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Journal Articles

Abstract A044: Immune profiling tools for adult and pediatric cancer: From whole genome and transcriptome sequencing to immunotherapy clinical trial design

Yaoqing Shen, Chelsea Mayoh, Kathleen Wee, Erin Pleasance, Emma Titmuss, Richard Corbett, Laura Williamson, Zakhar Krekhno, Arash Nabbi, Raoul Santiago, Stephanie Bianco, Scott Davidson, Adam Shlien, Kyoko E Yuki, Denise Connolly, Daniel Morgenstern, Melika Bonakdar, Greg Taylor, Veronika Csizmok, Cameron J Grisdale, Melissa McConechy, Jing Xu, John H Dupuis, Karen Mungall, Eric Chuah, Andrew Mungall, Jessica Nelson, Stephen Yip, Sophie Sun, Howard Lim, Daniel Renouf, Janessa Laskin, Sarah Cohen-Gogo, Shahrad R Rassekh, Rebecca J Deyell, Marco A Marra, Paul G Ekert, Steven JM Jones
Journal: Cancer Research
Cancer Res (2025) 85 (5_Supplement): A044.
https://doi.org/10.1158/1538-7445.GENFUNC25-A044
Published: 11 March 2025
View article titled, Abstract A044: Immune profiling tools for adult and pediatric cancer: From whole genome and transcriptome sequencing to immunotherapy clinical trial design
Journal Articles

Abstract A007 DNA damage response deficiency enhances neuroblastoma progression and sensitivity to combination PARP and ATR inhibition

Madeline N. Hayes, Sarah Cohen-Gogo, Lynn Kee, Mehdi Layeghifard, Ivette Valencia-Sama, Anisha Rajaselvam, David Kaplan, Anita Villani, Adam Shlien, Daniel A. Morgenstern, Meredith S Irwin
Journal: Cancer Research
Cancer Res (2024) 84 (17_Supplement): A007.
https://doi.org/10.1158/1538-7445.PEDIATRIC24-A007
Published: 05 September 2024
View article titled, Abstract A007 DNA damage response deficiency enhances neuroblastoma progression and sensitivity to combination PARP and ATR inhibition
Journal Articles

Abstract A034 LIBERTY: LIquid Biopsy for rElapsed/RefracTorY neuroblastoma - a pilot study of characterization of circulating tumor DNA alterations in patients with relapsed and refractory neuroblastoma using a clinically validated liquid biopsy platform

Sarah Cohen-Gogo, Gabriel Revon-Riviere, Jathishinie Jegathisawaran, Adam Shlien, Anita Villani, Meredith Irwin, Daniel A. Morgenstern
Journal: Cancer Research
Cancer Res (2024) 84 (17_Supplement): A034.
https://doi.org/10.1158/1538-7445.PEDIATRIC24-A034
Published: 05 September 2024
View article titled, Abstract A034 LIBERTY: LIquid Biopsy for rElapsed/RefracTorY neuroblastoma - a pilot study of characterization of circulating tumor DNA alterations in patients with relapsed and refractory neuroblastoma using a clinically validated liquid biopsy platform
Journal Articles

Abstract A035 Characterization of circulating tumor DNA in a pediatric oncology cohort and implementation into the SickKids Cancer Sequencing (KiCS) precision oncology program

Sarah Cohen-Gogo, Taegi Choi, Ryan Ripsman, Matt Hudson, Sandy Fong, Reem Khan, Rosemarie E. Venier, Tristan Charlinski, Anita Villani, David Malkin, Adam Shlien
Journal: Cancer Research
Cancer Res (2024) 84 (17_Supplement): A035.
https://doi.org/10.1158/1538-7445.PEDIATRIC24-A035
Published: 05 September 2024
View article titled, Abstract A035 Characterization of circulating tumor DNA in a pediatric oncology cohort and implementation into the SickKids Cancer Sequencing (KiCS) precision oncology program
Journal Articles

Abstract B001: Timing the development of chemoresistance in relapsed pediatric cancer with mutational signatures

Sasha Blay, Mehdi Layeghifard, Scott Davidson, David Chen, Astra Schwertschkow, Vijay Ramaswamy, Michael Taylor, Elli Papaemmanuil, Anita Villani, David Malkin, Ludmil Alexandrov, Mark Cowley, Adam Shlien
Journal: Cancer Research
Cancer Res (2024) 84 (17_Supplement): B001.
https://doi.org/10.1158/1538-7445.PEDIATRIC24-B001
Published: 05 September 2024
View article titled, Abstract B001: Timing the development of chemoresistance in relapsed pediatric cancer with mutational signatures
Journal Articles

