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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 E. Gross, Charles D. Haynes, Allison Heath, David M. Higgins, Prasanna Jagannathan, Karthik Kalletla, Priti Kumari, James R. Lindsay, Aaron Lisman, Bas Leenknegt, Pieter Lukasse, Divya Madala, Ramyasree Madupuri, Pim van Nierop, Oleguer Plantalech, Joyce Quach, Adam 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 Pillai, Chelsea Nichols, Stuart M. Gardos, John Philip, GENIE BPC Core Team, AACR Project GENIE Consortium, Kenneth L. Kehl, Gregory J. Riely, Deb 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)
https://doi.org/10.1158/0008-5472.CAN-23-0816
Published: 05 September 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 1908: Clinical genomic profiling identifies lower frequency of therapeutically actionable alterations and lower prognostic value of APC inactivation in colorectal cancer patients of African ancestry

Henry Walch, Anisha Luthra, Kanika S. Arora, Michele Waters, Samantha Chin, Christopher J. Fong, Doori Rose, Hannah Williams, Jeese J. Smith, Nikolaus Schultz, Michael F. Berger, Karuna Ganesh, Julio Garcia-Aguilar, Rona Yaeger, Walid K. Chatila, Francisco Sanchez-Vega
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 1908.
https://doi.org/10.1158/1538-7445.AM2023-1908
Published: 29 May 2023
View article titled, Abstract 1908: Clinical genomic profiling identifies lower frequency of therapeutically actionable alterations and lower prognostic value of APC inactivation in colorectal cancer patients of African ancestry
Journal Articles

Abstract 1053: Circulating tumor DNA from cerebrospinal fluid (CSF) allows for characterization and monitoring of glioma patients

Subhiksha Nandakumar, Christoph Kreitzer, Charli Ann Hertz, Johnathan Rafailov, Timothy Song, Nicholas D. Socci, A. Rose Brannon, Maria E. Arcila, David B. Solit, Michael F. Berger, Nikolaus Schultz, Ingo K. Mellinghoff, Alexandra M. Miller
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 1053.
https://doi.org/10.1158/1538-7445.AM2023-1053
Published: 04 April 2023
View article titled, Abstract 1053: Circulating tumor DNA from cerebrospinal fluid (CSF) allows for characterization and monitoring of glioma patients
Journal Articles

Abstract 2: Vertical MAPK pathway targeting in novel genetically engineered mouse and cell line models of NF1-altered melanoma: the mSK-Mel murine cohort

Alexis M. Jones, Aphrothiti J. Hanrahan, Moriah H. Nissan, Sebastien Monette, Ziyu Chen, Wenhuo Hu, Sandra Misale, Isabell Schulze, Naresh Vasani, Cailian Liu, Xia Yang, Mohsen Abu-Akeel, Elisa de Stanchina, Nikolaus Schultz, Michael F. Berger, Neal Rosen, Taha Merghoub, David B. Solit
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 2.
https://doi.org/10.1158/1538-7445.AM2023-2
Published: 04 April 2023
View article titled, Abstract 2: Vertical MAPK pathway targeting in novel genetically engineered mouse and cell line models of NF1-altered melanoma: the mSK-Mel murine cohort
Journal Articles

Abstract 2598: The DACH1 gene is frequently deleted in prostate cancer, restrains prostatic intraepithelial neoplasia, augments DNA damage repair and predicts therapy responses

Zhiping Li, Xuanmao Jiao, Gordon Robertson, Gabriele Di Sante, Anthony W. Ashton, Agnese DiRocco, Min Wang, Jun Zhao, Sankar Addya, Chenguang Wang, Peter A. McCue, Andrew P. South, Carlos Cordon-Cardo, Runzhi Liu, Kishan Patel, Rasha Hamid, Jorim Parmar, James B. DuHadaway, Nikolaus Schultz, Andrew Kossenkov, Lai Yee Phoon, Hao Chen, Li Lan, Yunguang Sun, Kenneth A. Iczkowski, Hallgeir Rui, Richard G. Pestell
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 2598.
https://doi.org/10.1158/1538-7445.AM2023-2598
Published: 04 April 2023
View article titled, Abstract 2598: The <em>DACH1</em> gene is frequently deleted in prostate cancer, restrains prostatic intraepithelial neoplasia, augments DNA damage repair and predicts therapy responses
Journal Articles

Correction: ARF Confers a Context-Dependent Response to Chemotherapy in Muscle-Invasive Bladder Cancer

