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Journal Articles

Abstract 1249: cBioPortal for Cancer Genomics

Tali Mazor, Ino de Bruijn, Rima AlHamad, Calla Chennault, Corey Dubin, Jeremy Easton-Marks, Zhaoyuan Fu, Benjamin Gross, Charles Haynes, David M. Higgins, Jason Hwee, Prasanna K. Jagannathan, Mirella Kalafati, Karthik Kalletla, James Ko, Tim Kuijpers, Sowmiyaa Kumar, Priti Kumari, Ritika Kundra, Bryan Lai, Xiang Li, James Lindsay, Aaron Lisman, Qi-Xuan Lu, Ramyasree Madupuri, Angelica Ochoa, Yusuf Z. Özgül, Oleguer Plantalech, Matthijs N. Pon, Baby A. Satravada, Jessica Singh, Selcuk Onur Sumer, Pim van Nierop, Floris Vleugels, Avery Wang, Manda Wilson, Hongxin Zhang, Gaofei Zhao, Ugur Dogrusoz, Allison Heath, Adam Resnick, Trevor J. Pugh, Chris Sander, Ethan Cerami, Jianjiong Gao, Nikolaus Schultz
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 1249.
https://doi.org/10.1158/1538-7445.AM2024-1249
Published: 22 March 2024
View article titled, Abstract 1249: cBioPortal for Cancer Genomics
Journal Articles

Abstract 6455: Investigating clinical trial eligibility criteria to improve MatchMiner trial matching

Harry Klein, Tali Mazor, Matthew Galvin, Jason Hansel, Emily Mallaber, Pavel Trukhanov, James Provencher, James Lindsay, Michael Hassett, Ethan Cerami
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 6455.
https://doi.org/10.1158/1538-7445.AM2024-6455
Published: 22 March 2024
View article titled, Abstract 6455: Investigating clinical trial eligibility criteria to improve MatchMiner trial matching
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 2142: Immune determinants of CAR-T expansion in solid tumor patients receiving GD2 CAR-T cell therapy

Tara Murty, Sabina Kaczanowska, Ahmad Alimadadi, Cristina Contreras, Caroline Duault, Priyanka Balasubrahmanyan, Warren Reynolds, Norma Gutierrez, Reema Baskar, Catherine Wu, Franziska Michor, Jennifer Altreuter, Yang Liu, Aashna Jhaveri, Vandon Duong, Hima Anbunathan, Radim Moravec, Joyce Hong, Roshni Biswas, Stephen Van Nostrand, James Lindsay, Mina Pichavant, Elena Sotillo, Bita Sahaf, Sean Bendall, Holden Maecker, Steven Highfill, David Stroncek, Melinda Merchant, John Glod, Catherine Hedrick, Crystal Mackall, Sneha Ramakrishna, Rosandra Kaplan
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 2142.
https://doi.org/10.1158/1538-7445.AM2023-2142
Published: 04 April 2023
View article titled, Abstract 2142: Immune determinants of CAR-T expansion in solid tumor patients receiving GD2 CAR-T cell therapy
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 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 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 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 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 CT142: GD2.Ox40.CD28.z CAR T cell trial in neuroblastoma and osteosarcoma

Sneha Ramakrishna, Sabina Kaczanowska, Tara Murty, Cristina F. Contreras, Melinda Merchant, John Glod, Norma Gutierrez, Ahmad Alimadadi, David Stroncek, Steven Highfill, Caroline Duault, Priyanka B. Subrahmanyam, Tyson Holmes, Warren Reynolds, Reema Baskar, Antoine Barge, Hayley Lyon, Radim Moravec, Srinika Ranasinghe, Joyce Yu, Roshni Biswas, Samuel Pollack, Stephen Van Nostrand, James Lindsay, Mina Pichavant, Bita Sahaf, Sean C. Bendall, Andrew J. Gentles, Holden Maecker, Catherine C. Hedrick, Crystal Mackall, Rosandra Kaplan
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): CT142.
https://doi.org/10.1158/1538-7445.AM2022-CT142
Published: 15 June 2022
View article titled, Abstract CT142: GD2.Ox40.CD28.z CAR T cell trial in neuroblastoma and osteosarcoma
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 2143: Clinicopathologic, genomic and immunophenotypic landscape of ATM mutations in non-small cell lung cancer

