neoplasia (HG-PanIN), we performed whole-genome copy number analysis using single nucleotide polymorphism microarrays and targeted next-generation sequencing of 11 microdissected HG-PanIN and two low-grade PanIN (LG-PanIN) lesions associated with HG-PanIN. HG-PanIN mutation profiles were compared to those of their associated invasive pancreatic ductal adenocarcinoma. All PanIN lesions harbored somatic KRAS mutations...
April 20, 2018: American Journal of Pathology
https://www.readbyqxmd.com/read/29656891/timing-the-landmark-events-in-the-evolution-of-clear-cell-renal-cell-cancer-tracerx-renal
#4
Thomas J Mitchell, Samra Turajlic, Andrew Rowan, David Nicol, James H R Farmery, Tim O'Brien, Inigo Martincorena, Patrick Tarpey, Nicos Angelopoulos, Lucy R Yates, Adam P Butler, Keiran Raine, Grant D Stewart, Ben Challacombe, Archana Fernando, Jose I Lopez, Steve Hazell, Ashish Chandra, Simon Chowdhury, Sarah Rudman, Aspasia Soultati, Gordon Stamp, Nicos Fotiadis, Lisa Pickering, Lewis Au, Lavinia Spain, Joanna Lynch, Mark Stares, Jon Teague, Francesco Maura, David C Wedge, Stuart Horswell, Tim Chambers, Kevin Litchfield, Hang Xu, Aengus Stewart, Reza Elaidi, Stéphane Oudard, Nicholas McGranahan, Istvan Csabai, Martin Gore, P Andrew Futreal, James Larkin, Andy G Lynch, Zoltan Szallasi, Charles Swanton, Peter J Campbell
Clear cell renal cell carcinoma (ccRCC) is characterized by near-universal loss of the short arm of chromosome 3, deleting several tumor suppressor genes. We analyzed whole genomes from 95 biopsies across 33 patients with clear cell renal cell carcinoma. We find hotspots of point mutations in the 5' UTR of TERT, targeting a MYC-MAX-MAD1 repressor associated with telomere lengthening. The most common structural abnormality generates simultaneous 3p loss and 5q gain (36% patients), typically through chromothripsis...
April 4, 2018: Cell
https://www.readbyqxmd.com/read/29564835/looking-for-broken-tad-boundaries-and-changes-on-dna-interactions-clinical-guide-to-3d-chromatin-change-analysis-in-complex-chromosomal-rearrangements-and-chromothripsis
#5
Kevin Yauy, Vincent Gatinois, Thomas Guignard, Satish Sati, Jacques Puechberty, Jean Baptiste Gaillard, Anouck Schneider, Franck Pellestor
Apparition of next-generation sequencing (NGS) was a breakthrough on knowledge of genome structure. Bioinformatic tools are a key point to analyze this huge amount of data from NGS and characterize the three-dimensional organization of chromosomes. This chapter describes usage of different browsers to explore publicly available online data and to search for possible 3D chromatin changes involved during complex chromosomal rearrangements as chromothripsis. Their pathogenic impact on clinical phenotype and gene misexpression can also be evaluated with annotated databases...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564834/experimental-induction-of-genome-chaos
#6
Christine J Ye, Guo Liu, Henry H Heng
Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564833/correlative-live-imaging-and-immunofluorescence-for-analysis-of-chromosome-segregation-in-mouse-preimplantation-embryos
#7
Cayetana Vázquez-Diez, Greg FitzHarris
Chromothripsis is a phenomenon observed in cancer cells, wherein a single or few chromosome(s) exhibit vast genomic rearrangements. Recent studies elucidated a striking series of events in which defective segregation of chromosomes causes their incorporation into micronuclei, where they are subject to extensive DNA damage prior to re-joining the main mass of chromosomes in a subsequent cell cycle, which provide an appealing mechanism for the etiology of chromothripsis. Micronuclei are well known to be common in human preimplantation embryos...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564832/time-lapse-imaging-for-the-detection-of-chromosomal-abnormalities-in-primate-preimplantation-embryos
#8
Brittany L Daughtry, Shawn L Chavez
The use of time-lapse microscopic imaging has proven to be a powerful tool for the study of mitotic divisions and other cellular processes across diverse species and cell types. Although time-lapse monitoring (TLM) of human preimplantation development was first introduced to the in vitro fertilization (IVF) community several decades ago, it was not until relatively recently that TLM systems were commercialized for clinical embryology purposes. Traditionally, human IVF embryos are assessed by successful progression and morphology under a stereomicroscope at distinct time points prior to selection for transfer...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564831/chromothripsisdb-a-curated-database-for-the-documentation-visualization-and-mining-of-chromothripsis-data
