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335 results on '"Mosquera, Juan Miguel"'

1. The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis

Author

Ohara, Kentaro, Rendeiro, André Figueiredo, Bhinder, Bhavneet, Eng, Kenneth Wha, Ravichandran, Hiranmayi, Nguyen, Duy, Pisapia, David, Vosoughi, Aram, Fernandez, Evan, Shohdy, Kyrillus S., Manohar, Jyothi, Beg, Shaham, Wilkes, David, Robinson, Brian D., Khani, Francesca, Bareja, Rohan, Tagawa, Scott T., Ouseph, Madhu M., Sboner, Andrea, Elemento, Olivier, Faltas, Bishoy M., and Mosquera, Juan Miguel

Published
2024
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2. Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers

Author

Setton, Jeremy, Hadi, Kevin, Choo, Zi-Ning, Kuchin, Katherine S., Tian, Huasong, Da Cruz Paula, Arnaud, Rosiene, Joel, Selenica, Pier, Behr, Julie, Yao, Xiaotong, Deshpande, Aditya, Sigouros, Michael, Manohar, Jyothi, Nauseef, Jones T., Mosquera, Juan-Miguel, Elemento, Olivier, Weigelt, Britta, Riaz, Nadeem, Reis-Filho, Jorge S., Powell, Simon N., and Imieliński, Marcin

Published
2023
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7. NIPBL: NACC1 Fusion Hepatic Carcinoma

Author

Hissong, Erika, Al Assaad, Majd, Bal, Munita, Reed, Katelyn A., Fornelli, Adele, Levine, Max F., Gundem, Gunes, Semaan, Alissa, Orr, Christine E., Sakhadeo, Uma, Manohar, Jyothi, Sigouros, Michael, Wilkes, David, Sboner, Andrea, Montgomery, Elizabeth A., Graham, Rondell P., Medina-Martínez, Juan S., Robine, Nicolas, Fang, Jiayun M., Choi, Eun-Young K., Westerhoff, Maria, Delgado-de la Mora, Jesús, Caudell, Patricia, Yantiss, Rhonda K., Papaemmanuil, Elli, Elemento, Olivier, Sigel, Carlie, Jessurun, José, and Mosquera, Juan Miguel

Published
2024
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8. NIPBL NACC1 Fusion Hepatic Carcinoma

Author

Hissong, Erika, Al Assaad, Majd, Bal, Munita, Reed, Katelyn A., Fornelli, Adele, Levine, Max F., Gundem, Gunes, Semaan, Alissa, Orr, Christine E., Sakhadeo, Uma, Manohar, Jyothi, Sigouros, Michael, Wilkes, David, Sboner, Andrea, Montgomery, Elizabeth A., Graham, Rondell P., Medina-Martínez, Juan S., Robine, Nicolas, Fang, Jiayun M., Choi, Eun-Young K., Westerhoff, Maria, Delgado-de la Mora, Jesús, Caudell, Patricia, Yantiss, Rhonda K., Papaemmanuil, Elli, Elemento, Olivier, Sigel, Carlie, Jessurun, José, and Mosquera, Juan Miguel

Published
2023
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11. Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing

Author

Deshpande, Aditya S., Ulahannan, Netha, Pendleton, Matthew, Dai, Xiaoguang, Ly, Lynn, Behr, Julie M., Schwenk, Stefan, Liao, Will, Augello, Michael A., Tyer, Carly, Rughani, Priyesh, Kudman, Sarah, Tian, Huasong, Otis, Hannah G., Adney, Emily, Wilkes, David, Mosquera, Juan Miguel, Barbieri, Christopher E., Melnick, Ari, Stoddart, David, Turner, Daniel J., Juul, Sissel, Harrington, Eoghan, and Imieliński, Marcin

Published
2022
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18. Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome

Author

Park, Kyung, Tran, Hung, Eng, Kenneth W., Ramazanoglu, Sinan, Rolon, Rebecca M. Marrero, Scognamiglio, Theresa, Borczuk, Alain, Mosquera, Juan Miguel, Pan, Qiulu, Sboner, Andrea, Rubin, Mark A., Elemento, Olivier, Rennert, Hanna, Fernandes, Helen, and Song, Wei

Subjects
Oncology, Experimental, Nucleotide sequencing -- Methods, RNA sequencing -- Methods, DNA sequencing -- Methods, Genetic variation -- Research, Molecular diagnostic techniques -- Methods, Cancer -- Research, Health
Abstract

