Search Results - "Bartha, Gábor"

A machine learning algorithm with subclonal sensitivity reveals widespread pan-cancer human leukocyte antigen loss of heterozygosity by Pyke, Rachel Marty, Mellacheruvu, Dattatreya, Dea, Steven, Abbott, Charles W., McDaniel, Lee, Bhave, Devayani P., Zhang, Simo V., Levy, Eric, Bartha, Gabor, West, John, Snyder, Michael P., Chen, Richard O., Boyle, Sean Michael

“…Human leukocyte antigen loss of heterozygosity (HLA LOH) allows cancer cells to escape immune recognition by deleting HLA alleles, causing the suppressed…”
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svclassify: a method to establish benchmark structural variant calls by Parikh, Hemang, Mohiyuddin, Marghoob, Lam, Hugo Y K, Iyer, Hariharan, Chen, Desu, Pratt, Mark, Bartha, Gabor, Spies, Noah, Losert, Wolfgang, Zook, Justin M, Salit, Marc

“…The human genome contains variants ranging in size from small single nucleotide polymorphisms (SNPs) to large structural variants (SVs). High-quality benchmark…”
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High prevalence of focal and multi-focal somatic genetic variants in the human brain by Keogh, Michael J., Wei, Wei, Aryaman, Juvid, Walker, Lauren, van den Ameele, Jelle, Coxhead, Jon, Wilson, Ian, Bashton, Matthew, Beck, Jon, West, John, Chen, Richard, Haudenschild, Christian, Bartha, Gabor, Luo, Shujun, Morris, Chris M., Jones, Nick S., Attems, Johannes, Chinnery, Patrick F.

“…Somatic mutations during stem cell division are responsible for several cancers. In principle, a similar process could occur during the intense cell…”
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Methane biogenesis during sodium azide-induced chemical hypoxia in rats by Tuboly, Eszter, Szabó, Andrea, Garab, Dénes, Bartha, Gábor, Janovszky, Ágnes, Erős, Gábor, Szabó, Anna, Mohácsi, Árpád, Szabó, Gábor, Kaszaki, József, Ghyczy, Miklós, Boros, Mihály

“…Previous studies demonstrated methane generation in aerobic cells. Our aims were to investigate the methanogenic features of sodium azide (NaN(3))-induced…”
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Activation of an Oncogenic MicroRNA Cistron by Provirus Integration by Wang, Clifford L., Wang, Bruce B., Bartha, Gábor, Li, Lauri, Channa, Namitha, Klinger, Mark, Killeen, Nigel, Wabl, Matthias

“…Retroviruses can cause tumors when they integrate near a protooncogene or tumor suppressor gene of the host. We infected >2,500 mice with the SL3-3 murine…”
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79 Extensively validated HLA LOH algorithm demonstrates an association between HLA LOH and genomic instability by Pyke, Rachel, Dea, Steven, Mellacheruvu, Dattatreya, Abbott, Charles, Zhang, Simo, McDaniel, Lee, Levy, Eric, Bartha, Gabor, West, John, Snyder, Michael, Chen, Richard, Boyle, Sean

“…BackgroundHuman Leukocyte Antigen (HLA) genes are critical for the presentation of neoantigens to the immune system by cancer cells. Deletion of HLA alleles,…”
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75 Comprehensive profiling of the tumor-immune microenvironment using an augmented transcriptome by Levy, Eric, Milani, Pamela, Navarro, Fabio, Bartha, Gabor, Abbott, Charles, Jacob, Jose, McClory, Rena, Li, Robin, West, John, Lyle, John, Boyle, Sean, Chen, Richard

“…BackgroundComprehensive profiling of both the tumor and tumor microenvironment (TME) can help further our understanding of tumor progression and response to…”
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73 Orthogonally and functionally validated algorithm for detecting HLA loss of heterozygosity by Pyke, Rachel, Mellacheruvu, Dattatreya, Abbott, Charles, Levy, Eric, Zhang, Simo, Bhave, Devayani, Chinnappa, Manjula, Bartha, Gabor, Lyle, John, West, John, Chen, Richard, Boyle, Sean

“…BackgroundHuman leukocyte antigen (HLA) genes facilitate communication between tumor cells and the immune system through the cell surface presentation of a…”
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29 Profiling tumor circulating cell-free DNA with an enhanced whole-exome to enable sensitive assessment of somatic mutations by Zhang, Simo, Tan, Mengyao, Navarro, Fabio CP, Northcott, Josette, Ma, Shuyuan, Nelson, Christopher, Bhave, Devayani, Gordon Bentley, L, Chinnappa, Manju, Norton, Dan, Bartha, Gabor, Harris, Jason, Lyle, John, Boyle, Sean, West, John, Chen, Richard

“…BackgroundAn increasing number of studies have demonstrated the potential use of circulating cell-free DNA (cfDNA) for diagnosis, prognosis, disease…”
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67 B-cell receptor heavy chain repertoire profiling using an augmented transcriptome by Levy, Eric, Milani, Pamela, Bartha, Gabor, Abbott, Charles, Power, Robert, McClory, Rena, Li, Robin, West, John, Lyle, John, Boyle, Sean, Chen, Richard

“…BackgroundComprehensive profiling of the tumor and tumor microenvironment (TME) is a critical tool for furthering our understanding of tumor progression and…”
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Retroviral activation of the mir-106a microRNA cistron in T lymphoma by Lum, Amy M, Wang, Bruce B, Li, Lauri, Channa, Namitha, Bartha, Gabor, Wabl, Matthias

“…Retroviral insertion into a host genome is a powerful tool not only for the discovery of cancer genes, but also for the discovery of potential oncogenic…”
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Abstract 3381: Analytical performance of an ultra-sensitive, tumor-informed liquid biopsy platform for molecular residual disease detection and clinical guidance by Chen, Rui, Bartha, Gábor, Lyle, John, Harris, Jason, Boyle, Sean M., Northcott, Josette, Norton, Dan, Pyke, Rachel M., Navarro, Fábio C., Abbott, Charles W., Haudenschild, Christian, Santiago, Rose, Nichols, Darren, Huang, Stephanie, Nelson, Christopher, Chinnappa, Manju, Chen, Yi, Wang, Yuker, Goodman, Laurie, Zhang, Qi, Hong, Manqing, Chen, Xiaoji, Ayash, Erin, Udar, Nitin, Saldivar, Sebastian, Yan, Jian, West, John, Chen, Richard O.

