Relevant bibliographies by topics / Cytogenomic and epigenomic characterization

Academic literature on the topic 'Cytogenomic and epigenomic characterization'

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Published: 9 March 2023

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Journal articles on the topic "Cytogenomic and epigenomic characterization"

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Baronchelli, Simona, Angela Bentivegna, Serena Redaelli, Gabriele Riva, Valentina Butta, Laura Paoletta, Giuseppe Isimbaldi, et al. "Delineating the Cytogenomic and Epigenomic Landscapes of Glioma Stem Cell Lines." PLoS ONE 8, no. 2 (February 28, 2013): e57462. http://dx.doi.org/10.1371/journal.pone.0057462.

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Redaelli, Serena, Angela Bentivegna, Dana Foudah, Mariarosaria Miloso, Juliana Redondo, Gabriele Riva, Simona Baronchelli, Leda Dalpra, and Giovanni Tredici. "From cytogenomic to epigenomic profiles: monitoring the biological behavior of in vitro cultured human bone marrow mesenchymal stem cells." Stem Cell Research & Therapy 3, no. 6 (2012): 47. http://dx.doi.org/10.1186/scrt138.

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Mathur, Radhika, Qixuan Wang, Patrick Schupp, Stephanie Hilz, Chibo Hong, Ivan Smirnov, Marisa Lafontaine, et al. "ECOA-5. Integrative 3D spatial characterization of genomic and epigenomic intratumoral heterogeneity in glioblastoma." Neuro-Oncology Advances 3, Supplement_2 (July 1, 2021): ii2. http://dx.doi.org/10.1093/noajnl/vdab070.005.

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Abstract Treatment failure in glioblastoma is often attributed to intratumoral heterogeneity (ITH), which fosters tumor evolution and selection of therapy-resistant clones. While genomic alterations are known contributors to ITH, emerging studies highlight functional roles for epigenomic ITH which integrates differentiation status, stochastic events, and microenvironmental inputs. Here, we have established a novel platform for integrative characterization of genomic and epigenomic ITH of glioblastoma in three-dimensional (3-D) space. In collaboration with neurosurgeons and biomedical imaging experts, we utilize 3-D surgical neuro-navigation to safely acquire ~10 tumor samples per patient representing maximal anatomical diversity. We conduct whole-exome sequencing, RNA sequencing, and assay for transposase-accessible chromatin using sequencing (ATAC-Seq) on each sample. The spatial location of each sample is mapped by its 3-D coordinates, allowing 360-degree visualization of genomic and epigenomic ITH for each patient. We demonstrate this approach on 8 patients with primary IDH-WT glioblastoma (83 spatially mapped samples), providing unprecedented insight into their spatial organization at the genomic and epigenomic levels. We link genetically defined tumor subclones to patterns of open chromatin and gene regulation, revealing underlying transcription factor binding at active promoters and enhancers. We also identify ITH in whole-genome doubling and focal oncogene amplification events in multiple patients, which we then link with epigenomic ITH. Further, to study microenvironmental inputs and their contribution to epigenomic ITH, we conduct deconvolution of RNA sequencing and ATAC-Seq data by analyzing feature co-variation. We resolve the 3-D spatial organization of immune, neural, and other nontumor cell types present in glioblastoma, characterizing their functional states and interactions with tumor cells. This work provides the most comprehensive spatial characterization of genomic and epigenomic ITH to date in glioblastoma. As a resource for further investigation, we have developed an interactive data sharing platform – The 3D Glioma Atlas – that enables 360-degree visualization of both genomic and epigenomic ITH.
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Siegel, Erin M., Steven Eschrich, Kathryn Winter, Bridget Riggs, Anders Berglund, Abidemi Ajidahun, Jeff Simko, et al. "Epigenomic Characterization of Locally Advanced Anal Cancer." Diseases of the Colon & Rectum 57, no. 8 (August 2014): 941–57. http://dx.doi.org/10.1097/dcr.0000000000000160.