* Context.--An increasing number of molecular laboratories are implementing next-generation sequencing platforms to identify clinically actionable and relevant genomic alterations for precision oncology. Objective.--To describe the validation studies as per New York State-Department of Health (NYS-DOH) guidelines for the Oncomine Comprehensive Panel v2, which was originally tailored to the National Cancer Institute Molecular Analysis for Therapy Choice (NCIMATCH) trial. Design.--Accuracy, precision, and reproducibility were investigated by using 130 DNA and 18 RNA samples from cytology cell blocks; formalin-fixed, paraffin-embedded tissues; and frozen samples. Analytic sensitivity and specificity were tested by using ATCC and HapMap cell lines. Results.--High accuracy and precision/reproducibility were observed for single nucleotide variants and insertion/ deletions. We also share our experience in the detection of gene fusions and copy number alterations from an amplicon-based sequencing platform. After sequencing analysis, variant annotation and report generation were performed by using the institutional knowledgebase. Conclusions.--This study serves as an example for validating a comprehensive targeted next-generation sequencing assay with both DNASeq and RNASeq components for NYS-DOH. doi: 10.5858/arpa.2019-0162-OA, Next-generation sequencing (NGS) has become the major tool in understanding the mutational landscape of many solid tumors and hematologic malignancies. (1,2) Specific genomic alterations in tumors can be used as [...]

Published
2020
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19. Genomic correlates of clinical outcome in advanced prostate cancer

Author

Abida, Wassim, Cyrta, Joanna, Heller, Glenn, Prandi, Davide, Armenia, Joshua, Coleman, Ilsa, Cieslik, Marcin, Benelli, Matteo, Robinson, Dan, Van Allen, Eliezer M., Sboner, Andrea, Fedrizzi, Tarcisio, Mosquera, Juan Miguel, Robinson, Brian D., De Sarkar, Navonil, Kunju, Lakshmi P., Tomlins, Scott, Wu, Yi Mi, Rodrigues, Daniel Nava, Loda, Massimo, Gopalan, Anuradha, Reuter, Victor E., Pritchard, Colin C., Mateo, Joaquin, Bianchini, Diletta, Miranda, Susana, Carreira, Suzanne, Rescigno, Pasquale, Filipenko, Julie, Vinson, Jacob, Montgomery, Robert B., Beltran, Himisha, Heath, Elisabeth I., Scher, Howard I., Kantoff, Philip W., Taplin, Mary-Ellen, Schultz, Nikolaus, deBono, Johann S., Demichelis, Francesca, Nelson, Peter S., Rubin, Mark A., Chinnaiyan, Arul M., and Sawyers, Charles L.

Published
2019

22. Targeting the epichaperome as an effective precision medicine approach in a novel PML-SYK fusion acute myeloid leukemia

Author

Sugita, Mayumi, Wilkes, David C., Bareja, Rohan, Eng, Kenneth W., Nataraj, Sarah, Jimenez-Flores, Reyna A., Yan, LunBiao, De Leon, Jeanne Pauline, Croyle, Jaclyn A., Kaner, Justin, Merugu, Swathi, Sharma, Sahil, MacDonald, Theresa Y., Noorzad, Zohal, Panchal, Palak, Pancirer, Danielle, Cheng, Shuhua, Xiang, Jenny Z., Olson, Luke, Van Besien, Koen, Rickman, David S., Mathew, Susan, Tam, Wayne, Rubin, Mark A., Beltran, Himisha, Sboner, Andrea, Hassane, Duane C., Chiosis, Gabriela, Elemento, Olivier, Roboz, Gail J., Mosquera, Juan Miguel, and Guzman, Monica L.

