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Journal Articles

Predicting Molecular Subtype and Survival of Rhabdomyosarcoma Patients Using Deep Learning of H&E Images: A Report from the Children's Oncology Group

Open Access
David Milewski, Hyun Jung, G. Thomas Brown, Yanling Liu, Ben Somerville, Curtis Lisle, Marc Ladanyi, Erin R. Rudzinski, Hyoyoung Choo-Wosoba, Donald A. Barkauskas, Tammy Lo, David Hall, Corinne M. Linardic, Jun S. Wei, Hsien-Chao Chou, Stephen X. Skapek, Rajkumar Venkatramani, Peter K. Bode, Seth M. Steinberg, George Zaki, Igor B. Kuznetsov, Douglas S. Hawkins, Jack F. Shern, Jack Collins, Javed Khan
Journal: Clinical Cancer Research
Clin Cancer Res (2023) 29 (2): 364–378.
https://doi.org/10.1158/1078-0432.CCR-22-1663
Published: 17 January 2023
View articletitled, Predicting Molecular Subtype and Survival of Rhabdomyosarcoma Patients Using Deep Learning of H&E Images: A Report from the Children's Oncology Group
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Includes: Supplementary data
Journal Articles

The Combination of Trametinib and Ganitumab is Effective in RAS-Mutated PAX-Fusion Negative Rhabdomyosarcoma Models

Available to Purchase
Katie E. Hebron, Xiaolin Wan, Jacob S. Roth, David J. Liewehr, Nancy E. Sealover, William J.E. Frye, Angela Kim, Stacey Stauffer, Olivia L. Perkins, Wenyue Sun, Kristine A. Isanogle, Christina M. Robinson, Amy James, Parirokh Awasthi, Priya Shankarappa, Xiaoling Luo, Haiyan Lei, Donna Butcher, Roberta Smith, Elijah F. Edmondson, Jin-Qiu Chen, Noemi Kedei, Cody J. Peer, Jack F. Shern, W. Douglas Figg, Lu Chen, Matthew D. Hall, Simone Difilippantonio, Frederic G. Barr, Robert L. Kortum, Robert W. Robey, Angelina V. Vaseva, Javed Khan, Marielle E. Yohe
Journal: Clinical Cancer Research
Clin Cancer Res (2023) 29 (2): 472–487.
https://doi.org/10.1158/1078-0432.CCR-22-1646
Published: 17 January 2023
View articletitled, The Combination of Trametinib and Ganitumab is Effective in RAS-Mutated PAX-Fusion Negative Rhabdomyosarcoma Models
Open the PDF for The Combination of Trametinib and Ganitumab is Effective in RAS-Mutated PAX-Fusion Negative Rhabdomyosarcoma Models in another window
Includes: Supplementary data
Journal Articles

Abstract IA023: Therapeutic efficacy of trametinib and ganitumab in RAS-mutated rhabdomyosarcoma

Free
Marielle E. Yohe, Katie E. Hebron, Xiaolin Wan, Jacob S. Roth, David J. Liewehr, Nancy E. Sealover, Stacey Stauffer, Olivia Feehan-Nelson, Wenyue Sun, Kristine A. Isanogle, Christina M. Robinson, Amy James, Parirokh Awasthi, Priya Shankarappa, Xiaoling Liu, Haiyan Lei, Donna Butcher, Roberta Smith, Elijah F. Edmonson, Jin-Qui Chen, Noemi Kedei, Cody S. Peer, Jack F. Shern, W. Douglas Figg, Lu Chen, Matthew D. Hall, Simone Difillipantonio, Frederic G. Barr, Robert L. Kortum, Angelina V. Vaseva, Javed Khan
Journal: Clinical Cancer Research
Clin Cancer Res (2022) 28 (18_Supplement): IA023.
https://doi.org/10.1158/1557-3265.SARCOMAS22-IA023
Published: 15 September 2022
View articletitled, Abstract IA023: Therapeutic efficacy of trametinib and ganitumab in RAS-mutated rhabdomyosarcoma
Journal Articles