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Sahajpal, Nikhil, Ashis Mondal, Suzanne Hurley, Alex Hastie, Alka Chaubey, Amyn Rojiani, Fariborz Rashid-Kolvear, and Ravindra Kolhe. "Next-generation cytogenomic characterization of prenatal cases by Optical Genome Mapping." Molecular Genetics and Metabolism 132 (April 2021): S322. http://dx.doi.org/10.1016/s1096-7192(21)00580-1.

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Roxo, Guilherme, Mónica Moura, Pedro Talhinhas, José Carlos Costa, Luís Silva, Raquel Vasconcelos, Miguel Menezes de Sequeira, and Maria Manuel Romeiras. "Diversity and Cytogenomic Characterization of Wild Carrots in the Macaronesian Islands." Plants 10, no. 9 (September 18, 2021): 1954. http://dx.doi.org/10.3390/plants10091954.

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The Macaronesian islands constitute an enormous reservoir of genetic variation of wild carrots (subtribe Daucinae; Apiaceae), including 10 endemic species, but an accurate understanding of the diversification processes within these islands is still lacking. We conducted a review of the morphology, ecology, and conservation status of the Daucinae species and, on the basis of a comprehensive dataset, we estimated the genome size variation for 16 taxa (around 320 samples) occurring in different habitats across the Macaronesian islands in comparison to mainland specimens. Results showed that taxa with larger genomes (e.g., Daucus crinitus: 2.544 pg) were generally found in mainland regions, while the insular endemic taxa from Azores and Cabo Verde have smaller genomes. Melanoselinum decipiens and Monizia edulis, both endemic to Madeira Island, showed intermediate values. Positive correlations were found between mean genome size and some morphological traits (e.g., spiny or winged fruits) and also with habit (herbaceous or woody). Despite the great morphological variation found within the Cabo Verde endemic species, the 2C-values obtained were quite homogeneous between these taxa and the subspecies of Daucus carota, supporting the close relationship among these taxa. Overall, this study improved the global knowledge of DNA content for Macaronesian endemics and shed light into the mechanisms underpinning diversity patterns of wild carrots in the western Mediterranean region.
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Azawi, Shaymaa, Stefanie Kankel, Thomas Liehr, and Martina Rincic. "First cytogenomic characterization of murine testis tumor cell line MLTC-1." Molecular and experimental biology in medicine 4, no. 1 (December 16, 2022): 10–14. http://dx.doi.org/10.33602/mebm.4.1.2.

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The cell line MLTC-1 was established in 1982 as a transplantable Leydig cell tumor from a C57BL/6 mouse. The cell line has already been applied in >100 studies: still, the only information about its genetic content is given in the first description: MLTC-1 initially had a polyploid karyotype. Here, a molecular karyotyping and multicolor banding-based molecular cytogenetic study was done to provide the first chromosomal/ (molecular) cytogenetic characterization of MLTC-1. A hexaploid karyotype with 72 to 105 chromosomes was hereby characterized. Besides polyploidy, unbalanced two- and three-way translocations, dicentrics and one neocentric derivative were identified. Also, no Y-chromosome could be detected in this clearly male derived cell line. Overall, a completely unbalanced genome is present in MLTC-1 with ~20 regions being subject to copy number losses or gains. After translating these imbalances into the human genome in a standardized way, a 40% match of imbalances with human Leydig cell tumors was evident; however, about the same rate of concordance was detectable for human spermatocytic seminomas and non-seminomas as well as testicular germ cell tumor. Accordingly, MLTC-1 is better suited as an advanced testicular germ cell tumor model in general, rather than specifically for human Leydig cell tumors.
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Nam, Chehyun, Benjamin Ziman, Megha Sheth, Hua Zhao, and De-Chen Lin. "Genomic and Epigenomic Characterization of Tumor Organoid Models." Cancers 14, no. 17 (August 24, 2022): 4090. http://dx.doi.org/10.3390/cancers14174090.

