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Elli Papaemmanuil
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Journal Articles

Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma

Michael D. Kinnaman, Simone Zaccaria, Alvin Makohon-Moore, Brian Arnold, Max F. Levine, Gunes Gundem, Juan E. Arango Ossa, Dominik Glodzik, M. Irene Rodríguez-Sánchez, Nancy Bouvier, Shanita Li, Emily Stockfisch, Marisa Dunigan, Cassidy Cobbs, Umesh K. Bhanot, Daoqi You, Katelyn Mullen, Jerry P. Melchor, Michael V. Ortiz, Tara J. O'Donohue, Emily K. Slotkin, Leonard H. Wexler, Filemon S. Dela Cruz, Meera R. Hameed, Julia L. Glade Bender, William D. Tap, Paul A. Meyers, Elli Papaemmanuil, Andrew L. Kung, Christine A. Iacobuzio-Donahue
Journal: Cancer Research
Cancer Res (2023) 83 (22): 3796–3812.
https://doi.org/10.1158/0008-5472.CAN-23-0385
Published: 15 November 2023
View article titled, Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma
Open the PDF for Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma in another window
Includes: Supplementary data
Journal Articles

Abstract 3437: Whole genome and transcriptome sequencing of a pan cancer cohort unearths novel therapeutic avenues

Majd Al Assaad, Hui-Hsuan Kuo, Jones Nauseef, Max F. Levine, Gunes Gundem, Juan S. Medina-Martínez, Jyothi Manohar, Michael Sigouros, Ahmed Elsaeed, David Wilkes, Elli Papaemmanuil, Eloise Chapman, Scott T. Tagawa, Allyson Ocean, Cora N. Sternberg, Eleni Andreopoulou, Manish Shah, Andrea Sboner, Kevin Holcomb, David Nanus, Laura Martin, Olivier Elemento, Juan Miguel Mosquera
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 3437.
https://doi.org/10.1158/1538-7445.AM2023-3437
Published: 04 April 2023
View article titled, Abstract 3437: Whole genome and transcriptome sequencing of a pan cancer cohort unearths novel therapeutic avenues
Journal Articles

Abstract 6168: Implementation and adoption of a web tool to support precision diagnostic and treatment decisions for patient with myelodysplastic syndromes

Elsa Bernard, Juan E. Arango Ossa, Heinz Tuechler, Peter L. Greenberg, Robert P. Hasserjian, Yasuhito Nannya, Sean M. Devlin, Maria Creignou, Philippe Pinel, Lily Monier, Juan S. Medina-Martinez, Dylan Domenico, Martin Jädersten, Ulrich Germing, Guillermo Sanz, Arjan A. van de Loosdrecht, Olivier Kosmider, Matilde Y. Follo, Felicitas Thol, Lurdes Zamora, Ronald F. Pinheiro, Andrea Pellagatti, Detlef Haase, Pierre Fenaux, Monika Belickova, Michael R. Savona, Virginia M. Klimek, Fabio P. Santos, Jacqueline Boultwood, Ioannis Kotsianidis, Valeria Santini, Francesc Solé, Uwe Platzbecker, Michael Heuser, Peter Valent, Kazuma Ohyashiki, Carlo Finelli, Maria Teresa Voso, Lee-Yung Shih, Michaela Fontenay, Joop H. Jansen, José Cervera, Norbert Gattermann, Benjamin L. Ebert, Rafael Bejar, Luca Malcovati, Mario Cazzola, Seishi Ogawa, Eva Hellström-Lindberg, Elli Papaemmanuil
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 6168.
https://doi.org/10.1158/1538-7445.AM2023-6168
Published: 04 April 2023
View article titled, Abstract 6168: Implementation and adoption of a web tool to support precision diagnostic and treatment decisions for patient with myelodysplastic syndromes
Journal Articles

Abstract 3142: Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology

Dylan Domenico, Gunes Gundem, Max F. Levine, Juanes E. Arango-Ossa, Pauline Robbe, Georgios Asimomitis, Cassidy Cobbs, Emily Stockfisch, Janine Senz, Dawn Cochrane, Neeman Mohibullah, Neerav Shukla, Sohrab P. Shah, Andrew McPherson, Anna Schuh, Andrew L. Kung, Elli Papaemmanuil
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 3142.
https://doi.org/10.1158/1538-7445.AM2023-3142
Published: 04 April 2023
View article titled, Abstract 3142: Enabling whole genome sequencing analysis from FFPE specimens in clinical oncology
Journal Articles