Abstract B012: Visualization of EWSR1’s colocalization with phosphorylated RNA-Polymerase II reveals its concentration at a subset of active regions of transcription in ewing sarcoma cells

Free
Natasha J. Caplen, Soumya Sundara Rajan, Vernon Ebegboni, Tamara L. Jones, Michael J. Kruhlak, Jan Wisniewski, Patricio Pichling, Katelyn R. Ludwig, Javed Khan, Raj Chari
Journal: Clinical Cancer Research
Clin Cancer Res (2022) 28 (18_Supplement): B012.
https://doi.org/10.1158/1557-3265.SARCOMAS22-B012
Published: 15 September 2022
View articletitled, Abstract B012: Visualization of EWSR1’s colocalization with phosphorylated RNA-Polymerase II reveals its concentration at a subset of active regions of transcription in ewing sarcoma cells
Journal Articles

Outcome-Related Signatures Identified by Whole Transcriptome Sequencing of Resectable Stage III/IV Melanoma Evaluated after Starting Hu14.18-IL2

Free
Richard K. Yang, Igor B. Kuznetsov, Erik A. Ranheim, Jun S. Wei, Sivasish Sindiri, Berkley E. Gryder, Vineela Gangalapudi, Young K. Song, Viharkumar Patel, Jacquelyn A. Hank, Cindy Zuleger, Amy K. Erbe, Zachary S. Morris, Renae Quale, KyungMann Kim, Mark R. Albertini, Javed Khan, Paul M. Sondel
Journal: Clinical Cancer Research
Series: Author Choice
Clin Cancer Res (2020) 26 (13): 3296–3306.
https://doi.org/10.1158/1078-0432.CCR-19-3294
Published: 01 July 2020
View articletitled, Outcome-Related Signatures Identified by Whole Transcriptome Sequencing of Resectable Stage III/IV Melanoma Evaluated after Starting Hu14.18-IL2
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Includes: Supplementary data
Journal Articles

Clinically Relevant Cytotoxic Immune Cell Signatures and Clonal Expansion of T-Cell Receptors in High-Risk MYCN-Not-Amplified Human Neuroblastoma

Free
Jun S. Wei, Igor B. Kuznetsov, Shile Zhang, Young K. Song, Shahab Asgharzadeh, Sivasish Sindiri, Xinyu Wen, Rajesh Patidar, Sushma Najaraj, Ashley Walton, Jaime M. Guidry Auvil, Daniela S. Gerhard, Aysen Yuksel, Daniel Catchpoole, Stephen M. Hewitt, Paul M. Sondel, Robert Seeger, John M. Maris, Javed Khan
Journal: Clinical Cancer Research
Clin Cancer Res (2018) 24 (22): 5673–5684.
https://doi.org/10.1158/1078-0432.CCR-18-0599
Published: 15 November 2018
View articletitled, Clinically Relevant Cytotoxic Immune Cell Signatures and Clonal Expansion of T-Cell Receptors in High-Risk MYCN-Not-Amplified Human Neuroblastoma
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Includes: Supplementary data
Journal Articles

Abstract B06: Targeting PI3K/mTOR in mouse rhabdomyosarcoma models driven by FGFR4 activation

Free
Timothy McKinnon, Rosemarie Venier, Marielle Yohe, Berkley E. Gryder, Brendan Dickson, Krista Schleicher, Dariush Davani, Winnie Wei, Cynthia Guidos, Abha Gupta, Javed Khan, Rebecca Gladdy
Journal: Clinical Cancer Research
Clin Cancer Res (2018) 24 (2_Supplement): B06.
https://doi.org/10.1158/1557-3265.SARCOMAS17-B06
Published: 15 January 2018
View articletitled, Abstract B06: Targeting PI3K/mTOR in mouse rhabdomyosarcoma models driven by FGFR4 activation
Journal Articles