Abstract B015: Transcriptome-based assessment of immune infiltration for molecular selection of pediatric patients with solid tumors for combination immune checkpoint inhibitor therapy

Yaoqing Shen, Chelsea Mayoh, Arash Nabbi, Raoul Santiago, Stephanie Bianco, Iain R. Bancarz, Laura Williamson, Richard Corbett, Zakhar Krekhno, Scott Davidson, Alexander Fortuna, Kyoko E. Yuki, Denise Connolly, Daniel Morgenstern, Paul G. Ekert, Adam Shlien, Steven J.M. Jones, Rebecca J. Deyell, Sarah Cohen-Gogo
Journal: Cancer Research
Cancer Res (2024) 84 (17_Supplement): B015.
https://doi.org/10.1158/1538-7445.PEDIATRIC24-B015
Published: 05 September 2024
View article titled, Abstract B015: Transcriptome-based assessment of immune infiltration for molecular selection of pediatric patients with solid tumors for combination immune checkpoint inhibitor therapy
Journal Articles

Abstract B026: Infant ALL without KMT2A rearrangements harbor clinically relevant alterations and share common origins with childhood ALL

Matthew Zatzman, Jennifer Seelisch, Federico Comitani, Fabio Fuligni, Scott Davidson, Kyoko E. Yuki, Lisa-Monique Edwards, Ledia Brunga, Erin Guest, Stephen P. Hunger, Mignon L. Loh, Elizabeth A. Raetz, John Chen, Jack Bartram, Johann K. Hitzler, Patrick A. Brown, Sumit Gupta, Adam Shlien
Journal: Cancer Research
Cancer Res (2024) 84 (17_Supplement): B026.
https://doi.org/10.1158/1538-7445.PEDIATRIC24-B026
Published: 05 September 2024
View article titled, Abstract B026: Infant ALL without KMT2A rearrangements harbor clinically relevant alterations and share common origins with childhood ALL
Journal Articles

Abstract B070: Chemotherapy is a major mutagen in relapsed childhood cancer

Mehdi Layeghifard, Nicholas Light, Erik Bergstrom, Marcos Diaz Gay, Mathepan J. Mahendralingam, Sasha Blay, Scott Davidson, Pedro L. Ballester, Rawan Hammad, Noemi Fuentes Bolanos, Shimaa Nassif, Nirav H. Thacker, Chelsea Mayoh, David Malkin, Elli Papaemmanuil, Mark J. Cowley, Anita Villani, Ludmil B. Alexandrov, Adam Shlien
Journal: Cancer Research
Cancer Res (2024) 84 (17_Supplement): B070.
https://doi.org/10.1158/1538-7445.PEDIATRIC24-B070
Published: 05 September 2024
View article titled, Abstract B070: Chemotherapy is a major mutagen in relapsed childhood cancer
Journal Articles

Abstract B034: A transcriptional atlas provides a universal diagnostic platform for mesenchymal tumors and validation of preclinical models

Joshua O. Nash, Pedro L. Ballestar, Scott Davidson, Astra Schwertschkow, Yael Babichev, Jodi Lees, Noa Alon, Nalan Gokgoz, Stephen M. Yu, Kyoko Yuki, Miranda Lorenti, Zhanqin Liu, Alaina McGoey, Famida Spatare, Bernard Castro, Kim Tsoi, Hagit Peretz-Soroka, Jack Brzezinski, Anita Villani, Albiruni Razaq, Abha Gupta, Elizabeth Demicco, Joanna Przybyl, Matt van de Rijn, Livia Garzia, Jay Wunder, Irene L. Andrulis, David Malkin, Rose Chami, Brendan C. Dickson, Rebecca A. Gladdy, Adam Shlien
Journal: Cancer Research
Cancer Res (2024) 84 (17_Supplement): B034.
https://doi.org/10.1158/1538-7445.PEDIATRIC24-B034
Published: 05 September 2024
View article titled, Abstract B034: A transcriptional atlas provides a universal diagnostic platform for mesenchymal tumors and validation of preclinical models
Journal Articles

Abstract 149: Modeling patient-specific CHEK2 genetic variants associated with high-risk neuroblastoma