Abstract 3556: Assessing patterns of genomic instability in recurrent osteosarcoma

Michael David Kinnaman, Simone Zaccaria, Alvin Makohon-Moore, Gunes Gundem, Juan E. Arango Ossa, Filemon S. Dela Cruz, Paul A. Meyers, Meera Hameed, William D. Tap, Julia Lynne Glade Bender, Elli Papaemmanuil, Andrew Kung, Christine Iacobuzio Donahue
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 3556.
https://doi.org/10.1158/1538-7445.AM2023-3556
Published: 04 April 2023
View article titled, Abstract 3556: Assessing patterns of genomic instability in recurrent osteosarcoma
Journal Articles

Abstract 2149: A whole genome sequencing classifier of homologous recombination deficiency

Kevin Hadi, Gunes Gundem, Max F. Levine, Aditya Deshpande, Minal Patel, Stan Skzrypczak, Majd Al Assaad, Juan Miguel Mosquera, Olivier Elemento, Andrew L. Kung, Juan S. Medina-Martínez, Elli Papaemmanuil
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 2149.
https://doi.org/10.1158/1538-7445.AM2023-2149
Published: 04 April 2023
View article titled, Abstract 2149: A whole genome sequencing classifier of homologous recombination deficiency
Journal Articles

Abstract 5747: Chemotherapy-related mutational signatures reveal the origins of therapy-related myeloid neoplasms

Benjamin Diamond, Bachisio Ziccheddu, Eileen M. Boyle, Kylee Maclachlan, Justin Taylor, Justin M. Watts, Sydney X. Lu, David G. Coffey, Niccolo Bolli, Elli Papaemmanuil, Kelly Bolton, Jae H. Park, Heather Landau, Karuna Ganesh, Mikkael A. Sekeres, Stephen Nimer, David J. Chung, Caleb H. Ho, Mikhail Roshal, Alexander Lesokhin, Gareth Morgan, Ola Landgren, Francesco Maura
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 5747.
https://doi.org/10.1158/1538-7445.AM2022-5747
Published: 15 June 2022
View article titled, Abstract 5747: Chemotherapy-related mutational signatures reveal the origins of therapy-related myeloid neoplasms
Journal Articles

Abstract 704: Development of a patient-derived xenograft (PDX) modeling program to enable pediatric precision medicine

Filemon S. Dela Cruz, Joseph G. McCarter, Daoqi You, Nancy Bouvier, Xinyi Wang, Kristina C. Guillan, Armaan H. Siddiquee, Katie B. Souto, Hongyan Li, Teng Gao, Dominik Glodzik, Daniel Diolaiti, Neerav N. Shukla, Joachim Silber, Umeshkumar K. Bhanot, Faruk Erdem Kombak, Diego F. Coutinho, Shanita Li, Juan E. Arango Ossa, Juan S. Medina-Martinez, Michael V. Ortiz, Emily K. Slotkin, Michael D. Kinnaman, Sameer F. Sait, Tara J. O'Donohue, Marissa Mattar, Maximiliano Meneses, Michael P. LaQuaglia, Todd E. Heaton, Justin T. Gerstle, Nicola Fabbri, Chelsey M. Burke, Irene M. Rodriquez-Sanchez, Christine A. Iacobuzio-Donahue, Julia L. Glade Bender, Ryan D. Roberts, Jason T. Yustein, Nino C. Rainusso, Brian D. Crompton, Elizabeth Stewart, Alejandro Sweet-Cordero, Leanne C. Sayles, Andrika D. Thomas, Michael H. Roehrl, Elisa de Stanchina, Elli Papaemmanuil, Andrew L. Kung
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 704.
https://doi.org/10.1158/1538-7445.AM2022-704
Published: 15 June 2022
View article titled, Abstract 704: Development of a patient-derived xenograft (PDX) modeling program to enable pediatric precision medicine
Journal Articles

Abstract 2590: Analysis of homologous recombination deficiency (HRD) scores in osteosarcoma

Michael David Kinnaman, Julia Pena, Max Levine, Nancy Bouvier, Elli Papaemmanuil, Suzanne Forrest, Katherine Janeway, Paul Meyers, Julia Glade Bender
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 2590.
https://doi.org/10.1158/1538-7445.AM2022-2590
Published: 15 June 2022
View article titled, Abstract 2590: Analysis of homologous recombination deficiency (HRD) scores in osteosarcoma
Journal Articles

