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Journal Articles

Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal

Ino de Bruijn, Ritika Kundra, Brooke Mastrogiacomo, Thinh Ngoc Tran, Luke Sikina, Tali Mazor, Xiang Li, Angelica Ochoa, Gaofei Zhao, Bryan Lai, Adam Abeshouse, Diana Baiceanu, Ersin Ciftci, Ugur Dogrusoz, Andrew Dufilie, Ziya Erkoc, Elena Garcia Lara, Zhaoyuan Fu, Benjamin Gross, Charles Haynes, Allison Heath, David Higgins, Prasanna Jagannathan, Karthik Kalletla, Priti Kumari, James Lindsay, Aaron Lisman, Bas Leenknegt, Pieter Lukasse, Divya Madela, Ramyasree Madupuri, Pim van Nierop, Oleguer Plantalech, Joyce Quach, Adam C. Resnick, Sander Y.A. Rodenburg, Baby A. Satravada, Fedde Schaeffer, Robert Sheridan, Jessica Singh, Rajat Sirohi, Selcuk Onur Sumer, Sjoerd van Hagen, Avery Wang, Manda Wilson, Hongxin Zhang, Kelsey Zhu, Nicole Rusk, Samantha Brown, Jessica A. Lavery, Katherine S. Panageas, Julia E. Rudolph, Michele L. LeNoue-Newton, Jeremy L. Warner, Xindi Guo, Haley Hunter-Zinck, Thomas V. Yu, Shirin Pilai, Chelsea Nichols, Stuart M. Gardos, John Philip, AACR Project GENIE BPC Core Team, AACR Project GENIE Consortium, Kenneth L. Kehl, Gregory J. Riely, Deborah Schrag, Jocelyn Lee, Michael V. Fiandalo, Shawn M. Sweeney, Trevor J. Pugh, Chris Sander, Ethan Cerami, Jianjiong Gao, Nikolaus Schultz
Journal: Cancer Research
Cancer Res (2023) 83 (23): 3861–3867.
https://doi.org/10.1158/0008-5472.CAN-23-0816
Published: 01 December 2023
View article titled, Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal
Open the PDF for Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal in another window
Includes: Supplementary data
Journal Articles

Abstract 4256: cBioPortal for Cancer Genomics

Ino de Bruijn, Tali Mazor, Adam Abeshouse, Diana Baiceanu, Stephanie Carrero, Elena Garcia Lara, Benjamin Gross, David M. Higgins, Prasanna K. Jagannathan, Priti Kumari, Ritika Kundra, Bryan Lai, Xiang Li, James Lindsay, Aaron Lisman, Divya Madala, Ramyasree Madupuri, Angelica Ochoa, Yusuf Ziya Özgül, Oleguer Plantalech, Sander Rodenburg, Baby Anusha Satravada, Robert Sheridan, Lucas Sikina, Jessica Singh, S Onur Sumer, Yichao Sun, Pim van Nierop, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Sjoerd van Hagen, Ugur Dogrusoz, Allison Heath, Adam Resnick, Trevor J. Pugh, Chris Sander, Ethan Cerami, Jianjiong Gao, Nikolaus Schultz
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 4256.
https://doi.org/10.1158/1538-7445.AM2023-4256
Published: 04 April 2023
View article titled, Abstract 4256: cBioPortal for Cancer Genomics
Journal Articles

Abstract 1067: MatchMiner: An open-source AI precision medicine trial matching platform

Harry Klein, Tali Mazor, Matthew Galvin, Jason Hansel, Emily Mallaber, Pavel Trukhanov, Joyce Yu, James Lindsay, Kenneth Kehl, Michael Hassett, Ethan Cerami
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 1067.
https://doi.org/10.1158/1538-7445.AM2023-1067
Published: 04 April 2023
View article titled, Abstract 1067: MatchMiner: An open-source AI precision medicine trial matching platform
Journal Articles

Abstract 5524: Persistent patient barriers to genomic testing in ambulatory oncology

