The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies

Autor: Basile Tessier‐Cloutier, Jasleen K Grewal, Martin R Jones, Erin Pleasance, Yaoqing Shen, Ellen Cai, Chris Dunham, Lynn Hoang, Basil Horst, David G Huntsman, Diana Ionescu, Anthony N Karnezis, Anna F Lee, Cheng Han Lee, Tae Hoon Lee, David DW Twa, Andrew J Mungall, Karen Mungall, Julia R Naso, Tony Ng, David F Schaeffer, Brandon S Sheffield, Brian Skinnider, Tyler Smith, Laura Williamson, Ellia Zhong, Dean A Regier, Janessa Laskin, Marco A Marra, C Blake Gilks, Steven JM Jones, Stephen Yip

Publikováno v: The Journal of Pathology: Clinical Research, Vol 8, Iss 4, Pp 395-407 (2022)

Abstract In this study, we evaluate the impact of whole genome and transcriptome analysis (WGTA) on predictive molecular profiling and histologic diagnosis in a cohort of advanced malignancies. WGTA was used to generate reports including molecular al

Externí odkaz: https://doaj.org/article/a901dba17e554a43930f20607375541d

The Precision Toxicology initiative

Autor: François Busquet, Jeanne Laperrouze, Katica Jankovic, Tamara Krsmanovic, Tomasz Ignasiak, Benedetta Leoni, Gordana Apic, Giovanni Asole, Roderic Guigó, Paolo Marangio, Emilio Palumbo, Silvia Perez-Lluch, Valentin Wucher, Anna Hendrika Vlot, Robert Anholt, Trudy Mackay, Beate I. Escher, Nico Grasse, Julia Huchthausen, Riccardo Massei, Thorsten Reemtsma, Stefan Scholz, Gerrit Schüürmann, Maria Bondesson, Peter Cherbas, Jonathan H. Freedman, Stephen Glaholt, Jessica Holsopple, Stephen C. Jacobson, Thomas Kaufman, Ellen Popodi, Joseph J. Shaw, Shannon Smoot, Jason M. Tennessen, Gary Churchill, Christina Cramer von Clausbruch, Thomas Dickmeis, Gaëlle Hayot, Giuseppina Pace, Ravindra Peravali, Carsten Weiss, Nadezda Cistjakova, Xin Liu, Andis Slaitas, James (Ben) Brown, Rafael Ayerbe, Joan Cabellos, Elena Cerro-Gálvez, María Diez-Ortiz, Verónica González, Rubén Martínez, Patricia Solórzano Vives, Rosemary Barnett, Thomas Lawson, Robert G. Lee, Elena Sostare, Mark Viant, Roland Grafström, Vesa Hongisto, Pekka Kohonen, Konrad Patyra, Pradeep Kumar Bhaskar, Marcial Garmendia-Cedillos, Ibraheem Farooq, Brian Oliver, Tom Pohida, Ghadi Salem, Daniel Jacobson, Elisabeth Andrews, Marianne Barnard, Aleksandra Čavoški, Anurag Chaturvedi, John K. Colbourne, David J.T. Epps, Laura Holden, Martin R. Jones, Xiaojing Li, Ferenc Müller, Agata Ormanin-Lewandowska, Luisa Orsini, Ruth Roberts, Ralf J.M. Weber, Jiarui Zhou, Mu-En Chung, Juan Carlos Gonzalez Sanchez, Gaurav D. Diwan, Gurdeep Singh, Uwe Strähle, Robert B. Russell, Dominique Batista, Susanna-Assunta Sansone, Philippe Rocca-Serra, David Du Pasquier, Gregory Lemkine, Barbara Robin-Duchesne, Andrew Tindall

The goal of PrecisionTox is to overcome conceptual barriers to replacing traditional mammalian chemical safety testing by accelerating the discovery of evolutionarily conserved toxicity pathways that are shared by descent among humans and more distan

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::876b7659dcbf87711644cfc5deccdefc
https://ora.ox.ac.uk/objects/uuid:bed21c1b-b26c-4b6d-aea0-dce1e848c810

Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes

Autor: Cameron J. Grisdale, Scott D. Brown, Kevin Y. Fan, Wei Zhang, Caralyn Reisle, Zoltan Bozoky, Robert A. Holt, Tariq Vira, Richard Corbett, Melika Bonakdar, My Linh Thibodeau, Kathleen Wee, Dean Cheng, Luka Culibrk, Marcus Carreira, David F. Schaeffer, Deirdre Weymann, Anna V. Tinker, Eric Y. Zhao, Michael K.C. Lee, Karen A. Gelmon, Karen Mungall, Richard A. Moore, Dean A. Regier, Daniel J. Renouf, Zusheng Zong, Reva Shenwai, Stephen Chia, Jahanshah Ashkani, Ana Fisic, Stephen Yip, Darryl D’Souza, Yussanne Ma, Daniel MacMillan, Erin Pleasance, Steve Bilobram, Alexandra Fok, Amir Muhammadzadeh, Jean-Michel Lavoie, Martin R. Jones, Hillary Pearson, Simon K. Chan, Balvir Deol, Steven J.M. Jones, Andrew J. Mungall, Mya Warren, Gregory A. Taylor, Elisa Majounie, Harwood H. Kwan, Eric Chuah, Howard John Lim, Sara Sadeghi, Dustin Bleile, Emma Titmuss, Reanne Bowlby, Anna Davies, Laura Williamson, Jessica Nelson, Caleb Choo, Jasleen K. Grewal, Katherine Dixon, Yongjun Zhao, Shehara Mendis, Yaoqing Shen, Janessa Laskin, Joanna M. Karasinska, Veronika Csizmok, Tina Wong, Sophie Sun, Kasmintan A. Schrader, Marco A. Marra

Publikováno v: Nature Cancer. 1:452-468

Advanced and metastatic tumors with complex treatment histories drive cancer mortality. Here we describe the POG570 cohort, a comprehensive whole-genome, transcriptome and clinical dataset, amenable for exploration of the impacts of therapies on geno

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::e551cd8d2e575de2b268eb76510c5700
https://doi.org/10.1038/s43018-020-0050-6

NRG1 Gene Fusions Are Recurrent, Clinically Actionable Gene Rearrangements in KRAS Wild-Type Pancreatic Ductal Adenocarcinoma

Autor: Janessa Laskin, Sharlene Gill, Jennifer J. Knox, David F. Schaeffer, Martin R. Jones, Marco A. Marra, Howard John Lim, Daniel J. Renouf, James T. Topham, Steven Gallinger, Hui-Li Wong, Karen Mungall, Julie Ho, Richard A. Moore, Angela Goytain, Malcolm J. Moore, Steven J.M. Jones, Yussanne Ma, Andrew J. Mungall, Laura Williamson, Wei Zhang, Robert E. Denroche, Yaoquing Shen, Michael K.C. Lee, Erin Pleasance, Sara Sadeghi, Gun-Ho Jang, Stephen Yip, Joanna M. Karasinska, Carolyn Reisle, Tony Ng, John Paul McGhie

Publikováno v: Clinical Cancer Research. 25:4674-4681

Purpose: Gene fusions involving neuregulin 1 (NRG1) have been noted in multiple cancer types and have potential therapeutic implications. Although varying results have been reported in other cancer types, the efficacy of the HER-family kinase inhibit

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::19debca6775c2b09129419b58accd2ee
https://doi.org/10.1158/1078-0432.ccr-19-0191

Fluorouracil sensitivity in a head and neck squamous cell carcinoma with a somatic DPYD structural variant

Autor: Cheryl Ho, Kathleen Wee, Laura Williamson, Daniel J. Renouf, Stephen Yip, Erin Pleasance, Martin R. Jones, Marco A. Marra, Elisa Majounie, Steven J.M. Jones, Janessa Laskin, Howard John Lim

Publikováno v: Cold Spring Harbor Molecular Case Studies

Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers worldwide and represents a heterogeneous group of tumors, the majority of which are treated with a combination of surgery, radiation, and chemotherapy. Fluoropyrimidine (

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce5846a69f9b150ad5430fa120ecdec1
http://europepmc.org/articles/PMC6996515