Abstract 1515: Tracking the origins and drivers of metastatic expansion in osteosarcoma

Michael David Kinnaman, Alvin Makohon-Moore, Dominik Glodzik, Max Levine, Nancy Bouvier, Filemon Dela Cruz, Meera Hameed, Paul Meyers, Elli Papaemmanuil, Andrew Kung, Christine Iacobuzio-Donahue
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 1515.
https://doi.org/10.1158/1538-7445.AM2020-1515
Published: 15 August 2020
View article titled, Abstract 1515: Tracking the origins and drivers of metastatic expansion in osteosarcoma
Journal Articles

Abstract 5703: Oncologic therapy shapes the fitness landscape of clonal hematopoiesis

Kelly L. Bolton, Ryan N. Ptashkin, Teng Gao, Lior Braunstein, Sean M. Devlin, Minal Patel, Antonin Berthon, Aijazuddin Syed, Mariko Yabe, Catherine Coombs, Nicole M. Caltabellotta, Mike Walsh, Ken Offit, Zsofia Stadler, Choonsik Lee, Paul Pharoah, Konrad H. Stopsack, Barbara Spitzer, Simon Mantha, James Fagin, Laura Boucai, Christopher J. Gibson, Benjamin Ebert, Andrew L. Young, Todd Druley, Koichi Takahashi, Nancy Gillis, Markus Ball, Eric Padron, David Hyman, Jose Baselga, Larry Norton, Stuart Gardos, Virginia Klimek, Howard Scher, Dean Bajorin, Eder Paraiso, Ryma Benayed, Maria Arcilla, Marc Ladanyi, David Solit, Michael Berger, Martin Tallman, Montserrat Garcia-Closas, Nilanjan Chatterjee, Luis Diaz, Ross Levine, Lindsay Morton, Ahmet Zehir, Elli Papaemmanuil
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 5703.
https://doi.org/10.1158/1538-7445.AM2020-5703
Published: 15 August 2020
View article titled, Abstract 5703: Oncologic therapy shapes the fitness landscape of clonal hematopoiesis
Journal Articles

Abstract 5105: A plug-and-play infrastructure for scalable bioinformatics operations

Juan S. Medina-Martínez, Juan E. Arango-Ossa, Gunes Gundem, Max F. Levine, Minal Patel, Noushin R. Farnoud, Venkata D. Yellapantula, Gao Teng, Joseph G. Mccarter, Elsa Bernard, Franck Rapaport, Dominik Glodzik, Ross L. Levine, Andrew Kung, Elli Papaemmanuil
Journal: Cancer Research
Cancer Res (2019) 79 (13_Supplement): 5105.
https://doi.org/10.1158/1538-7445.AM2019-5105
Published: 01 July 2019
View article titled, Abstract 5105: A plug-and-play infrastructure for scalable bioinformatics operations
Journal Articles

Abstract LB-304: Oncologic therapy for solid tumors alters the risk of clonal hematopoiesis

Kelly Bolton, Ryan Ptashkin, Lior Braunstein, Teng Gao, Sean M. Devlin, Daniel Kelly, Catherine Coombs, Minal Patel, Matahi Moarii, Elsa Bernard, Antonin Berthon, Laura Boucai, Dominik Glodzik, Axel Martin, Zsofia Stadler, Michael Walsh, Diana Mandelker, Akshar Patel, Jessica Schulman, Gunes Gundem, Aijazuddin Syed, Maria Arcila, David B. Solit, Mark E. Robson, Marc Ladanyi, Choonsik Lee, John Philip, Dean Bajorin, Montserrat Garcia-Closas, Stuart Gardos, David Hyman, Martin Tallman, Mariko Yabe, Kenneth Offit, Howard Scher, Virginia Klimek, Luis Diaz, Nilanjan Chatterjee, Michael F. Berger, Lindsay Morton, Ross Levine, Ahmet Zehir, Elli Papaemmanuil
Journal: Cancer Research
Cancer Res (2019) 79 (13_Supplement): LB-304.
https://doi.org/10.1158/1538-7445.AM2019-LB-304
Published: 01 July 2019
View article titled, Abstract LB-304: Oncologic therapy for solid tumors alters the risk of clonal hematopoiesis
Journal Articles