#9
Haoyang Cai
ChromothripsisDB ( http://cgma.scu.edu.cn/ChromothripsisDB ) is a manually curated database containing a unified description of published chromothripsis cases and relevant genomic aberrations. Available data includes copy number alterations, chromosome structural variations, and gene annotations. The criteria used for detecting chromothripsis in each study are also provided. At present, the molecular mechanisms involved in chromothripsis phenomenon are not fully understood. Thus, further studies with large number of identified chromothripsis samples are needed...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564830/chromothripsis-detection-and-characterization-using-the-ctlpscanner-web-server
#10
Jian Yang, Bo Liu, Haoyang Cai
Accurate detection of chromothripsis event is important to study the mechanisms underlying this phenomenon. CTLPScanner ( http://cgma.scu.edu.cn/CTLPScanner/ ) is a web-based tool for identification and annotation of chromothripsis-like pattern (CTLP) in genomic array data. In this chapter, we illustrate the utility of CTLPScanner for screening chromosome pulverization regions and give interpretation of the results. The web interface offers a set of parameters and thresholds for customized screening. We also provide practical recommendations for effective chromothripsis detection...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564828/genes-proteins-and-biological-pathways-preventing-chromothripsis
#11
Martin Poot
The highly complex structural genome variations chromothripsis, chromoanasynthesis, and chromoplexy are subsumed under the term chromoanagenesis, which means chromosome rebirth. Precipitated by numerous DNA double-strand breaks, they differ in number of and distances between breakpoints, associated copy number variations, order and orientation of segments, and flanking sequences at joining points. Results from patients with the autosomal dominant cancer susceptibility disorder Li-Fraumeni syndrome implicated somatic TP53 mutations in chromothripsis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564826/detection-of-impaired-dna-replication-and-repair-in-micronuclei-as-indicators-of-genomic-instability-and-chromothripsis
#12
Mariona Terradas, Marta Martín, Anna Genescà
The physical isolation of chromosomes within micronuclei offers an attractive mechanistic explanation for the local DNA fragmentation and clustered genome rearrangements that characterize chromothripsis. Localized shattering of the chromatin confined in micronuclei can be a consequence of defects in micronuclei basic general functions, such as DNA replication and repair. The detection of DNA repair and replication defects in micronuclei is described here, as well as the analysis of chromosome breakage and inaccurate reassembly of broken segments in the daughter cells, as indirect methods to detect chromothripsis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564825/generation-of-micronuclei-and-detection-of-chromosome-pulverization
#13
Monique N H Luijten, Jeannie X T Lee, Sixun Chen, Karen C Crasta
Lagging chromosomes that arise after chromosome mis-segregation during cell division can be encapsulated within small structures known as micronuclei. A link between whole-chromosome mis-segregation and chromothripsis has been demonstrated via micronuclear chromosome pulverization. Here, we describe methods to efficiently generate micronuclei and examine downstream cell fates, specifically with regard to DNA damage and chromosome pulverization.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564824/a-role-for-retrotransposons-in-chromothripsis
#14
Dustin C Hancks
Chromothripsis is a mutational event driven by tens to hundreds of double-stranded DNA breaks which occur in a single event between a limited number of chromosomes. Following chromosomal shattering, DNA fragments are stitched together in a seemingly random manner resulting in complex genomic rearrangements including sequence shuffling, deletions, and inversions of varying size. This genomic catastrophe has been observed in cancer genomes and the genomes of patients harboring developmental and congenital defects...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564823/experimental-determination-of-checkpoint-adaptation-by-mitotic-shake-off-and-microscopy