Xueting Xiong, Sarah Cohen-Gogo, Anita Villani, Adam Shlien, Meredith S. Irwin, Madeline Hayes
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 149.
https://doi.org/10.1158/1538-7445.AM2024-149
Published: 22 March 2024
View article titled, Abstract 149: Modeling patient-specific <em>CHEK2</em> genetic variants associated with high-risk neuroblastoma
Journal Articles

Abstract 5466: In vivo characterization of neuroblastoma intratumoral heterogeneity

Willow R. Squires, Alex Weiss, Sarah Cohen-Gogo, Adam Shlien, David Kaplan, Meredith S. Irwin, Madeline N. Hayes
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 5466.
https://doi.org/10.1158/1538-7445.AM2024-5466
Published: 22 March 2024
View article titled, Abstract 5466: <em>In vivo</em> characterization of neuroblastoma intratumoral heterogeneity
Journal Articles

Abstract 3951: Timing the development of chemoresistance in relapsed pediatric cancer

Sasha Blay, Mehdi Layeghifard, Scott Davidson, David Chen, Astra Schwertschkow, Vijay Ramaswamy, Michael Taylor, Elli Papaemmanuil, Anita Villani, David Malkin, Ludmil Alexandrov, Mark Cowley, Adam Shlien
Journal: Cancer Research
Cancer Res (2024) 84 (6_Supplement): 3951.
https://doi.org/10.1158/1538-7445.AM2024-3951
Published: 22 March 2024
View article titled, Abstract 3951: Timing the development of chemoresistance in relapsed pediatric cancer
Journal Articles

The BRD4–NUT Fusion Alone Drives Malignant Transformation of NUT Carcinoma

R. Taylor Durall, Julianna Huang, Luke Wojenski, Yeying Huang, Prafulla C. Gokhale, Brittaney A. Leeper, Joshua O. Nash, Pedro L. Ballester, Scott Davidson, Adam Shlien, Emmanuel Sotirakis, Fabien Bertaux, Vincent Dubus, Jia Luo, Catherine J. Wu, Derin B. Keskin, Kyle P. Eagen, Geoffrey I. Shapiro, Christopher A. French
Journal: Cancer Research
Cancer Res (2023) 83 (23): 3846–3860.
https://doi.org/10.1158/0008-5472.CAN-23-2545
Published: 01 December 2023
View article titled, The BRD4–NUT Fusion Alone Drives Malignant Transformation of NUT Carcinoma
Open the PDF for The BRD4–NUT Fusion Alone Drives Malignant Transformation of NUT Carcinoma in another window
Includes: Supplementary data
Journal Articles

Abstract 6545: Investigating secondary findings in a pediatric cancer cohort: preliminary findings

Safa Majeed, Stephenie Prokopec, Brianne Laverty, Vallijah Subasri, Michael Taylor, Yvonne Bombard, Trevor Pugh, Adam Shlien, Anita Villani, David Malkin
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 6545.
https://doi.org/10.1158/1538-7445.AM2023-6545
Published: 04 April 2023
View article titled, Abstract 6545: Investigating secondary findings in a pediatric cancer cohort: preliminary findings
Journal Articles

Abstract 4509: A pan-Canadian precision oncology program for children, adolescents and young adults with hard-to-cure cancer: The PRecision Oncology For Young peopLE (PROFYLE) Program

Stephanie A. Grover, Lesleigh Abbott, Jason N. Berman, Guillaume Bourque, Jennifer A. Chan, Avram E. Denburg, Rebecca J. Deyell, Conrad V. Fernandez, Cynthia Hawkins, Jan-Willem Henning, Meredith S. Irwin, Nada Jabado, Steven J. Jones, Philipp F. Lange, Paul Moorehead, Michael F. Moran, Daniel A. Morgenstern, Sapna Oberoi, Antonia Palmer, Shahrad R. Rassekh, Donna L. Senger, Adam Shlien, Daniel Sinnett, Caron Strahlendorf, Patrick J. Sullivan, Michael D. Taylor, Suzanne Vercauteren, Anita Villani, Stephanie Villeneuve, James A. Whitlock, David Malkin, on behalf of the PROFYLE Consortium
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 4509.
https://doi.org/10.1158/1538-7445.AM2023-4509
Published: 04 April 2023
View article titled, Abstract 4509: A pan-Canadian precision oncology program for children, adolescents and young adults with hard-to-cure cancer: The PRecision Oncology For Young peopLE (PROFYLE) Program
Journal Articles