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Tumor organoid modeling has been recognized as a state-of-the-art system for in vitro research on cancer biology and precision oncology. Organoid culture technologies offer distinctive advantages, including faithful maintenance of physiological and pathological characteristics of human disease, self-organization into three-dimensional multicellular structures, and preservation of genomic and epigenomic landscapes of the originating tumor. These features effectively position organoid modeling between traditional cell line cultures in two dimensions and in vivo animal models as a valid, versatile, and robust system for cancer research. Here, we review recent advances in genomic and epigenomic characterization of tumor organoids and the novel findings obtained, highlight significant progressions achieved in organoid modeling of gene–drug interactions and genotype–phenotype associations, and offer perspectives on future opportunities for organoid modeling in basic and clinical cancer research.
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Graff-Baker, Amanda N., Javier I. J. Orozco, Diego M. Marzese, Matthew P. Salomon, Dave S. B. Hoon, and Melanie Goldfarb. "Epigenomic and Transcriptomic Characterization of Secondary Breast Cancers." Annals of Surgical Oncology 25, no. 10 (June 28, 2018): 3082–87. http://dx.doi.org/10.1245/s10434-018-6582-7.

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Rodríguez Paredes, M., L. Solé Boldo, G. Raddatz, J. Gutekunst, M. Liberio, J. Mallm, K. Rippe, A. S. Lonsdorf, and F. Lyko. "469 Epigenomic characterization of non-melanoma skin cancer." Journal of Investigative Dermatology 139, no. 9 (September 2019): S295. http://dx.doi.org/10.1016/j.jid.2019.07.519.

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Dissertations / Theses on the topic "Cytogenomic and epigenomic characterization"

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BARONCHELLI, SIMONA. "Cytogenetic, genimic, epigenomic and drug sensitivity landscapes to unravel the complexity of glioma stem cell lines: a multi-level approach." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2011. http://hdl.handle.net/10281/27138.

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BACKGROUND. Glioblastoma multiforme (GBM) is the most common and malignant type of glioma and it is characterized by extensive heterogeneity, both at the cellular and molecular level. The poor prognosis and the lack of an effective treatment are due to the presence of a small sub-population of cells with stem-like properties, termed glioma stem cells (GSCs). At the genomic level, heterogeneity is characterized by multiple levels of alterations, including cytogenetic, genomic and epigenomic alterations. Drug sensitivity is an additional level of GSC complexity and heterogeneity and the identification of an effective treatment for GBM depends on the depletion of the GSC pool. Valproic acid (VPA) is a histone deacetylase inhibitor and so it can be used for an epigenetic therapy for cancer. Besides, a differentiation inducing ability of VPA on cancer cells was demonstrated. Paclitaxel (PTX) is a conventional chemotherapeutic agent and in the last years it was shown to be a potential therapeutic drug for gliomas. AIMS AND PROJECT DESIGN. Six GSC lines were studied, as they represent a valuable tool for the investigation of cytogenomic and epigenomic landscapes of GBM, in order to unravel specific molecular pathways, involved in the stem-like counterpart. Drug sensitivity profiles were assessed, evaluating cell viability and cytomorphological parameters (mitotic index, ploidy and polymorphic nuclei), after VPA and PTX administration. The reliability of differentiation and epigenetic therapy through the use of VPA was further investigated by morphological and molecular epigenomic analysis, investigating the DNA methylation status. RESULTS AND DISCUSSION. Several shared cytogenetic and genomic alterations linked to GBM pathogenesis were found among the GSC lines. Specifically, polysomy of chromosome 7, loss of chromosome 10, CDKN2A and CDKN2B deletions are aberrations related to highly relevant pathways in GBM tumorigenesis. Moreover, a minimal deleted region at 1p36.31 was common among the six GSC lines, including CAMTA1 gene, a putative tumor suppressor gene, specific for cancer stem-like cells. Disregulated cytogenenomic pathways in GSCs were preferentially linked to the control of stem cell proliferation, invasion, cellular development and differentiation. The evaluation of the methylation profiles of GSC lines revealed aberrant methylation of developmental genes, which are targeted by Polycomb Repressive Complex 2 in embryonic stem cells and involved in cellular development and nervous system differentiation, evidencing a specific impairment of these processes in cancer stem-like cells. VPA is able to begin a differentiation process in GSCs, as demonstrated by the study of methylation changes caused by VPA, through the methylation of pathways which are involved in self-renewal maintenance, such as Wnt/β-catenin, and several cancer-related mechanisms. Anyway, terminal differentiation was impaired, due to an intrinsic characteristic of cancer cells endowed with stem like properties. GSCs viability was severely affected by dual drug treatment, combining VPA and PTX: VPA caused an initial differentiation, enabling PTX to induce cell death of downstream cells in tumor hierarchy. Thus, a dual approach with drugs affecting different features of malignancy could be a successful approach to GBM treatment. CONCLUSIONS. A multi-level study for the evaluation of cytogenomic and epigenomic landscapes of GSCs is an effective approach for the identification of molecular pathways, specifically de-regulated in stem-like cells, giving an outstanding contribution in the identification of key mechanisms sustaining self-renewal. GSC lines are a valuable tool to evaluate the potentiality of new therapeutical approaches, which should be able to overwhelm the stem-like related counterpart. VPA and PTX combined treatment was found to fulfill the therapeutical potential of VPA and might be a successful approach to unlock the self-renewal loop, typical of GSCs and affect their growth.
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Ribeiro, Maria Margarida Sá. "Cytogenomic characterization and DNA methylation patterns of laryngeal cancer." Master's thesis, 2017. http://hdl.handle.net/10316/81422.