Published
2021
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24. Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer

Author

Beltran, Himisha, Romanel, Alessandro, Conteduca, Vincenza, Casiraghi, Nicola, Sigouros, Michael, Franceschini, Gian Marco, Orlando, Francesco, Fedrizzi, Tarcisio, Ku, Sheng-Yu, Dann, Emma, Alonso, Alicia, Mosquera, Juan Miguel, Sboner, Andrea, Xiang, Jenny, Elemento, Olivier, Nanus, David M., Tagawa, Scott T., Benelli, Matteo, and Demichelis, Francesca

Subjects
Cancer treatment, Epigenetic inheritance, Cancer genetics -- Diagnosis -- Development and progression, Enzalutamide, Abiraterone, Methylation, Genomes, Genomics, Genetic research, Tumor proteins -- Diagnosis -- Development and progression, DNA, Prostate cancer -- Development and progression -- Diagnosis, Cancer metastasis -- Diagnosis -- Development and progression, Adenocarcinoma, Androgens, Tumors, Sulfites, Health care industry
Abstract

Loss of androgen receptor (AR) signaling dependence occurs in approximately 15%-20% of advanced treatment-resistant prostate cancers, and this may manifest clinically as transformation from a prostate adenocarcinoma histology to a castration-resistant neuroendocrine prostate cancer (CRPC-NE). The diagnosis of CRPC-NE currently relies on a metastatic tumor biopsy, which is invasive for patients and sometimes challenging to diagnose due to morphologic heterogeneity. By studying whole-exome sequencing and whole-genome bisulfite sequencing of cell free DNA (cfDNA) and of matched metastatic tumor biopsies from patients with metastatic prostate adenocarcinoma and CRPC-NE, we identified CRPC-NE features detectable in the circulation. Overall, there was markedly higher concordance between cfDNA and biopsy tissue genomic alterations in patients with CRPC-NE compared with castration-resistant adenocarcinoma, supporting greater intraindividual genomic consistency across metastases. Allele-specific copy number and serial sampling analyses allowed for the detection and tracking of clonal and subclonal tumor cell populations. cfDNA methylation was indicative of circulating tumor content fraction, reflective of methylation patterns observed in biopsy tissues, and was capable of detecting CRPCNE-associated epigenetic changes (e.g., hypermethylation of ASXL3 and SPDEF; hypomethylation of INSM1 and CDH2). A targeted set combining genomic (TP53, RB1, CYLD, AR) and epigenomic (hypo- and hypermethylation of 20 differential sites) alterations applied to ctDNA was capable of identifying patients with CRPC-NE., Introduction Prostate cancer is a leading cause of cancer death for men worldwide (1). Despite significant advances in therapy for patients with metastatic disease, the emergence of treatment resistance remains [...]

Published
2020
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27. Common germline-somatic variant interactions in advanced urothelial cancer

Author

Vosoughi, Aram, Zhang, Tuo, Shohdy, Kyrillus S., Vlachostergios, Panagiotis J., Wilkes, David C., Bhinder, Bhavneet, Tagawa, Scott T., Nanus, David M., Molina, Ana M., Beltran, Himisha, Sternberg, Cora N., Motanagh, Samaneh, Robinson, Brian D., Xiang, Jenny, Fan, Xiao, Chung, Wendy K., Rubin, Mark A., Elemento, Olivier, Sboner, Andrea, Mosquera, Juan Miguel, and Faltas, Bishoy M.

Published
2020
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31. SPOP mutation drives prostate neoplasia without stabilizing oncogenic transcription factor ERG

Author

Shoag, Jonathan, Liu, Deli, Blattner, Mirjam, Sboner, Andrea, Park, Kyung, Deonarine, Lesa, Robinson, Brian D., Mosquera, Juan Miguel, Chen, Yu, Rubin, Mark A., and Barbieri, Christopher E.

Subjects
Mutation -- Research, Adenocarcinoma -- Care and treatment, Prostate cancer -- Genetic aspects -- Care and treatment, Health care industry
Abstract

Nearly 50% of prostate cancers harbor gene fusions that lead to overexpression of the transcription factor ERG, while a mutually exclusive 10% of prostate cancers harbor recurrent mutations in the gene encoding the E3 ubiquitin ligase SPOP. Recent reports suggest that SPOP acts as a ubiquitin ligase for ERG and propose that ERG stabilization is the oncogenic effector of SPOP mutation. Here, we used human prostate cancer samples and showed that the vast majority of human SPOP-mutant cancers do not express ERG. Comparison of SPOP-mutant and ERG-fusion organoid models showed evidence of divergent, rather than common, transcriptional programs. Furthermore, expression of prostate cancer-associated SPOP mutations in genetically engineered mouse models of SPOP-mutant prostate cancer did not result in the expression of ERG protein in histologically normal prostate glands, high-grade prostatic intraepithelial neoplasia, invasive adenocarcinoma, or prostate organoids. In summary, we found no evidence that ERG is an effector of SPOP mutation in human prostate cancer or mouse models., Introduction Over the past decade, there has been remarkable progress in the molecular classification of prostate cancer, with the delineation of multiple distinct subclasses defined by recurrent genomic aberrations. Recurrent [...]