Abstract 956: The evolutionary history of lethal metastatic prostate cancer

Gunes Gundem, Peter Van Loo, Barbara Kremeyer, Ludmil B. Alexandrov, Jose M.C. Tubio, Elli Papaemmanuil, Daniel S. Brewer, Heini Kallio, Gunilla Högnäs, Matti Annala, Kati Kivinummi, Victoria Goody, Calli Latimer, Sarah O'Meara, Kevin J. Dawson, William Isaacs, Michael R. Emmert-Buck, Matti Nykter, Christopher Foster, Zsofia Kote-Jarai, Douglas Easton, Hayley C. Whitaker, David E. Neal, Colin S. Cooper, Rosalind A. Eeles, Tapio Visakorpi, Peter J. Campbell, Ultan McDermott, David C. Wedge, G. S. Bova
Journal: Cancer Research
Cancer Res (2015) 75 (15_Supplement): 956.
https://doi.org/10.1158/1538-7445.AM2015-956
Published: 01 August 2015
View article titled, Abstract 956: The evolutionary history of lethal metastatic prostate cancer
Journal Articles

Abstract 5143: From sequencing data to mutation spectra: a high throughput analysis pipeline.

David Jones, Adam P. Butler, Jon W. Teague, Keiran M. Raine, Andrew Menzies, John Marshall, Jonathan Hinton, Serge Dronov, Lucy Stebbings, Alagu Jayakumar, Catherine Leroy, Jorge Zamora, Manasa Ramakrishna, Elli Papaemmanuil, Helen Davies, Susanna L. Cooke, Serena Nik-Zainal, Ultan McDermott, Michael R. Stratton, Peter Campbell
Journal: Cancer Research
Cancer Res (2013) 73 (8_Supplement): 5143.
https://doi.org/10.1158/1538-7445.AM2013-5143
Published: 15 April 2013
View article titled, Abstract 5143: From sequencing data to mutation spectra: a high throughput analysis pipeline.
Journal Articles

Abstract 2993: Patterns of recurrent mutations in SETBP1 mutated and wild-type atypical Chronic Myeloid Leukemia patients.

Sara Redaelli, Simona Valletta, Rocco Piazza, Nils Winkelmann, Roberta Spinelli, Alessandra Pirola, Laura Antolini, Luca Mologni, Carla Donadoni, Elli Papaemmanuil, Susanne Schnittger, Kim Dong-Wook, Jacqueline Boultwood, Fabio Rossi, Giuseppe Gaipa, Greta De Martini, Paola Francia di Celle, Hyun Gyung Jang, Valeria Fantin, Graham R. Bignell, Vera Magistroni, Torsten Haferlach, Enrico Maria Pogliani, Peter Campbell, Andrew J. Chase, William J. Tapper, Nick C.P. Cross, Carlo Gambacorti Passerini
Journal: Cancer Research
Cancer Res (2013) 73 (8_Supplement): 2993.
https://doi.org/10.1158/1538-7445.AM2013-2993
Published: 15 April 2013
View article titled, Abstract 2993: Patterns of recurrent mutations in SETBP1 mutated and wild-type atypical Chronic Myeloid Leukemia patients.
Journal Articles

Abstract 3176: Recurrent SETBP1 mutations in atypical chronic myeloid leukemia abrogate an ubiquitination site and dysregulate SETBP1 protein levels.

Rocco Piazza, Simona Valletta, Nils Winkelmann, Sara Redaelli, Roberta Spinelli, Alessandra Pirola, Laura Antolini, Luca Mologni, Carla Donadoni, Elli Papaemmanuil, Susanne Schnittger, Kim Dong-Wook, Jacqueline Boultwood, Fabio Rossi, Giuseppe Gaipa, Greta De Martini, Paola Francia di Celle, Hyun Gyung Jang, Valeria Fantin, Graham R. Bignell, Vera Magistroni, Torsten Haferlach, Enrico Maria Pogliani, Peter Campbell, Andrew J. Chase, William J. Tapper, Nick C.P. Cross, Carlo Gambacorti Passerini
Journal: Cancer Research
Cancer Res (2013) 73 (8_Supplement): 3176.
https://doi.org/10.1158/1538-7445.AM2013-3176
Published: 15 April 2013
View article titled, Abstract 3176: Recurrent SETBP1 mutations in atypical chronic myeloid leukemia abrogate an ubiquitination site and dysregulate SETBP1 protein levels.