Ellana K. Haakenstad, Jane Roberts, Anna C. Revette, Wendy Loeser, Joseph Grider, Andrea Kruse, Alissa Gentile, Rachel Freedman, Neal I. Lindeman, Olga Kozyreva, Pedro Sanz-Altamira, Christopher S. Lathan, Michael Hassett, Ethan Cerami, Annette S. Kim, Danielle K. Manning, Jonathan Nowak, Marios Giannakis, R Coleman Lindsley, William C. Hahn, Barrett J. Rollins, Levi Garraway, Bruce E. Johnson, Nadine Jackson McCleary
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 5524.
https://doi.org/10.1158/1538-7445.AM2023-5524
Published: 04 April 2023
View article titled, Abstract 5524: Persistent patient barriers to genomic testing in ambulatory oncology
Journal Articles

Abstract 5706: ImmunoPROFILE: A prospective implementation of clinically validated, quantitative immune cell profiling test identifies tumor-infiltrating CD8+ and PD-1+ cell densities as prognostic biomarkers across a 2,023 patient pan-cancer cohort treated with different therapies

James Lindsay, Bijaya Sharma, Kristen D. Felt, Anita Giobbie-Hurder, Ian Dryg, Jason L. Weirather, Jennifer Altreuter, Tali Mazor, Priti Kumari, Joao V. Alessi, Ajit J. Nirmal, Michael P. Manos, Ananth R. Kumar, William Lotter, Ethan Cerami, Burce E. Johnson, Neil I. Lindeman, Lynette M. Sholl, Jonathan A. Nowak, Scott J. Rodig
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 5706.
https://doi.org/10.1158/1538-7445.AM2023-5706
Published: 04 April 2023
View article titled, Abstract 5706: ImmunoPROFILE: A prospective implementation of clinically validated, quantitative immune cell profiling test identifies tumor-infiltrating CD8<sup>+</sup> and PD-1<sup>+</sup> cell densities as prognostic biomarkers across a 2,023 patient pan-cancer cohort treated with different therapies
Journal Articles

Abstract 2131: Curating cartography: Enabling the harmonisation, visualisation, and reuse of diverse multiplexed imaging data through the Human Tumor Atlas Network Data Coordinating Center

Adam J. Taylor, Milen Nikolov, Ino de Brujin, Jeremy Muhlich, Mialy De Felice, Artem Sokolov, Denis Schapiro, Peter Sorger, Julie Bletz, Nikolaus Schultz, Vésteinn Thorsson, James Eddy, Ethan Cerami
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 2131.
https://doi.org/10.1158/1538-7445.AM2022-2131
Published: 15 June 2022
View article titled, Abstract 2131: Curating cartography: Enabling the harmonisation, visualisation, and reuse of diverse multiplexed imaging data through the Human Tumor Atlas Network Data Coordinating Center
Journal Articles

Abstract 5026: Dynamic changes in circulating protein levels reveal an association between ipilimumab and nivolumab combination treatment (SWOG Lung-MAP S1400I trial) with outcomes in squamous cell lung cancer

Edgar Gonzalez-Kozlova, Hsin-Hui Huang, Mary Redman, Roy Herbst, Scott Gettinger, Luda Bazhenova, Hui Xie, Manishkumar Patel, Kai Nie, Jocelyn Harris, Kimberly Argueta, Karen Kelly, Ethan Cerami, James Lindsay, Joyce Yu, Roshni Biswas, Stephen Van Nostrand, Radim Moravec, Diane Marie Del Valle, Seunghee Kim-schulze, Sacha Gnjatic
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 5026.
https://doi.org/10.1158/1538-7445.AM2022-5026
Published: 15 June 2022
View article titled, Abstract 5026: Dynamic changes in circulating protein levels reveal an association between ipilimumab and nivolumab combination treatment (SWOG Lung-MAP S1400I trial) with outcomes in squamous cell lung cancer
Journal Articles

Abstract 1974: Immune gene expression signatures associated clinical benefit from nivolumab and ipilimumab for previously treated patients with stage IV squamous cell lung cancer: An immune biomarker analysis of phase III SWOG LungMAP S1400I trial