Tomasz B. Owczarek, Takashi Kobayashi, Ricardo Ramirez, Lijie Rong, Anna M. Puzio-Kuter, Gopa Iyer, Min Yuen Teo, Francisco Sánchez-Vega, Jingqiang Wang, Nikolaus Schultz, Tian Zheng, David B. Solit, Hikmat A. Al-Ahmadie, Cory Abate-Shen
Journal: Cancer Research
Cancer Res (2023) 83 (7): 1159.
https://doi.org/10.1158/0008-5472.CAN-23-0518
Published: 04 April 2023
View article titled, Correction: ARF Confers a Context-Dependent Response to Chemotherapy in Muscle-Invasive Bladder Cancer
Open the PDF for Correction: ARF Confers a Context-Dependent Response to Chemotherapy in Muscle-Invasive Bladder Cancer in another window
Journal Articles

Abstract 4260: Understanding genomic and social determinants of cancer immunotherapy outcome across ancestry

Christopher J. Fong, Michele Waters, Karl Pichotta, Justin Jee, Devika R. Jutagir, David Ma, Tomin Perea-Chamblee, Susie Kim, Kanika Arora, Brooke Mastrogiacomo, Thinh Tran, Steven Maron, Mirella Altoe, Anisha Luthra, Joseph Kholodenko, Arfath Patha, Doori Rose, Michael F. Berger, Gregory J. Riely, Nikolaus Schultz, Sanna Goyert, Adam Schoenfeld, Francesca Gany, Jian Carrot-Zhang
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 4260.
https://doi.org/10.1158/1538-7445.AM2023-4260
Published: 04 April 2023
View article titled, Abstract 4260: Understanding genomic and social determinants of cancer immunotherapy outcome across ancestry
Journal Articles

Abstract 4259: Identification of anti-neoplastic therapy given before initial visit at a referral center using natural language processing applied to medical oncology initial consultation notes

Thinh N. Tran, Karl B. Pichotta, Si-Yang Liu, Christopher Fong, Anisha Luthra, Brooke Mastrogiacomo, Steven Maron, Deborah Schrag, Sohrab P. Shah, Pedram Razavi, Bob T. Li, Gregory J. Riely, Nikolaus Schultz, Justin Jee
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 4259.
https://doi.org/10.1158/1538-7445.AM2023-4259
Published: 04 April 2023
View article titled, Abstract 4259: Identification of anti-neoplastic therapy given before initial visit at a referral center using natural language processing applied to medical oncology initial consultation notes
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 6063: Genomic characterization of non-small cell lung cancer (NSCLC) brain metastasis (BM) patients identifies novel alterations associated with tropisms and disease progression

Henry Walch, Anna Skakodub, Kathryn R. Tringale, Harish N. Vasudevan, Jordan Eichholz, Daniel W. Kelly, Emily Lebow, Nelson S. Moss, Kenny Kwok Hei Yu, Bob T. Li, Boris Mueller, Atif Khan, Yao Yu, Simon Powell, Jorge S. Reis-Filho, Brandon S. Imber, Pedram Razavi, Daniel R. Gomez, Nikolaus Schultz, Luke R. Pike
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 6063.
https://doi.org/10.1158/1538-7445.AM2023-6063
Published: 04 April 2023
View article titled, Abstract 6063: Genomic characterization of non-small cell lung cancer (NSCLC) brain metastasis (BM) patients identifies novel alterations associated with tropisms and disease progression
Journal Articles

Abstract 5721: Automated annotation for large-scale clinicogenomic models of lung cancer treatment response and overall survival

Justin Jee, Chris Fong, Karl Pichotta, Thinh Tran, Anisha Luthra, Mirella Altoe, Steven Maron, Ronglai Shen, Si-Yang Liu, Michele Waters, Joseph Kholodenko, Brooke Mastrogiacomo, Susie Kim, A Rose Brannon, Michael F. Berger, Axel Martin, Jason Chang, Anton Safonov, Jorge S. Reis-Filho, Deborah Schrag, Sohrab P. Shah, Pedram Razavi, Bob T. Li, Gregory J. Riely, Nikolaus Schultz
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 5721.
https://doi.org/10.1158/1538-7445.AM2023-5721
Published: 04 April 2023
View article titled, Abstract 5721: Automated annotation for large-scale clinicogenomic models of lung cancer treatment response and overall survival
Journal Articles

Abstract 6585: OncoKB, MSK’s precision oncology knowledge base

Sarah P. Suehnholz, Moriah Nissan, Hongxin Zhang, Ritika Kundra, Calvin Lu, Amanda Dhaneshwar, Nicole Fernandez, Stephanie Carrero, Maria E. Arcila, Marc Ladanyi, Michael F. Berger, Aijazuddin Syed, Rose Brannon, Ross Levine, Ahmet Dogan, Ezra Rosen, Alexander Drilon, David B. Solit, Nikolaus Schultz, Debyani Chakravarty
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 6585.
https://doi.org/10.1158/1538-7445.AM2023-6585
Published: 04 April 2023
View article titled, Abstract 6585: OncoKB, MSK’s precision oncology knowledge base
Journal Articles

