Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

by Soroush Samadian, Jeff P Bruce, Trevor J Pugh
Published 2018-03-01

Elevation in viral entry genes and innate immunity compromise underlying increased infectivity and severity of COVID-19 in cancer patients

by Jennifer Yin Yee Kwan, Liang-Tzung Lin, Rachel Bell, Jeffrey P. Bruce, Christopher Richardson, Trevor J. Pugh, Fei-Fei Liu
Published 2021-02-01

Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data [version 2; peer review: 1 approved, 2 approved with reservations]

by J. Javier Diaz-Mejia, Elaine C. Meng, Alexander R. Pico, Sonya A. MacParland, Troy Ketela, Trevor J. Pugh, Gary D. Bader, John H. Morris
Published 2019-08-01

Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data [version 3; peer review: 2 approved, 1 approved with reservations]

by J. Javier Diaz-Mejia, Elaine C. Meng, Alexander R. Pico, Sonya A. MacParland, Troy Ketela, Trevor J. Pugh, Gary D. Bader, John H. Morris
Published 2019-10-01

The DEAD-box helicase DDX56 is a conserved stemness regulator in normal and cancer stem cells

by Michael Pryszlak, Mallory Wiggans, Xin Chen, Julia E. Jaramillo, Sarah E. Burns, Laura M. Richards, Trevor J. Pugh, David R. Kaplan, Xi Huang, Peter B. Dirks, Bret J. Pearson
Published 2021-03-01

Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates

by Olena Kis, Rayan Kaedbey, Signy Chow, Arnavaz Danesh, Mark Dowar, Tiantian Li, Zhihua Li, Jessica Liu, Mark Mansour, Esther Masih-Khan, Tong Zhang, Scott V. Bratman, Amit M. Oza, Suzanne Kamel-Reid, Suzanne Trudel, Trevor J. Pugh
Published 2017-05-01

Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor

by Rene Quevedo, Anna Spreafico, Jeff Bruce, Arnavaz Danesh, Samah El Ghamrasni, Amanda Giesler, Youstina Hanna, Cherry Have, Tiantian Li, S. Y. Cindy Yang, Tong Zhang, Sylvia L. Asa, Benjamin Haibe-Kains, Monika Krzyzanowska, Adam C. Smith, Simron Singh, Lillian L. Siu, Trevor J. Pugh
Published 2020-04-01

Therapeutic radiation for childhood cancer drives structural aberrations of NF2 in meningiomas

by Sameer Agnihotri, Suganth Suppiah, Peter D. Tonge, Shahrzad Jalali, Arnavaz Danesh, Jeffery P. Bruce, Yasin Mamatjan, George Klironomos, Lior Gonen, Karolyn Au, Sheila Mansouri, Sharin Karimi, Felix Sahm, Andreas von Deimling, Michael D. Taylor, Normand J. Laperriere, Trevor J. Pugh, Kenneth D. Aldape, Gelareh Zadeh
Published 2017-08-01

Landscape of genomic alterations in high-grade serous ovarian cancer from exceptional long- and short-term survivors

by S. Y. Cindy Yang, Stephanie Lheureux, Katherine Karakasis, Julia V. Burnier, Jeffery P. Bruce, Derek L. Clouthier, Arnavaz Danesh, Rene Quevedo, Mark Dowar, Youstina Hanna, Tiantian Li, Lin Lu, Wei Xu, Blaise A. Clarke, Pamela S. Ohashi, Patricia A. Shaw, Trevor J. Pugh, Amit M. Oza
Published 2018-10-01

Whole Exome Sequencing Identifies TSC1/TSC2 Biallelic Loss as the Primary and Sufficient Driver Event for Renal Angiomyolipoma Development.

by Krinio Giannikou, Izabela A Malinowska, Trevor J Pugh, Rachel Yan, Yuen-Yi Tseng, Coyin Oh, Jaegil Kim, Magdalena E Tyburczy, Yvonne Chekaluk, Yang Liu, Nicola Alesi, Geraldine A Finlay, Chin-Lee Wu, Sabina Signoretti, Matthew Meyerson, Gad Getz, Jesse S Boehm, Elizabeth P Henske, David J Kwiatkowski
Published 2016-08-01