Dzifa Y. Duose, Jiexin Zhang, Mary Redman, Baili Zhang, Ethan Cerami, James Lindsay, Joyce Yu, Roshni Biswas, Stephen Van Nostrand, Radim Moravec, Rajyalakshmi Luthra, Gheath Al-Atrash, Karen Kelly, Roy Herbst, Ignacio Wistuba, Scott Gettinger, Lyudmila Bazhenova, J. Jack Lee, Jianjun Zhang, Cara Haymaker
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1974.
https://doi.org/10.1158/1538-7445.AM2022-1974
Published: 15 June 2022
View article titled, Abstract 1974: Immune gene expression signatures associated clinical benefit from nivolumab and ipilimumab for previously treated patients with stage IV squamous cell lung cancer: An immune biomarker analysis of phase III SWOG LungMAP S1400I trial
Journal Articles

Abstract 4091: Design and adoption of MatchMiner at Dana-Farber Cancer Institute

Harry Klein, Tali Mazor, Priti Kumari, Andrea Ovalle, Pavel Trukhanov, Jason Hansel, Joyce Yu, James Lindsay, Michael Hassett, Ethan Cerami
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 4091.
https://doi.org/10.1158/1538-7445.AM2022-4091
Published: 15 June 2022
View article titled, Abstract 4091: Design and adoption of MatchMiner at Dana-Farber Cancer Institute
Journal Articles

Abstract 3890: Sequencing of 888 pediatric solid tumors informs precision oncology trial design and data sharing initiatives in pediatric cancer

Suzanne J. Forrest, Hersh Gupta, Abigail Ward, Yvonne Li, Duong Doan, Alyaa Al-Ibraheemi, Sanda Alexandrescu, Pratiti Bandopadhayay, Suzanne Shusterman, Elizabeth A. Mullen, Natalie Collins, Susan N. Chi, Karen D. Wright, Priti Kumari, Tali Mazor, Keith L. Ligon, Priyanka Shivdasani, Phani Davineni, Monica Manam, Richard L. Schilsky, Suanna S. Bruinooge, Jaime M. Guidry Auvil, Ethan Cerami, Barrett J. Rollins, Matthew L. Meyerson, Neal I. Lindeman, Laura MacConaill, Bruce E. Johnson, Andrew D. Cherniack, Alanna J. Church, Katherine A. Janeway
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 3890.
https://doi.org/10.1158/1538-7445.AM2022-3890
Published: 15 June 2022
View article titled, Abstract 3890: Sequencing of 888 pediatric solid tumors informs precision oncology trial design and data sharing initiatives in pediatric cancer
Journal Articles

Abstract 2580: Infiltration and spatial distribution of immune cells are associated clinical benefit from Nivolumab and Ipilimumab for previously treated patients with stage IV squamous cell lung cancer: an immune biomarker analysis of Phase III SWOG LungMAP S1400I trial

Edwin Roger Parra, Jiexin Zhang, Mary Redman, Rossana Lazcano, Piubelli Mario, Caddie Laberiano Fernandez, Renganayaki K. Krishna, Shanyu Zhang, Hong Chen, Ganiraju Manyam, Radim Moravec, Ethan Cerami, James Lindsay, Joyce Yu, Roshni Biswas, Stephen Van Nostrand, Dzifa Y. Duose, Jianjun Zhang, Roy Herbst, Gheath Al-Atrash, Kasthuri Kannan, Ignacio I. Wistuba, Scott Gettinger, Lyudmila Bazhenova, Jack Lee, Jianhua Zhang, Cara Haymaker
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 2580.
https://doi.org/10.1158/1538-7445.AM2022-2580
Published: 15 June 2022
View article titled, Abstract 2580: Infiltration and spatial distribution of immune cells are associated clinical benefit from Nivolumab and Ipilimumab for previously treated patients with stage IV squamous cell lung cancer: an immune biomarker analysis of Phase III SWOG LungMAP S1400I trial
Journal Articles