Abstract 6578: reVUE: repository for variants with unexpected effects

Ino de Bruijn, Aditi Gopalan, Xiang Li, Hongxin Zhang, Onur Sumer, Thomas Y. Cong, Tona Gonzalez, Madelaine Rangel, Nikolaus Schultz, Debyani Chakravarty
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 6578.
https://doi.org/10.1158/1538-7445.AM2023-6578
Published: 04 April 2023
View article titled, Abstract 6578: reVUE: repository for variants with unexpected effects
Journal Articles

Abstract A005: Genomic profiling identifies differences in the distribution of APC mutations in non-Hispanic black and non-Hispanic white patients with colorectal cancer

Henry Walch, Anisha Luthra, Walid Chatila, Kanika Arora, Samantha Chin, Michele Waters, Jesse J. Smith, Nikolaus Schultz, Michael F. Berger, Karuna Ganesh, Julio Garcia-Aguilar, Rona Yaeger, Francisco Sanchez-Vega
Journal: Cancer Research
Cancer Res (2022) 82 (23_Supplement_1): A005.
https://doi.org/10.1158/1538-7445.CRC22-A005
Published: 01 December 2022
View article titled, Abstract A005: Genomic profiling identifies differences in the distribution of APC mutations in non-Hispanic black and non-Hispanic white patients with colorectal cancer
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 82: Molecular characterization of gallbladder cancer

Nicolas A. Giraldo, Abhinita Mohanty, Chad Vanderbilt, Rose Brannon, Ryma Benayed, Efsevia Vakiani, Ghassan Abou-Alfa, James Harding, Imane El Dika, Nikolaus Schultz, Bob Li, Michael F. Berger, Marc Ladanyi, Eileen O'Reilly, William Jarnagin, Olca Basturk, Maria Arcila
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 82.
https://doi.org/10.1158/1538-7445.AM2022-82
Published: 15 June 2022
View article titled, Abstract 82: Molecular characterization of gallbladder cancer
Journal Articles

Abstract 3634: Integrative analysis of the contribution of genomic and clinical factors to worse clinical outcomes in non-Hispanic Black patients with colorectal cancer

Henry Walch, Anisha Luthra, Walid K. Chatila, Fan Wu, Debyani Chakravarty, Chin-Tung Chen, Rupa Sood, Dana M. Omer, Jesse J. Smith, Nikolaus Schultz, Karuna Ganesh, Julio Garcia-Aguilar, Rona Yaeger, Francisco Sanchez-Vega
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 3634.
https://doi.org/10.1158/1538-7445.AM2022-3634
Published: 15 June 2022
View article titled, Abstract 3634: Integrative analysis of the contribution of genomic and clinical factors to worse clinical outcomes in non-Hispanic Black patients with colorectal cancer
Journal Articles

Abstract 1189: OncoKB, MSK’s precision oncology knowledge base

Sarah P. Suehnholz, Moriah Nissan, Hongxin Zhang, Ritika Kundra, Calvin Lu, Benjamin Xu, Maria E. Arcila, Marc Ladanyi, Michael F. Berger, Ahmet Zehir, Aijaz Syed, Julia E. Rudolph, Ross L. Levine, Ahmet Dogan, Jianjiong Gao, David B. Solit, Nikolaus Schultz, Debyani Chakravarty
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1189.
https://doi.org/10.1158/1538-7445.AM2022-1189
Published: 15 June 2022
View article titled, Abstract 1189: OncoKB, MSK’s precision oncology knowledge base
Journal Articles

Abstract 1156: Genome Nexus: A comprehensive resource for the annotation and interpretation of genomic variants in cancer

Ino de Bruijn, Xiang Li, Onur Sumer, Benjamin Gross, Robert Sheridan, Angelica Ochoa, Manda Wilson, Avery Wang, Hongxin Zhang, Aaron Lisman, Adam Abeshouse, Sander Rodenburg, Sjoerd van Hagen, Remond Fijneman, Gerrit Meijer, Nikolaus Schultz, Jianjiong Gao
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 1156.
https://doi.org/10.1158/1538-7445.AM2022-1156
Published: 15 June 2022
View article titled, Abstract 1156: Genome Nexus: A comprehensive resource for the annotation and interpretation of genomic variants in cancer
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