Trevor Pugh

Trevor Pugh

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Trevor Pugh

Trevor Pugh

Publications by authors named "Trevor Pugh"

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High efficiency error suppression for accurate detection of low-frequency variants.

Nucleic Acids Res 2019 Sep;47(15):e87

Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1093/nar/gkz474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6735726PMC
September 2019

Translational genomics of nasopharyngeal cancer.

Semin Cancer Biol 2019 Sep 12. Epub 2019 Sep 12.

Department of Anatomical and cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region. Electronic address:

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http://dx.doi.org/10.1016/j.semcancer.2019.09.006DOI Listing
September 2019

Early Initiation of Tocilizumab in Clinically Isolated Aortitis.

Cureus 2019 Apr 16;11(4):e4479. Epub 2019 Apr 16.

Rheumatology, University of Washington, Seattle, USA.

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http://dx.doi.org/10.7759/cureus.4479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6579327PMC
April 2019

Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data.

F1000Res 2019 15;8. Epub 2019 Mar 15.

Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, USA.

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http://dx.doi.org/10.12688/f1000research.18490.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6720041PMC
March 2019

Regulatory T Cells in Ovarian Cancer Are Characterized by a Highly Activated Phenotype Distinct from that in Melanoma.

Clin Cancer Res 2018 11 31;24(22):5685-5696. Epub 2018 Jul 31.

The Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1158/1078-0432.CCR-18-0554DOI Listing
November 2018

Patient-Derived Xenografts for Prognostication and Personalized Treatment for Head and Neck Squamous Cell Carcinoma.

Cell Rep 2018 10;25(5):1318-1331.e4

Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.10.004DOI Listing
October 2018

Prediction of acute myeloid leukaemia risk in healthy individuals.

Nature 2018 07 9;559(7714):400-404. Epub 2018 Jul 9.

Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/s41586-018-0317-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485381PMC
July 2018

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

PLoS Comput Biol 2018 03 28;14(3):e1006080. Epub 2018 Mar 28.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1006080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5891060PMC
March 2018

Circulating Tumour DNA for Detecting Minimal Residual Disease in Multiple Myeloma.

Authors:
Trevor J Pugh

Semin Hematol 2018 01 7;55(1):38-40. Epub 2018 Mar 7.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada. Electronic address:

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http://dx.doi.org/10.1053/j.seminhematol.2018.03.002DOI Listing
January 2018

Integration of Technical, Bioinformatic, and Variant Assessment Approaches in the Validation of a Targeted Next-Generation Sequencing Panel for Myeloid Malignancies.

Arch Pathol Lab Med 2017 Jun 9;141(6):759-775. Epub 2017 Mar 9.

From the Laboratory Medicine Program, Advanced Molecular Diagnostics Laboratory, Departments of Pathology and Genetics (Drs Thomas, Sukhai, Garg, Misyura, Stockley, and Kamel-Reid), the Princess Margaret Cancer Centre (Drs Thomas, Sukhai, Garg, Misyura, Pugh, Stockley, and Kamel-Reid and Ms Zhang), and High Performance Computing and Bioinformatics Services, Princess Margaret Genomics Centre (Dr Harbi and Mr Dolatshahi), University Health Network, Toronto, Ontario, Canada; and the Departments of Medical Biophysics (Drs Pugh and Kamel-Reid) and Laboratory Medicine and Pathobiology (Drs Stockley and Kamel-Reid), The University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.5858/arpa.2016-0547-RADOI Listing
June 2017

Somatic BRCA1/2 Recovery as a Resistance Mechanism After Exceptional Response to Poly (ADP-ribose) Polymerase Inhibition.

J Clin Oncol 2017 Apr 21;35(11):1240-1249. Epub 2017 Feb 21.

Stephanie Lheureux, Jeff P. Bruce, Julia V. Burnier, Katherine Karakasis, S.Y. Cindy Yang, Rene Quevedo, Tiantian Li, Mark Dowar, Valerie Bowering, Trevor J. Pugh, and Amit M. Oza, Princess Margaret Cancer Centre; Stephanie Lheureux, Patricia A. Shaw, Blaise A. Clarke, S.Y. Cindy Yang, Rene Quevedo, Trevor J. Pugh, and Amit M. Oza, University of Toronto; Patricia A. Shaw and Blaise A. Clarke, University Health Network, Toronto, Canada.