Biagio Ricciuti, Joao Victor Alessi, Xinan Wang, Arrien A. Bertram, Victor R. Vaz, Mizuki Nishino, James Lindsay, Kristen D. Felt, Bijaya Sharma, Lynette M. Sholl, Rodig Scott, Mark M. Awad, Michael L. Cheng
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 2143.
https://doi.org/10.1158/1538-7445.AM2022-2143
Published: 15 June 2022
View article titled, Abstract 2143: Clinicopathologic, genomic and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Journal Articles

Abstract 4117: Clinicopathologic and molecular characterization of KRASG12D lung cancers

Jia Luo, Biagio Ricciuti, Joao V. Alessi, Xinan Wang, Victor Vaz, Federica Pecci, Tom Nguyen, James Lindsay, Bijaya Sharma, Kristen D. Felt, Scott J. Rodig, Mizuki H. Nishino, Lynette M. Sholl, David A. Barbie, Pasi A. Jänne, Mark M. Awad
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 4117.
https://doi.org/10.1158/1538-7445.AM2022-4117
Published: 15 June 2022
View article titled, Abstract 4117: Clinicopathologic and molecular characterization of KRAS<sup>G12D</sup> lung cancers
Journal Articles

Abstract 506: Dissecting the genomic and tumor immune microenvironment factors associated with disease recurrence in resected stage I NSCLC

Joao Victor Alessi, Zihan Wei, Biagio Ricciuti, James Lindsay, Victor R. Vaz, Adriana Barrichello, Bijaya Sharma, Kristen D. Felt, Fangxin Hong, Lynette M. Sholl, Scott J. Rodig, Mark M. Awad
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 506.
https://doi.org/10.1158/1538-7445.AM2022-506
Published: 15 June 2022
View article titled, Abstract 506: Dissecting the genomic and tumor immune microenvironment factors associated with disease recurrence in resected stage I NSCLC
Journal Articles

Abstract 26: Association of aneuploidy score with clinical outcomes to immunotherapy in NSCLC

João Victor Alessi, Biagio Ricciuti, Yvonne Y. Li, Hersh Gupta, Giuseppe Lamberti, Gonzalo Recondo, Mizuki Nishino, Lynette M. Sholl, Andrew D. Cherniak, James Lindsay, Bijaya Sharma, Kathleen Pfaff, Kristen Felt, Scott Rodig, Mark M. Awad
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 26.
https://doi.org/10.1158/1538-7445.AM2021-26
Published: 01 July 2021
View article titled, Abstract 26: Association of aneuploidy score with clinical outcomes to immunotherapy in NSCLC
Journal Articles

Abstract 490: A very high tumor mutational burden (TMB) is associated with improved efficacy of PD-(L)1 inhibition across different PD-L1 expression subgroups and a distinct immunophenotype in NSCLC

Biagio Ricciuti, Kathryn C. Arbour, Navin R. Mahadevan, Joao V. Alessi, James Lindsay, Renato Umeton, Rileen Sinha, Amir Hoojghan, Natalie Vokes, Gonzalo Recondo, Giuseppe Lamberti, Andrew Polio1, Hira Rizvi, Giulia Leonardi, Andrew J. Plodkowski, Kristen Felt, Bijaya Sharma, Michael Y. Tolstorukov, Pasi A. Janne, Eliezer M. Van Allen, Lynette M. Sholl, Scott J. Rodig, Matthew D. Hellmann, Mark M. Awad
Journal: Cancer Research
Cancer Res (2021) 81 (13_Supplement): 490.
https://doi.org/10.1158/1538-7445.AM2021-490
Published: 01 July 2021
View article titled, Abstract 490: A very high tumor mutational burden (TMB) is associated with improved efficacy of PD-(L)1 inhibition across different PD-L1 expression subgroups and a distinct immunophenotype in NSCLC
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 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