Abstract 1155: cBioPortal for cancer genomics

Jianjiong Gao, Tali Mazor, Ino de Bruijn, Adam Abeshouse, Diana Baiceanu, Ziya Erkoc, Elena Garcia Lara, Benjamin Gross, David M. Higgins, Prasanna K. Jagannathan, Priti Kumari, Ritika Kundra, Xiang Li, James Lindsay, Aaron Lisman, Divya Madala, Ramyasree Madupuri, Angelica Ochoa, Oleguer Plantalech, Sander Rodenburg, Baby A. Satravada, Robert Sheridan, Lucas Sikina, Jessica Singh, S. Onur Sumer, Yichao Sun, Pim van Nierop, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Sjoerd van Hagen, Kees van Bochove, Ugur Dogrusoz, Allison Heath, Adam Resnick, Trevor J. Pugh, Chris Sander, Ethan Cerami, Nikolaus Schultz
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1155.
https://doi.org/10.1158/1538-7445.AM2022-1155
Published: 15 June 2022
View article titled, Abstract 1155: cBioPortal for cancer genomics
Journal Articles

Abstract 207: The cBioPortal for Cancer Genomics

Jianjiong Gao, Tali Mazor, Ino de Bruijn, Adam Abeshouse, Diana Baiceanu, Ziya Erkoc, Benjamin Gross, David Higgins, Prasanna K. Jagannathan, Karthik Kalletla, Priti Kumari, Ritika Kundra, Xiang Li, James Lindsay, Aaron Lisman, Pieter Lukasse, Divya Madala, Ramyasree Madupuri, Angelica Ochoa, Oleguer Plantalech, Joyce Quach, Sander Rodenburg, Anusha Satravada, Fedde Schaeffer, Robert Sheridan, Lucas Sikina, S. Onur Sumer, Yichao Sun, Paul van Dijk, Pim van Nierop, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Sjoerd van Hagen, Kees van Bochove, Ugur Dogrusoz, Allison Heath, Adam Resnick, Trevor J. Pugh, Chris Sander, Ethan Cerami, Nikolaus Schultz
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 207.
https://doi.org/10.1158/1538-7445.AM2021-207
Published: 01 July 2021
View article titled, Abstract 207: The cBioPortal for Cancer Genomics
Journal Articles

Abstract 171: Cloud-based bulk and single-cell RNAseq pipelines in the Terra platform for the Lung PCA

Chris Husted, François Aguet, Conor Shea, Adam Gower, William Mischler, Yusuke Koga, Rui Hong, Steven Dubinett, Avrum Spira, Sarah A. Mazzilli, Ethan Cerami, Ignaty Leshchiner, Marc E. Lenburg, Gad Getz, Jennifer E. Beane, Joshua D. Campbell
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 171.
https://doi.org/10.1158/1538-7445.AM2021-171
Published: 01 July 2021
View article titled, Abstract 171: Cloud-based bulk and single-cell RNAseq pipelines in the Terra platform for the Lung PCA
Journal Articles

Abstract 1198: MatchMiner: An open-source computational platform that accelerates patient enrollment on to precision medicine trials

Harry Klein, Tali Mazor, Priti Kumari, James Lindsay, Andrea Ovalle, Ethan Siegel, Pavel Trukhanov, Joyce Yu, Michael Hassett, Ethan Cerami
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 1198.
https://doi.org/10.1158/1538-7445.AM2021-1198
Published: 01 July 2021
View article titled, Abstract 1198: MatchMiner: An open-source computational platform that accelerates patient enrollment on to precision medicine trials
Journal Articles

Abstract 1097: FGFR2 in-frame indels: A novel targetable alteration in intrahepatic cholangiocarcinoma