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http://dx.doi.org/10.1200/JCO.2016.71.3677DOI Listing
April 2017

An Anaplastic Lymphoma Kinase Immunohistochemistry-Negative but Fluorescence In Situ Hybridization-Positive Lung Adenocarcinoma Is Resistant to Crizotinib.

J Thorac Oncol 2016 12 6;11(12):2248-2252. Epub 2016 Sep 6.

University Health Network, Ontario Cancer Institute/Princess Margaret Cancer Centre, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.jtho.2016.08.139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5573599PMC
December 2016

VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data.

Genet Med 2016 07 17;18(7):712-9. Epub 2015 Dec 17.

Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/gim.2015.156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940431PMC
July 2016

Human Papillomavirus Genotype Association With Survival in Head and Neck Squamous Cell Carcinoma.

JAMA Oncol 2016 Jun;2(6):823-6

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada2Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1001/jamaoncol.2015.6587DOI Listing
June 2016

Next generation sequencing-based copy number analysis reveals low prevalence of deletions and duplications in 46 genes associated with genetic cardiomyopathies.

Mol Genet Genomic Med 2016 Mar 16;4(2):143-51. Epub 2015 Dec 16.

Laboratory for Molecular MedicinePartners HealthCare Personalized MedicineCambridgeMassachusetts; Department of PathologyMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts.

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http://dx.doi.org/10.1002/mgg3.187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4799872PMC
March 2016

Divergent clonal selection dominates medulloblastoma at recurrence.

Authors:
A Sorana Morrissy Livia Garzia David J H Shih Scott Zuyderduyn Xi Huang Patryk Skowron Marc Remke Florence M G Cavalli Vijay Ramaswamy Patricia E Lindsay Salomeh Jelveh Laura K Donovan Xin Wang Betty Luu Kory Zayne Yisu Li Chelsea Mayoh Nina Thiessen Eloi Mercier Karen L Mungall Yusanne Ma Kane Tse Thomas Zeng Karey Shumansky Andrew J L Roth Sohrab Shah Hamza Farooq Noriyuki Kijima Borja L Holgado John J Y Lee Stuart Matan-Lithwick Jessica Liu Stephen C Mack Alex Manno K A Michealraj Carolina Nor John Peacock Lei Qin Juri Reimand Adi Rolider Yuan Y Thompson Xiaochong Wu Trevor Pugh Adrian Ally Mikhail Bilenky Yaron S N Butterfield Rebecca Carlsen Young Cheng Eric Chuah Richard D Corbett Noreen Dhalla An He Darlene Lee Haiyan I Li William Long Michael Mayo Patrick Plettner Jenny Q Qian Jacqueline E Schein Angela Tam Tina Wong Inanc Birol Yongjun Zhao Claudia C Faria José Pimentel Sofia Nunes Tarek Shalaby Michael Grotzer Ian F Pollack Ronald L Hamilton Xiao-Nan Li Anne E Bendel Daniel W Fults Andrew W Walter Toshihiro Kumabe Teiji Tominaga V Peter Collins Yoon-Jae Cho Caitlin Hoffman David Lyden Jeffrey H Wisoff James H Garvin Duncan S Stearns Luca Massimi Ulrich Schüller Jaroslav Sterba Karel Zitterbart Stephanie Puget Olivier Ayrault Sandra E Dunn Daniela P C Tirapelli Carlos G Carlotti Helen Wheeler Andrew R Hallahan Wendy Ingram Tobey J MacDonald Jeffrey J Olson Erwin G Van Meir Ji-Yeoun Lee Kyu-Chang Wang Seung-Ki Kim Byung-Kyu Cho Torsten Pietsch Gudrun Fleischhack Stephan Tippelt Young Shin Ra Simon Bailey Janet C Lindsey Steven C Clifford Charles G Eberhart Michael K Cooper Roger J Packer Maura Massimino Maria Luisa Garre Ute Bartels Uri Tabori Cynthia E Hawkins Peter Dirks Eric Bouffet James T Rutka Robert J Wechsler-Reya William A Weiss Lara S Collier Adam J Dupuy Andrey Korshunov David T W Jones Marcel Kool Paul A Northcott Stefan M Pfister David A Largaespada Andrew J Mungall Richard A Moore Nada Jabado Gary D Bader Steven J M Jones David Malkin Marco A Marra Michael D Taylor

Nature 2016 Jan 13;529(7586):351-7. Epub 2016 Jan 13.