Published
2018
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36. SPOP Mutations in Prostate Cancer across Demographically Diverse Patient Cohorts

Author

Blattner, Mirjam, Lee, Daniel J., O'Reilly, Catherine, Park, Kyung, MacDonald, Theresa Y., Khani, Francesca, Turner, Kevin R., Chiu, Ya-Lin, Wild, Peter J., Dolgalev, Igor, Heguy, Adriana, Sboner, Andrea, Ramazangolu, Sinan, Hieronymus, Haley, Sawyers, Charles, Tewari, Ashutosh K., Moch, Holger, Yoon, Ghil Suk, Known, Yong Chul, Andrén, Ove, Fall, Katja, Demichelis, Francecsa, Mosquera, Juan Miguel, Robinson, Brian D., Barbieri, Christopher E., and Rubin, Mark A.

Published
2014
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37. Bone biopsy protocol for advanced prostate cancer in the era of precision medicine

Author

Sailer, Verena, Schiffman, Marc H., Kossai, Myriam, Cyrta, Joanna, Beg, Shaham, Sullivan, Brian, Pua, Bradley B., Lee, Kyungmouk Steve, Talenfeld, Adam D., Nanus, David M., Tagawa, Scott T., Robinson, Brian D., Rao, Rema A., Pauli, Chantal, Bareja, Rohan, Beltran, Luis S., Sigaras, Alexandros, Eng, Kenneth Wa, Elemento, Olivier, Sboner, Andrea, Rubin, Mark A., Beltran, Himisha, and Mosquera, Juan Miguel

Published
2018
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39. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer

Author

Beltran, Himisha, Prandi, Davide, Mosquera, Juan Miguel, Benelli, Matteo, Puca, Loredana, Cyrta, Joanna, Marotz, Clarisse, Giannopoulou, Eugenia, Chakravarthi, Balabhadrapatruni V.S.K., Varambally, Sooryanarayana, Tomlins, Scott A., Nanus, David M., Tagawa, Scott T., Van Allen, Eliezer M., Elemento, Olivier, Sboner, Andrea, Garraway, Levi A., Rubin, Mark A., and Demichelis, Francesca

Subjects
Prostate cancer -- Analysis -- Health aspects -- Genetic aspects -- Care and treatment -- Patient outcomes -- Research, Hormone receptors -- Physiological aspects -- Genetic aspects -- Research, Androgens -- Physiological aspects -- Genetic aspects -- Research, Biological sciences, Health
Abstract

An increasingly recognized resistance mechanism to androgen receptor (AR)-directed therapy in prostate cancer involves epithelial plasticity, in which tumor cells demonstrate low to absent AR expression and often have neuroendocrine features. The etiology and molecular basis for this 'alternative' treatment-resistant cell state remain incompletely understood. Here, by analyzing whole-exome sequencing data of metastatic biopsies from patients, we observed substantial genomic overlap between castration-resistant tumors that were histologically characterized as prostate adenocarcinomas (CRPC-Adeno) and neuroendocrine prostate cancer (CRPC-NE); analysis of biopsy samples from the same individuals over time points to a model most consistent with divergent clonal evolution. Genome-wide DNA methylation analysis revealed marked epigenetic differences between CRPC-NE tumors and CRPC-Adeno, and also designated samples of CRPC-Adeno with clinical features of AR independence as CRPC-NE, suggesting that epigenetic modifiers may play a role in the induction and/or maintenance of this treatment-resistant state. This study supports the emergence of an alternative, 'AR-indifferent' cell state through divergent clonal evolution as a mechanism of treatment resistance in advanced prostate cancer., Prostate cancer remains a leading cause of cancer death in males worldwide (1). The mainstay of therapy for patients with metastatic spread, including castration-resistant disease, is hormonal therapy that targets [...]

Published
2016

44. MAGI3-AKT3 fusion in breast cancer amended

Author

Mosquera, Juan-Miguel, Varma, Sonal, Pauli, Chantal, MacDonald, Theresa Y., Yashinskie, Jossie J., Varga, Zsuzsanna, Sboner, Andrea, Moch, Holger, Rubin, Mark A., and Shin, Sandra J.