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Dissertação de Mestrado em Investigação Biomédica apresentada à Faculdade de Medicina
Background: Laryngeal cancer is the second most common malignancy of the head and neck, accounting for approximately 20% of cases. In Portugal, the third European country with the highest incidence of laryngeal cancer, approximately 600 new cases are diagnosed per year. With a low 5 year-survival rate, mainly explained by a late diagnosis, tumour aggressiveness and rapid metastatic process, it is essential to identify biomarkers to anticipate the cancer detection in an early stage.Aim: The main goal of this study was the cytogenomic evaluation and DNA methylation patterns characterization of laryngeal cancer in order to identify putative diagnostic and prognostic biomarkers.Methods: Tumour and non-tumour laryngeal tissue samples obtained from twenty one patients that undergone surgical treatment for laryngeal cancer were used. Detection of copy number variations (CNVs) was performed using array Comparative Genomic Hybridization (aCGH) and Methylation Specific Multiplex Ligation-dependent Probe Amplification (MS-MLPA). Furthermore, methylation patterns of target genes were assessed by MS-MLPA analysis.Results: aCGH revealed frequent gains of chromosomes 3q, 7p, 8, 9q, 11q, 12p,17q and 18p while losses were frequently found in chromosome 3p, 9p, 11p and Y. Amplifications of GATA5 and CDK6 were the most common events among tumour samples. VHL, CDKN2A, ATM and CADM genes were found to be frequently deleted. Methylation of GATA5 was frequent in tumour samples being associated with late stages while WT1 was highly methylated in non-tumour samples, being an early epigenetic event in laryngeal cancer. The methylation of MGMT was associated with tobacco consumption.Conclusion: This study confirmed genetic variations associated with laryngeal carcinoma that have already been reported as well as identified alterations that have been associated with tumour development and progression. Genes found altered are candidate genes as biomarkers for laryngeal cancer.
O cancro da laringe é o segundo tumor mais comum dentro da família de tumores com origem na cabeça e pescoço, contribuindo para aproximadamente 20% dos casos. Em Portugal, o terceiro país europeu com maior incidência de cancro da laringe, cerca de 600 novos casos são diagnosticados por ano. Com uma baixa taxa de sobrevivência após 5 anos, explicada principalmente por um diagnóstico tardio, agressividade tumoral e por um processo metastático rápido, é essencial identificar biomarcadores para antecipar a deteção do cancro num estadio inicial.O principal objetivo deste estudo foi a avaliação citogenética e a caracterização dos padrões de metilação do DNA do cancro da laringe, a fim de identificar biomarcadores putativos de valor diagnóstico e prognóstico. Foram utilizadas amostras de tecido tumoral e não tumoral da laringe, obtidas de vinte e um pacientes submetidos a tratamento cirúrgico para o cancro da laringe. A deteção de variações de número de cópias foi realizada através das técnicas de array Comparative Genomic Hybridization (aCGH) e Methylation Specific Multiplex Ligation-dependent Probe Amplification (MS-MLPA). Além disso, os padrões de metilação dos genes alvo foram avaliados pela análise MS-MLPA.O aCGH revelou ganhos frequentes dos cromossomas 3q, 7p, 8, 9q, 11q, 12p,17q e 18p enquanto as perdas foram frequentemente encontradas nos cromossomas 3p, 9p, 11p e Y. As amplificações dos genes GATA5 e CDK6 foram os eventos mais comuns entre amostras tumorais. A perda dos genes VHL, CDKN2A, ATM e CADM foi frequentemente detetada. A metilação do GATA5 foi frequente em amostras de tumores associados a estadios avançados, enquanto o WT1 foi altamente metilado em amostras não tumorais, sendo um evento epigenético precoce no cancro da laringe. A metilação da MGMT foi associada ao consumo de tabaco. Este estudo confirmou variações genéticas associadas ao carcinoma laríngeo já anteriormente relatadas, bem como alterações identificadas como estando associadas ao desenvolvimento e progressão do tumor. Os genes encontrados alterados são genes candidatos ao seu uso como biomarcadores do cancro da laringe.
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Book chapters on the topic "Cytogenomic and epigenomic characterization"