“…Abstract Most circulating tumor DNA (ctDNA)-based molecular residual disease (MRD) detection methods leverage a limited genomic footprint, restricting…”
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Abstract 3788: Sensitive detection of oncoviruses integrated into a comprehensive tumor immuno-genomics platform by Bartha, Gabor, Li, Robin, Luo, Shujun, West, John, Chen, Richard

“…Abstract Introduction HPV, HBV, HCV and EBV viruses are causally linked to over 11% of cancers worldwide while KSHV, HTLV and MCV are linked to an additional…”
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Abstract 363: Investigating the potential clinical predictive value of virus genotype, menopausal status and mutational landscape in cervical cancer tissue using a NGS based human papillomavirus (HPV) assay and whole exome sequencing (WES) by Pignon, Jean-Christophe, Giese, Heidi, Foernzler, Dorothee, McDaniel, Lee D., Bartha, Gabor, Scheuenpflug, Juergen, Feng, Zheng

“…Abstract Purpose: Persistent HPV infections are associated with nearly all cervical cancers and some head & neck and genitourinary cancers. In cervical cancer,…”
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Prediction of immunotherapy response by integrating immune infiltration and neoantigen presentation score in late-stage melanoma by Li, Bailiang, Abbott, Charles, McDaniel, Lee, Pyke, Rachel Marty, Navarro, Fabio, Anbunathan, Hima, Bartha, Gabor, Harris, Jason, Snyder, Michael, Jang, Sekwon, Boyle, Sean Michael, Chen, Richard

“…e21554 Background: Single modality biomarkers such as tumor mutational burden (TMB) fail to reliably predict response to immune checkpoint blockade (ICB) in…”
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Personalized neoantigen vaccine and pembrolizumab in advanced hepatocellular carcinoma: a phase 1/2 trial by Yarchoan, Mark, Gane, Edward J., Marron, Thomas U., Perales-Linares, Renzo, Yan, Jian, Cooch, Neil, Shu, Daniel H., Fertig, Elana J., Kagohara, Luciane T., Bartha, Gabor, Northcott, Josette, Lyle, John, Rochestie, Sarah, Peters, Joann, Connor, Jason T., Jaffee, Elizabeth M., Csiki, Ildiko, Weiner, David B., Perales-Puchalt, Alfredo, Sardesai, Niranjan Y.

“…Programmed cell death protein 1 (PD-1) inhibitors have modest efficacy as a monotherapy in hepatocellular carcinoma (HCC). A personalized therapeutic cancer…”
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Large healthy donor dataset demonstrates high analytical specificity and repeatability for the NeXT Personal molecular residual disease assay by Navarro, Fabio, Bartha, Gabor, Lyle, John, Harris, Jason, Northcott, Josette, Norton, Dan, Pyke, Rachel Marty, Abbott, Charles, Chen, Rui, Boyle, Sean Michael, Haudenschild, Christian, Santiago, Rose, Nelson, Christopher, Huo, Yelia, Chinnappa, Manju, Zhang, Qi, Chen, Richard

“…e15031 Background: Residual and recurrent cancer detection using circulating cell-free DNA (cfDNA) in liquid biopsy samples has proven promising in the past…”
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Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation by Pyke, Rachel Marty, Mellacheruvu, Dattatreya, Dea, Steven, Abbott, Charles W., Zhang, Simo V., Phillips, Nick A., Harris, Jason, Bartha, Gabor, Desai, Sejal, McClory, Rena, West, John, Snyder, Michael P., Chen, Richard, Boyle, Sean Michael

“…This article has been withdrawn by the authors. A publication of the manuscript with the correct figures and tables has been approved and the authors state the…”
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Prediction of Immunotherapy Response in Melanoma through Combined Modeling of Neoantigen Burden and Immune-Related Resistance Mechanisms by Abbott, Charles W, Boyle, Sean M, Pyke, Rachel Marty, McDaniel, Lee D, Levy, Eric, Navarro, Fábio C P, Mellacheruvu, Dattatreya, Zhang, Simo V, Tan, Mengyao, Santiago, Rose, Rusan, Zeid M, Milani, Pamela, Bartha, Gabor, Harris, Jason, McClory, Rena, Snyder, Michael P, Jang, Sekwon, Chen, Richard

“…While immune checkpoint blockade (ICB) has become a pillar of cancer treatment, biomarkers that consistently predict patient response remain elusive due to the…”
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Abstract 2227: Pan-cancer shedding patterns of tumor circulating cell free DNA by Navarro, Fabio C. P., Zhang, Simo, Tan, Mengyao, Abbott, Charles, Northcott, Josette, Lyle, John, Bartha, Gabor, Harris, Jason, West, John, Chen, Richard, Boyle, Sean Michael

“…Abstract Introduction: Tumor circulating cell-free DNA (ctDNA) comprises DNA molecules cast from tumors that reach and survive in a patient's bloodstream…”
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