Subjects
Tumor proteins -- Health aspects, Breast cancer -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Banerji et al. (1) described a novel MAGI3-AKT3 rearrangement in breast cancer, enriched in triple-negative tumours; the report was highly encouraging as targeted therapies could potentially serve as a new [...]

Published
2015

45. Oncogene-mediated alterations in chromatin conformation

Author

Rickman, David S., Soong, T. David, Moss, Benjamin, Mosquera, Juan Miguel, Dlabal, Jan, Terry, Stéphane, MacDonald, Theresa Y., Tripodi, Joseph, Bunting, Karen, Najfeld, Vesna, Demichelis, Francesca, Melnick, Ari M., Elemento, Olivier, and Rubin, Mark A.

Published
2012

49. Whole-genome characterization of myoepithelial carcinomas of the soft tissue.

Author

Cyrta, Joanna, Rosiene, Joel, Bareja, Rohan, Kudman, Sarah, Al Zoughbi, Wael, Motanagh, Samaneh, Wilkes, David C., Eng, Kenneth, Tuo Zhang, Sticca, Evan, Mathew, Susan, Rubin, Mark A., Sboner, Andrea, Elemento, Olivier, Rubin, Brian P., Imielinski, Marcin, and Mosquera, Juan Miguel

Subjects
WHOLE genome sequencing, SOFT tissue tumors, RNA sequencing, IMMUNOHISTOCHEMISTRY, CELL morphology
Abstract

Myoepithelial carcinomas (MECs) of soft tissue are rare and aggressive tumors affecting young adults and children, but their molecular landscape has not been comprehensively explored through genome sequencing. Here, we present the whole-exome sequencing (WES), whole-genome sequencing (WGS), and RNA sequencing findings of two MECs. Patients 1 and 2 (P1, P2), both male, were diagnosed at 27 and 37 yr of age, respectively, with shoulder (P1) and inguinal (P2) soft tissue tumors. Both patients developed metastatic disease, and P2 died of disease. P1 tumor showed a rhabdoid cytomorphology and a complete loss of INI1 (SMARCB1) expression, associated with a homozygous SMARCB1 deletion. The tumor from P2 showed a clear cell/small cell morphology, retained INI1 expression and strong S100 positivity. By WES and WGS, tumors from both patients displayed low tumor mutation burdens, and no targetable alterations in cancer genes were detected. P2's tumor harbored an EWSR1::KLF15 rearrangement, whereas the tumor from P1 showed a novel ASCC2::GGNBP2 fusion. WGS evidenced a complex genomic event involving mainly Chromosomes 17 and 22 in the tumor from P1, which was consistent with chromoplexy. These findings are consistent with previous reports of EWSR1 rearrangements (50% of cases) in MECs and provide a genetic basis for the loss of SMARCB1 protein expression observed through immunohistochemistry in 10% of 40% of MEC cases. The lack of additional driver mutations in these tumors supports the hypothesis that these alterations are the key molecular events in MEC evolution. Furthermore, the presence of complex structural variant patterns, invisible to WES, highlights the novel biological insights that can be gained through the application of WGS to rare cancers. [ABSTRACT FROM AUTHOR]

Published
2022
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50. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

Author

Frampton, Garrett M, Fichtenholtz, Alex, Otto, Geoff A, Wang, Kai, Downing, Sean R, He, Jie, Schnall-Levin, Michael, White, Jared, Sanford, Eric M, An, Peter, Sun, James, Juhn, Frank, Brennan, Kristina, Iwanik, Kiel, Maillet, Ashley, Buell, Jamie, White, Emily, Zhao, Mandy, Balasubramanian, Sohail, Terzic, Selmira, Richards, Tina, Banning, Vera, Garcia, Lazaro, Mahoney, Kristen, Zwirko, Zac, Donahue, Amy, Beltran, Himisha, Mosquera, Juan Miguel, Rubin, Mark A, Dogan, Snjezana, Hedvat, Cyrus V, Berger, Michael F, Pusztai, Lajos, Lechner, Matthias, Boshoff, Chris, Jarosz, Mirna, Vietz, Christine, Parker, Alex, Miller, Vincent A, Ross, Jeffrey S, Curran, John, Cronin, Maureen T, Stephens, Philip J, Lipson, Doron, and Yelensky, Roman

Published
2013
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