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Ramaswamy, Vijay, and Michael D. Taylor. "Bioinformatic Strategies for the Genomic and Epigenomic Characterization of Brain Tumors." In Methods in Molecular Biology, 37–56. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8805-1_4.

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Conference papers on the topic "Cytogenomic and epigenomic characterization"

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Rodríguez-Paredes, Manuel, Stefanie Geyh, Mahshid Gazorpak, Julian Gutekunst, Felix Bormann, Rainer Haas, Thomas Schröder, and Frank Lyko. "Abstract 2408: Epigenomic characterization of MSC from myeloid malignancies." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-2408.

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Mukherjee, Seema, Bonnie S. Glisson, John D. Minna, Robert J. Cardnell, Luc Girard, Adi Gazdar, Lixia Diao, Jing Wang, and Lauren A. Byers. "Abstract 2961: Characterization of methylation profiles reveals distinct epigenomic patterns in SCLC and NSCLC." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-2961.

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Battle, Stephanie L., Antti Larjo, Joling Liao, Harri Lähdesmäki, Andre Lieber, and R. David Hawkins. "Abstract AS04: Epigenomic characterization of gene regulatory networks in human ovarian cancer stem cells." In Abstracts: 10th Biennial Ovarian Cancer Research Symposium; September 8-9, 2014; Seattle, WA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1557-3265.ovcasymp14-as04.

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Zhang, Wa, David Klinkebiel, Sanjit Pandey, Dan Wang, Song Liu, Chittibabu Guda, Kunle Odunsi, and Adam R. Karpf. "Abstract B12: Genomic and epigenomic characterization of global DNA hypomethylation in human epithelial ovarian cancer." In Abstracts: AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; September 18-21, 2013; Miami, FL. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1078-0432.ovca13-b12.

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Desmedt, C., S. Nik-Zainal, D. Fumagalli, F. Rothé, S. Singhal, S. Majjaj, D. Brown, et al. "Abstract S6-2: Characterization of different foci of multifocal breast cancer using genomic, transcriptomic and epigenomic data." In Abstracts: Thirty-Fifth Annual CTRC‐AACR San Antonio Breast Cancer Symposium‐‐ Dec 4‐8, 2012; San Antonio, TX. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/0008-5472.sabcs12-s6-2.

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