Abstract PR11: SSX-mediated chromatin engagement and targeting of BAF complexes activates oncogenic transcription in synovial sarcoma

Free
Matthew J. McBride, John L. Pulice, Robert T. Nakayama, Nazar Mashtalir, Davis R. Ingram, Jacob D. Jaffe, Jack F. Shern, Javed Khan, Jason L. Hornick, Alexander J. Lazar, Cigall Kadoch
Journal: Clinical Cancer Research
Clin Cancer Res (2018) 24 (2_Supplement): PR11.
https://doi.org/10.1158/1557-3265.SARCOMAS17-PR11
Published: 15 January 2018
View articletitled, Abstract PR11: SSX-mediated chromatin engagement and targeting of BAF complexes activates oncogenic transcription in synovial sarcoma
Journal Articles

MultiDimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research

Free
Wendy Chang, Andrew S. Brohl, Rajesh Patidar, Sivasish Sindiri, Jack F. Shern, Jun S. Wei, Young K. Song, Marielle E. Yohe, Berkley Gryder, Shile Zhang, Kathleen A. Calzone, Nityashree Shivaprasad, Xinyu Wen, Thomas C. Badgett, Markku Miettinen, Kip R. Hartman, James C. League-Pascual, Toby N. Trahair, Brigitte C. Widemann, Melinda S. Merchant, Rosandra N. Kaplan, Jimmy C. Lin, Javed Khan
Journal: Clinical Cancer Research
Series: Author Choice
Clin Cancer Res (2016) 22 (15): 3810–3820.
https://doi.org/10.1158/1078-0432.CCR-15-2717
Published: 31 July 2016
View articletitled, MultiDimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research
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Includes: Supplementary data
Journal Articles

SLFN11 Is a Transcriptional Target of EWS-FLI1 and a Determinant of Drug Response in Ewing Sarcoma

Free
Sai-Wen Tang, Sven Bilke, Liang Cao, Junko Murai, Fabricio G. Sousa, Mihoko Yamade, Vinodh Rajapakse, Sudhir Varma, Lee J. Helman, Javed Khan, Paul S. Meltzer, Yves Pommier
Journal: Clinical Cancer Research
Clin Cancer Res (2015) 21 (18): 4184–4193.
https://doi.org/10.1158/1078-0432.CCR-14-2112
Published: 14 September 2015
View articletitled, SLFN11 Is a Transcriptional Target of EWS-FLI1 and a Determinant of Drug Response in Ewing Sarcoma
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Includes: Supplementary data
Journal Articles

PBX1 Is a Favorable Prognostic Biomarker as It Modulates 13-cis Retinoic Acid–Mediated Differentiation in Neuroblastoma

Free
Nilay Shah, Jianjun Wang, Julia Selich-Anderson, Garrett Graham, Hasan Siddiqui, Xin Li, Javed Khan, Jeffrey Toretsky
Journal: Clinical Cancer Research
Clin Cancer Res (2014) 20 (16): 4400–4412.
https://doi.org/10.1158/1078-0432.CCR-13-1486
Published: 13 August 2014
View articletitled, PBX1 Is a Favorable Prognostic Biomarker as It Modulates 13-cis Retinoic Acid–Mediated Differentiation in Neuroblastoma
Open the PDF for PBX1 Is a Favorable Prognostic Biomarker as It Modulates 13-cis Retinoic Acid–Mediated Differentiation in Neuroblastoma in another window
Includes: Supplementary data
Journal Articles

microRNA Profiling Identifies Cancer-Specific and Prognostic Signatures in Pediatric Malignancies

Free
Jun S. Wei, Peter Johansson, Qing-Rong Chen, Young K. Song, Steffen Durinck, Xinyu Wen, Adam T.C. Cheuk, Malcolm A. Smith, Peter Houghton, Christopher Morton, Javed Khan
Journal: Clinical Cancer Research
Clin Cancer Res (2009) 15 (17): 5560–5568.
https://doi.org/10.1158/1078-0432.CCR-08-3287
Published: 31 August 2009
View articletitled, microRNA Profiling Identifies Cancer-Specific and Prognostic Signatures in Pediatric Malignancies
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Includes: Supplementary data
Journal Articles