#15
Lucy H Swift, Roy M Golsteyn
Cells that undergo checkpoint adaptation arrest at and then abrogate the G2/M cell cycle checkpoint to enter mitosis with damaged DNA. Cells surviving this process frequently contain micronuclei, which can lead to genomic change and chromothripsis. In this chapter we describe how to induce checkpoint adaptation and detect it by time-lapse video and immunofluorescence microscopy and how to isolate cells undergoing checkpoint adaptation from a total cell population.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564822/rna-seq-analysis-to-detect-abnormal-fusion-transcripts-linked-to-chromothripsis
#16
Anne-Laure Bougé, Florence Rufflé, Sébastien Riquier, Benoit Guibert, Jérôme Audoux, Thérèse Commes
RNA-Seq approach enables the detection and characterization of fusion or chimeric transcript associated to complex genome rearrangement. Until now, these events are classically identified at DNA level.Here we describe a complete procedure including a novel way of analyzing reads that combines genomic locations and local coverage to directly infer chimeric junctions with a high sensitivity and specificity, allowing identification of different classes of chimeric RNA events. We also recommend the best practices for the bioinformatics analysis and describe the experimental process for RNA validation using real-time PCR and sequencing...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564821/detection-of-chromothripsis-in-plants
#17
Isabelle M Henry, Luca Comai, Ek Han Tan
Chromothripsis, or chromosome shattering, occurs after chromosomes missegregate, are pulverized and subsequently repaired erroneously, leading to highly complex structural rearrangements. In plants, chromothripsis has been observed as a result of mitotic malfunction connected with the incomplete loss of haploid inducer chromosomes during uniparental genome elimination. Uniparental genome elimination, a process that results in haploid induction, is a phenomenon that typically results in the loss of an entire parental chromosome set in early embryos, resulting in haploid plants...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564820/identification-of-chromothripsis-in-biopsy-using-snp-based-microarray
#18
Veronica Ortega, Christina Mendiola, Gopalrao V N Velagaleti
One of the well-known hallmarks of cancer is genomic instability. Although gradualism is a well-established process of cancer evolution, recent studies have shown that chromothripsis or chromoanasynthesis can result in complex genomic rearrangements by a single catastrophic event rather than several incremental steps. These two novel phenomena suggest an evolutionary modality for cancer cells to circumvent individual mutational events with one simultaneous shattering of chromosomes or chromosome regions resulting in the random reassembling of shattered genetic material to form complex derivative chromosomes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564819/chromothripsis-detectable-in-small-supernumerary-marker-chromosomes-ssmc-using-fluorescence-in-situ-hybridization-fish
#19
Thomas Liehr
The formation of small supernumerary marker chromosomes (sSMC) still remains enigmatic. However, it is suggested that majority of all kinds of de novo sSMC (inverted duplication-, ring-, and centric-minute-shaped ones) are products of incomplete trisomic rescue during early embryogenesis. Recent work, based on molecular cytogenetics, suggests that these trisomic rescue events are going together with chromothripsis, directed against the supernumerary chromosome to be degraded. Here we present a protocol how to characterize so-called discontinuous sSMC by means of fluorescence in situ hybridization (FISH)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29564818/analysis-of-chromothripsis-by-combined-fish-and-microarray-analysis
#20
Ruth N MacKinnon
Fluorescence in situ hybridization (FISH) to metaphase chromosomes, in conjunction with SNP array, array CGH, or whole genome sequencing, can help determine the organization of abnormal genomes after chromothripsis and other types of complex genome rearrangement. DNA microarrays can identify the changes in copy number, but they do not give information on the organization of the abnormal chromosomes, balanced rearrangements, or abnormalities of the centromeres and other regions comprised of highly repetitive DNA...
2018: Methods in Molecular Biology
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