Yvonne Y. Li, James M. Cleary, Srivatsan Raghavan, Liam F. Spurr, Qibiao Wu, Lei Shi, Lauren K. Brais, Maureen Loftus, Lipika Goyal, Anuj K. Patel, Atul B. Shinagare, Thomas E. Clancy, Geoffrey Shapiro, Ethan Cerami, William R. Sellers, William C. Hahn, Matthew Meyerson, Nabeel Bardeesy, Andrew D. Cherniack, Brian M. Wolpin
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 1097.
https://doi.org/10.1158/1538-7445.AM2020-1097
Published: 15 August 2020
View article titled, Abstract 1097: FGFR2 in-frame indels: A novel targetable alteration in intrahepatic cholangiocarcinoma
Journal Articles

Abstract 3209: The cBioPortal for Cancer Genomics

Jianjiong Gao, Tali Mazor, Adam Abeshouse, Ino de Bruijn, Benjamin Gross, Karthik Kalletla, Priti Kumari, Ritika Kundra, Xiang Li, James Lindsay, Aaron Lisman, Pieter Lukasse, Ramyasree Madupuri, Angelica Ochoa, Oleguer Plantalech, Sander Rodenburg, Fedde Schaeffer, Robert Sheridan, Lucas Sikina, Jing Su, S. Onur Sumer, Yichao Sun, Paul van Dijk, Sjoerd van Hagen, Pim van Nierop, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Kelsey Zhu, Kees van Bochove, Ugur Dogrusoz, Allison Heath, Adam Resnick, Trevor J. Pugh, Chris Sander, Ethan Cerami, Nikolaus Schultz
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 3209.
https://doi.org/10.1158/1538-7445.AM2020-3209
Published: 15 August 2020
View article titled, Abstract 3209: The cBioPortal for Cancer Genomics
Journal Articles

Abstract 3382: MatchMiner: An open-source computational platform for genomically-driven matching of cancer patients to precision medicine clinical trials

Tali Mazor, Rachel B. Keller, Priti Kumai, James Lindsay, Eric Marriott, Andrea Ovalle, Ethan Siegel, Joyce Yu, Michael Hassett, Ethan Cerami
Journal: Cancer Research
Cancer Res (2020) 80 (16_Supplement): 3382.
https://doi.org/10.1158/1538-7445.AM2020-3382
Published: 15 August 2020
View article titled, Abstract 3382: MatchMiner: An open-source computational platform for genomically-driven matching of cancer patients to precision medicine clinical trials
Journal Articles

Abstract 910: The cBioPortal for cancer genomics

Jianjiong Gao, Tali Mazor, Adam Abeshouse, Ersin Ciftci, Ino de Bruijn, Benjamin Gross, Karthik Kalletla, Priti Kumari, Ritika Kundra, James Lindsay, Aaron Lisman, Pieter Lukasse, Ramyasree Madupuri, Angelica Ochoa, Oleguer Plantalech, Pichai Raman, Fedde Schaeffer, Robert Sheridan, Jing Su, S. Onur Sumer, Yichao Sun, Sander Tan, Sjoerd van Hagen, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Kelsey Zhu, Kees van Bochove, Ugur Dogrusoz, Trevor J. Pugh, Adam Resnick, Chris Sander, Ethan Cerami, Nikolaus Schultz
Journal: Cancer Research
Cancer Res (2019) 79 (13_Supplement): 910.
https://doi.org/10.1158/1538-7445.AM2019-910
Published: 01 July 2019
View article titled, Abstract 910: The cBioPortal for cancer genomics
Journal Articles

Abstract 2288: Assessing patient trial readiness for precision cancer medicine clinical trials through computational trial matching and rule-based logic applied to genomic and clinical data

Catherine Del Vecchio Fitz, Khanh Do, James Lindsay, Suzanne Hector-Barry, Zachary Zwiesler, Priti Kumari, Tali Mazor, Tamba Monrose, Adem Albayrak, John Methot, Michael Hassett, Geoffrey Shapiro, Ethan Cerami
Journal: Cancer Research
Cancer Res (2018) 78 (13_Supplement): 2288.
https://doi.org/10.1158/1538-7445.AM2018-2288
Published: 01 July 2018
View article titled, Abstract 2288: Assessing patient trial readiness for precision cancer medicine clinical trials through computational trial matching and rule-based logic applied to genomic and clinical data