Developmental &Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.

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http://dx.doi.org/10.1038/nature16478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936195PMC
January 2016

Oncotator: cancer variant annotation tool.

Hum Mutat 2015 Apr 16;36(4):E2423-9. Epub 2015 Mar 16.

Cancer Program, Broad Institute, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.

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http://doi.wiley.com/10.1002/humu.22771
Publisher Site
http://dx.doi.org/10.1002/humu.22771DOI Listing
April 2015

Pugh et al. reply.

Nature 2015 Apr;520(7547):E12-4

1] Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Cancer Program, Broad Institute, Cambridge, Massachusetts, 02142, USA.

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http://dx.doi.org/10.1038/nature14266DOI Listing
April 2015

Comprehensive diagnostic testing for stereocilin: an approach for analyzing medically important genes with high homology.

J Mol Diagn 2014 Nov 23;16(6):639-47. Epub 2014 Aug 23.

Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts. Electronic address:

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http://dx.doi.org/10.1016/j.jmoldx.2014.06.003DOI Listing
November 2014

The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing.

Genet Med 2014 Aug 6;16(8):601-8. Epub 2014 Feb 6.

1] Laboratory for Molecular Medicine, Partners HealthCare Center for Personalized Molecular Medicine, Cambridge, Massachusetts, USA [2] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/gim.2013.204DOI Listing
August 2014

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition.

Cancer Cell 2014 Mar;25(3):393-405

Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.ccr.2014.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493053PMC
March 2014

Landscape of genomic alterations in cervical carcinomas.

Nature 2014 Feb 25;506(7488):371-5. Epub 2013 Dec 25.

1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142, USA [3] Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [4].

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http://dx.doi.org/10.1038/nature12881DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161954PMC
February 2014

Activation of the PD-1 pathway contributes to immune escape in EGFR-driven lung tumors.

Cancer Discov 2013 Dec 27;3(12):1355-63. Epub 2013 Sep 27.

Departments of 1Medicine and 2Medical Oncology and Cancer Vaccine Center, Dana-Farber Cancer Institute; 3Harvard Medical School; 4Ludwig Institute for Cancer Research; 5Department of Neurosurgery, Massachusetts General Hospital; 6Belfer Institute for Applied Cancer Science; 7Department of Pathology, Brigham and Women's Hospital, Boston; 8Broad Institute, Cambridge, Massachusetts; 9UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and 10Department of Molecular Pharmacology and Therapeutics, Oncology Institute, Loyola University, Chicago, Illinois; 11Department of Physiology, University of Valencia, Valencia, Spain.

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http://dx.doi.org/10.1158/2159-8290.CD-13-0310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864135PMC
December 2013

A comprehensive assay for CFTR mutational analysis using next-generation sequencing.

Clin Chem 2013 Oct 17;59(10):1481-8. Epub 2013 Jun 17.

Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH, and Dartmouth-Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH;

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http://dx.doi.org/10.1373/clinchem.2013.206466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570467PMC
October 2013

Dissecting the genomic complexity underlying medulloblastoma.

Nature 2012 Aug;488(7409):100-5

Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.

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http://dx.doi.org/10.1038/nature11284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3662966PMC
August 2012

Sequence variant discovery in DNA repair genes from radiosensitive and radiotolerant prostate brachytherapy patients.

Clin Cancer Res 2009 Aug 28;15(15):5008-16. Epub 2009 Jul 28.

Genome Sciences Centre, Provincial Prostate Brachytherapy Program, and Medical Biophysics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1158/1078-0432.CCR-08-3357DOI Listing
August 2009