Tumor genomic, transcriptomic, and immune profiling characterizes differential response to first‐line platinum chemotherapy in high grade serous ovarian cancer

by Johanne I. Weberpals, Trevor J. Pugh, Paola Marco‐Casanova, Glenwood D. Goss, Natalie Andrews Wright, Prisni Rath, Jonathon Torchia, Alexander Fortuna, Gemma N. Jones, Martine P. Roudier, Laurence Bernard, Bryan Lo, Dax Torti, Alberto Leon, Kayla Marsh, Darren Hodgson, Marc Duciaume, William J. Howat, Natalia Lukashchuk, Stanley E. Lazic, Doreen Whelan, Harmanjatinder S. Sekhon
Published 2021-05-01

Landscape mapping of shared antigenic epitopes and their cognate TCRs of tumor-infiltrating T lymphocytes in melanoma

by Kenji Murata, Munehide Nakatsugawa, Muhammed A Rahman, Linh T Nguyen, Douglas G Millar, David T Mulder, Kenji Sugata, Hiroshi Saijo, Yukiko Matsunaga, Yuki Kagoya, Tingxi Guo, Mark Anczurowski, Chung-Hsi Wang, Brian D Burt, Dalam Ly, Kayoko Saso, Alexandra Easson, David P Goldstein, Michael Reedijk, Danny Ghazarian, Trevor J Pugh, Marcus O Butler, Tak W Mak, Pamela S Ohashi, Naoto Hirano
Published 2020-04-01

Wnt activation as a therapeutic strategy in medulloblastoma

by Branavan Manoranjan, Chitra Venugopal, David Bakhshinyan, Ashley A. Adile, Laura Richards, Michelle M. Kameda-Smith, Owen Whitley, Anna Dvorkin-Gheva, Minomi Subapanditha, Neil Savage, Nazanin Tatari, Dillon McKenna, Blessing Bassey-Archibong, Neil Winegarden, Robin Hallett, John P. Provias, Blake Yarascavitch, Olufemi Ajani, Adam Fleming, Gary D. Bader, Trevor J. Pugh, Bradley W. Doble, Sheila K. Singh
Published 2020-08-01

Prospective observational study and serosurvey of SARS-CoV-2 infection in asymptomatic healthcare workers at a Canadian tertiary care center.

by Victor H Ferreira, Andrzej Chruscinski, Vathany Kulasingam, Trevor J Pugh, Tamara Dus, Brad Wouters, Amit Oza, Matthew Ierullo, Terrance Ku, Beata Majchrzak-Kita, Sonika T Humar, Ilona Bahinskaya, Natalia Pinzon, Jianhua Zhang, Lawrence E Heisler, Paul M Krzyzanowski, Bernard Lam, Ilinca M Lungu, Dorin Manase, Krista M Pace, Pouria Mashouri, Michael Brudno, Michael Garrels, Tony Mazzulli, Myron Cybulsky, Atul Humar, Deepali Kumar
Published 2021-01-01

Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer

by Stanley Zhou, James R. Hawley, Fraser Soares, Giacomo Grillo, Mona Teng, Seyed Ali Madani Tonekaboni, Junjie Tony Hua, Ken J. Kron, Parisa Mazrooei, Musaddeque Ahmed, Christopher Arlidge, Hwa Young Yun, Julie Livingstone, Vincent Huang, Takafumi N. Yamaguchi, Shadrielle M. G. Espiritu, Yanyun Zhu, Tesa M. Severson, Alex Murison, Sarina Cameron, Wilbert Zwart, Theodorus van der Kwast, Trevor J. Pugh, Michael Fraser, Paul C. Boutros, Robert G. Bristow, Housheng Hansen He, Mathieu Lupien
Published 2020-01-01

Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity

by S. Y. Cindy Yang, Scott C. Lien, Ben X. Wang, Derek L. Clouthier, Youstina Hanna, Iulia Cirlan, Kelsey Zhu, Jeffrey P. Bruce, Samah El Ghamrasni, Marco A. J. Iafolla, Marc Oliva, Aaron R. Hansen, Anna Spreafico, Philippe L. Bedard, Stephanie Lheureux, Albiruni Razak, Vanessa Speers, Hal K. Berman, Alexey Aleshin, Benjamin Haibe-Kains, David G. Brooks, Tracy L. McGaha, Marcus O. Butler, Scott V. Bratman, Pamela S. Ohashi, Lillian L. Siu, Trevor J. Pugh
Published 2021-08-01