Whole Chromosome Alterations Predict Survival in High-Risk Neuroblastoma without MYCN Amplification

Free
Sven Bilke, Qing-Rong Chen, Jun S. Wei, Javed Khan
Journal: Clinical Cancer Research
Clin Cancer Res (2008) 14 (17): 5540–5547.
https://doi.org/10.1158/1078-0432.CCR-07-4461
Published: 02 September 2008
View articletitled, Whole Chromosome Alterations Predict Survival in High-Risk Neuroblastoma without MYCN Amplification
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Journal Articles

Molecular Characterization of the Pediatric Preclinical Testing Panel

Free
Geoffrey Neale, Xiaoping Su, Christopher L. Morton, Doris Phelps, Richard Gorlick, Richard B. Lock, C. Patrick Reynolds, John M. Maris, Henry S. Friedman, Jeffrey Dome, Joseph Khoury, Timothy J. Triche, Robert C. Seeger, Richard Gilbertson, Javed Khan, Malcolm A. Smith, Peter J. Houghton
Journal: Clinical Cancer Research
Clin Cancer Res (2008) 14 (14): 4572–4583.
https://doi.org/10.1158/1078-0432.CCR-07-5090
Published: 15 July 2008
View articletitled, Molecular Characterization of the Pediatric Preclinical Testing Panel
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Includes: Supplementary data
Journal Articles

High Skp2 Expression Characterizes High-Risk Neuroblastomas Independent of MYCN Status

Free
Frank Westermann, Kai-Oliver Henrich, Jun S. Wei, Werner Lutz, Matthias Fischer, Rainer König, Ruprecht Wiedemeyer, Volker Ehemann, Benedikt Brors, Karen Ernestus, Ivo Leuschner, Axel Benner, Javed Khan, Manfred Schwab
Journal: Clinical Cancer Research
Clin Cancer Res (2007) 13 (16): 4695–4703.
https://doi.org/10.1158/1078-0432.CCR-06-2818
Published: 15 August 2007
View articletitled, High Skp2 Expression Characterizes High-Risk Neuroblastomas Independent of MYCN Status
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Includes: Supplementary data
Journal Articles

Reduced Expression of CAMTA1 Correlates with Adverse Outcome in Neuroblastoma Patients

Free
Kai-Oliver Henrich, Matthias Fischer, Daniel Mertens, Axel Benner, Ruprecht Wiedemeyer, Benedikt Brors, André Oberthuer, Frank Berthold, Jun Stephen Wei, Javed Khan, Manfred Schwab, Frank Westermann
Journal: Clinical Cancer Research
Clin Cancer Res (2006) 12 (1): 131–138.
https://doi.org/10.1158/1078-0432.CCR-05-1431
Published: 05 January 2006
View articletitled, Reduced Expression of CAMTA1 Correlates with Adverse Outcome in Neuroblastoma Patients
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Journal Articles

Gene Expression Profiles Associated with Response to Chemotherapy in Epithelial Ovarian Cancers

Free
Amir A. Jazaeri, Christopher S. Awtrey, Gadisetti V.R. Chandramouli, Yao Eric Chuang, Javed Khan, Christos Sotiriou, Olga Aprelikova, Cindy J. Yee, Kristin K. Zorn, Michael J. Birrer, J. Carl Barrett, Jeff Boyd
Journal: Clinical Cancer Research
Clin Cancer Res (2005) 11 (17): 6300–6310.
https://doi.org/10.1158/1078-0432.CCR-04-2682
Published: 06 September 2005
View articletitled, Gene Expression Profiles Associated with Response to Chemotherapy in Epithelial Ovarian Cancers
Open the PDF for Gene Expression Profiles Associated with Response to Chemotherapy in Epithelial Ovarian Cancers in another window
Includes: Supplementary data