Abstract 53: Zebrafish tp53 mutants recapitulate Li-Fraumeni syndrome phenotypes and provide a preclinical platform for evaluating tumor preventive compounds

Kim Kobar, Erin Burnley, Lissandra Tuzi, Craig Midgen, Adam Shlien, David Malkin, Sergey V. Prykhozhij, Jason N. Berman
Journal: Cancer Research
Cancer Res (2023) 83 (7_Supplement): 53.
https://doi.org/10.1158/1538-7445.AM2023-53
Published: 04 April 2023
View article titled, Abstract 53: Zebrafish <em>tp53</em> mutants recapitulate Li-Fraumeni syndrome phenotypes and provide a preclinical platform for evaluating tumor preventive compounds
Journal Articles

Abstract 5224: The PRecision Oncology For Young peopLE (PROFYLE) Program: A national precision oncology program for children, adolescents and young adults with hard-to-cure cancer in Canada

Stephanie A. Grover, Lesleigh Abbott, Jason N. Berman, Jennifer A. Chan, Avram E. Denburg, Rebecca J. Deyell, Conrad V. Fernandez, Cynthia Hawkins, Jan-Willem Henning, Meredith S. Irwin, Nada Jabado, Steven J. Jones, Philipp F. Lange, Michael F. Moran, Daniel A. Morgenstern, Antonia Palmer, Shahrad R. Rassekh, Donna L. Senger, Adam Shlien, Daniel Sinnett, Caron Strahlendorf, Patrick J. Sullivan, Michael D. Taylor, Suzanne Vercauteren, Anita Villani, James A. Whitlock, David Malkin, on behalf of the Terry Fox PROFYLE Consortium
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 5224.
https://doi.org/10.1158/1538-7445.AM2022-5224
Published: 15 June 2022
View article titled, Abstract 5224: The PRecision Oncology For Young peopLE (PROFYLE) Program: A national precision oncology program for children, adolescents and young adults with hard-to-cure cancer in Canada
Journal Articles

Abstract 2021: Wilms tumor and pure erythroid leukemia arising from the same clone in an adolescent

Anita Villani, Winnie Lo, Yisu Li, Mohamed Abdelhaleem, Mary Shago, Federico Comitani, My Linh Thibodeau, Sarah Alexander, Uri Tabori, David Malkin, Adam Shlien, Jack Brzezinski
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): 2021.
https://doi.org/10.1158/1538-7445.AM2022-2021
Published: 15 June 2022
View article titled, Abstract 2021: Wilms tumor and pure erythroid leukemia arising from the same clone in an adolescent
Journal Articles

Abstract LB177: Widespread hypertranscription in aggressive human cancer

Matthew Zatzman, Fabio Fuligni, Ryan Ripsman, Tannu Suwal, Lisa-Monique Edward, Rob Denroche, Gun Ho Jang, Faiyaz Notta, Steven Gallinger, Saravana P. Selvanathan, Jeffrey Toretsky, Matthew D. Hellmann, Uri Tabori, Annie Huang, Adam Shlien
Journal: Cancer Research
Cancer Res (2022) 82 (12_Supplement): LB177.
https://doi.org/10.1158/1538-7445.AM2022-LB177
Published: 15 June 2022
View article titled, Abstract LB177: Widespread hypertranscription in aggressive human cancer
Journal Articles

Diverse Oncogenic Fusions and Distinct Gene Expression Patterns Define the Genomic Landscape of Pediatric Papillary Thyroid Carcinoma

Ana Stosic, Fabio Fuligni, Nathaniel D. Anderson, Scott Davidson, Richard de Borja, Meryl Acker, Vito Forte, Paolo Campisi, Evan J. Propst, Nikolaus E. Wolter, Rose Chami, Ozgur Mete, David Malkin, Adam Shlien, Jonathan D. Wasserman
Journal: Cancer Research
Cancer Res (2021) 81 (22): 5625–5637.
https://doi.org/10.1158/0008-5472.CAN-21-0761
Published: 15 November 2021
View article titled, Diverse Oncogenic Fusions and Distinct Gene Expression Patterns Define the Genomic Landscape of Pediatric Papillary Thyroid Carcinoma
Open the PDF for Diverse Oncogenic Fusions and Distinct Gene Expression Patterns Define the Genomic Landscape of Pediatric Papillary Thyroid Carcinoma in another window
Includes: Supplementary data