An interim report on the investigator-initiated phase 2 study of pembrolizumab immunological response evaluation (INSPIRE)

by Derek L. Clouthier, Scott C. Lien, S. Y. Cindy Yang, Linh T. Nguyen, Venkata S. K. Manem, Diana Gray, Michael Ryczko, Albiruni R. A. Razak, Jeremy Lewin, Stephanie Lheureux, Ilaria Colombo, Philippe L. Bedard, David Cescon, Anna Spreafico, Marcus O. Butler, Aaron R. Hansen, Raymond W. Jang, Sangeet Ghai, Ilan Weinreb, Valentin Sotov, Ramy Gadalla, Babak Noamani, Mengdi Guo, Sawako Elston, Amanda Giesler, Sevan Hakgor, Haiyan Jiang, Tracy McGaha, David G. Brooks, Benjamin Haibe-Kains, Trevor J. Pugh, Pamela S. Ohashi, Lillian L. Siu
Published 2019-03-01

Molecular profiling of advanced solid tumors and patient outcomes with genotype-matched clinical trials: the Princess Margaret IMPACT/COMPACT trial

by Tracy L. Stockley, Amit M. Oza, Hal K. Berman, Natasha B. Leighl, Jennifer J. Knox, Frances A. Shepherd, Eric X. Chen, Monika K. Krzyzanowska, Neesha Dhani, Anthony M. Joshua, Ming-Sound Tsao, Stefano Serra, Blaise Clarke, Michael H. Roehrl, Tong Zhang, Mahadeo A. Sukhai, Nadia Califaretti, Mateya Trinkaus, Patricia Shaw, Theodorus van der Kwast, Lisa Wang, Carl Virtanen, Raymond H. Kim, Albiruni R. A. Razak, Aaron R. Hansen, Celeste Yu, Trevor J. Pugh, Suzanne Kamel-Reid, Lillian L. Siu, Philippe L. Bedard
Published 2016-10-01

Whole-genome profiling of nasopharyngeal carcinoma reveals viral-host co-operation in inflammatory NF-κB activation and immune escape

by Jeff P. Bruce, Ka-Fai To, Vivian W. Y. Lui, Grace T. Y. Chung, Yuk-Yu Chan, Chi Man Tsang, Kevin Y. Yip, Brigette B. Y. Ma, John K. S. Woo, Edwin P. Hui, Michael K. F. Mak, Sau-Dan Lee, Chit Chow, Sharmila Velapasamy, Yvonne Y. Y. Or, Pui Kei Siu, Samah El Ghamrasni, Stephenie Prokopec, Man Wu, Johnny S. H. Kwan, Yuchen Liu, Jason Y. K. Chan, C. Andrew van Hasselt, Lawrence S. Young, Christopher W. Dawson, Ian C. Paterson, Lee-Fah Yap, Sai-Wah Tsao, Fei-Fei Liu, Anthony T. C. Chan, Trevor J. Pugh, Kwok-Wai Lo
Published 2021-07-01

PRMT5 inhibition disrupts splicing and stemness in glioblastoma

by Patty Sachamitr, Jolene C. Ho, Felipe E. Ciamponi, Wail Ba-Alawi, Fiona J. Coutinho, Paul Guilhamon, Michelle M. Kushida, Florence M. G. Cavalli, Lilian Lee, Naghmeh Rastegar, Victoria Vu, María Sánchez-Osuna, Jasmin Coulombe-Huntington, Evgeny Kanshin, Heather Whetstone, Mathieu Durand, Philippe Thibault, Kirsten Hart, Maria Mangos, Joseph Veyhl, Wenjun Chen, Nhat Tran, Bang-Chi Duong, Ahmed M. Aman, Xinghui Che, Xiaoyang Lan, Owen Whitley, Olga Zaslaver, Dalia Barsyte-Lovejoy, Laura M. Richards, Ian Restall, Amy Caudy, Hannes L. Röst, Zahid Quyoom Bonday, Mark Bernstein, Sunit Das, Michael D. Cusimano, Julian Spears, Gary D. Bader, Trevor J. Pugh, Mike Tyers, Mathieu Lupien, Benjamin Haibe-Kains, H. Artee Luchman, Samuel Weiss, Katlin B. Massirer, Panagiotis Prinos, Cheryl H. Arrowsmith, Peter B. Dirks
Published 2021-02-01