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JOURNAL ARTICLE
Simon Haile, Richard D Corbett, Veronique G LeBlanc, Lisa Wei, Stephen Pleasance, Steve Bilobram, Ka Ming Nip, Kirstin Brown, Eva Trinh, Jillian Smith, Diane L Trinh, Miruna Bala, Eric Chuah, Robin J N Coope, Richard A Moore, Andrew J Mungall, Karen L Mungall, Yongjun Zhao, Martin Hirst, Samuel Aparicio, Inanc Birol, Steven J M Jones, Marco A Marra
RNA sequencing (RNAseq) has been widely used to generate bulk gene expression measurements collected from pools of cells. Only relatively recently have single-cell RNAseq (scRNAseq) methods provided opportunities for gene expression analyses at the single-cell level, allowing researchers to study heterogeneous mixtures of cells at unprecedented resolution. Tumors tend to be composed of heterogeneous cellular mixtures and are frequently the subjects of such analyses. Extensive method developments have led to several protocols for scRNAseq but, owing to the small amounts of RNA in single cells, technical constraints have required compromises...
2021: Frontiers in Genetics
#22
JOURNAL ARTICLE
T Roderick Docking, Jeremy D K Parker, Martin Jädersten, Gerben Duns, Linda Chang, Jihong Jiang, Jessica A Pilsworth, Lucas A Swanson, Simon K Chan, Readman Chiu, Ka Ming Nip, Samantha Mar, Angela Mo, Xuan Wang, Sergio Martinez-Høyer, Ryan J Stubbins, Karen L Mungall, Andrew J Mungall, Richard A Moore, Steven J M Jones, İnanç Birol, Marco A Marra, Donna Hogge, Aly Karsan
As more clinically-relevant genomic features of myeloid malignancies are revealed, it has become clear that targeted clinical genetic testing is inadequate for risk stratification. Here, we develop and validate a clinical transcriptome-based assay for stratification of acute myeloid leukemia (AML). Comparison of ribonucleic acid sequencing (RNA-Seq) to whole genome and exome sequencing reveals that a standalone RNA-Seq assay offers the greatest diagnostic return, enabling identification of expressed gene fusions, single nucleotide and short insertion/deletion variants, and whole-transcriptome expression information...
April 30, 2021: Nature Communications
#23
Justin T Reese, Ben Coleman, Lauren Chan, Hannah Blau, Tiffany J Callahan, Luca Cappelletti, Tommaso Fontana, Katie Rebecca Bradwell, Nomi L Harris, Elena Casiraghi, Giorgio Valentini, Guy Karlebach, Rachel Deer, Julie A McMurry, Melissa A Haendel, Christopher G Chute, Emily Pfaff, Richard Moffitt, Heidi Spratt, Jasvinder Singh, Christopher J Mungall, Andrew E Williams, Peter N Robinson
BACKGROUND: Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly used to reduce pain, fever, and inflammation but have been associated with complications in community-acquired pneumonia. Observations shortly after the start of the COVID-19 pandemic in 2020 suggested that ibuprofen was associated with an increased risk of adverse events in COVID-19 patients, but subsequent observational studies failed to demonstrate increased risk and in one case showed reduced risk associated with NSAID use...
December 22, 2021: medRxiv
#24
JOURNAL ARTICLE
Patryk Skowron, Hamza Farooq, Florence M G Cavalli, A Sorana Morrissy, Michelle Ly, Liam D Hendrikse, Evan Y Wang, Haig Djambazian, Helen Zhu, Karen L Mungall, Quang M Trinh, Tina Zheng, Shizhong Dai, Ana S Guerreiro Stucklin, Maria C Vladoiu, Vernon Fong, Borja L Holgado, Carolina Nor, Xiaochong Wu, Diala Abd-Rabbo, Pierre Bérubé, Yu Chang Wang, Betty Luu, Raul A Suarez, Avesta Rastan, Aaron H Gillmor, John J Y Lee, Xiao Yun Zhang, Craig Daniels, Peter Dirks, David Malkin, Eric Bouffet, Uri Tabori, James Loukides, François P Doz, Franck Bourdeaut, Olivier O Delattre, Julien Masliah-Planchon, Olivier Ayrault, Seung-Ki Kim, David Meyronet, Wieslawa A Grajkowska, Carlos G Carlotti, Carmen de Torres, Jaume Mora, Charles G Eberhart, Erwin G Van Meir, Toshihiro Kumabe, Pim J French, Johan M Kros, Nada Jabado, Boleslaw Lach, Ian F Pollack, Ronald L Hamilton, Amulya A Nageswara Rao, Caterina Giannini, James M Olson, László Bognár, Almos Klekner, Karel Zitterbart, Joanna J Phillips, Reid C Thompson, Michael K Cooper, Joshua B Rubin, Linda M Liau, Miklós Garami, Peter Hauser, Kay Ka Wai Li, Ho-Keung Ng, Wai Sang Poon, G Yancey Gillespie, Jennifer A Chan, Shin Jung, Roger E McLendon, Eric M Thompson, David Zagzag, Rajeev Vibhakar, Young Shin Ra, Maria Luisa Garre, Ulrich Schüller, Tomoko Shofuda, Claudia C Faria, Enrique López-Aguilar, Gelareh Zadeh, Chi-Chung Hui, Vijay Ramaswamy, Swneke D Bailey, Steven J Jones, Andrew J Mungall, Richard A Moore, John A Calarco, Lincoln D Stein, Gary D Bader, Jüri Reimand, Jiannis Ragoussis, William A Weiss, Marco A Marra, Hiromichi Suzuki, Michael D Taylor
Sonic hedgehog medulloblastoma encompasses a clinically and molecularly diverse group of cancers of the developing central nervous system. Here, we use unbiased sequencing of the transcriptome across a large cohort of 250 tumors to reveal differences among molecular subtypes of the disease, and demonstrate the previously unappreciated importance of non-coding RNA transcripts. We identify alterations within the cAMP dependent pathway (GNAS, PRKAR1A) which converge on GLI2 activity and show that 18% of tumors have a genetic event that directly targets the abundance and/or stability of MYCN...
March 19, 2021: Nature Communications
#25
Jian Carrot-Zhang, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S Damrauer, Tiago Chedraoui Silva, Christopher K Wong, Hyo Young Choi, Ina Felau, A Gordon Robertson, Mauro A A Castro, Lisui Bao, Esther Rheinbay, Eric Minwei Liu, Tuan Trieu, David Haan, Christina Yau, Toshinori Hinoue, Yuexin Liu, Ofer Shapira, Kiran Kumar, Karen L Mungall, Hailei Zhang, Jake June-Koo Lee, Ashton Berger, Galen F Gao, Binyamin Zhitomirsky, Wen-Wei Liang, Meng Zhou, Sitapriya Moorthi, Alice H Berger, Eric A Collisson, Michael C Zody, Li Ding, Andrew D Cherniack, Gad Getz, Olivier Elemento, Christopher C Benz, Josh Stuart, J C Zenklusen, Rameen Beroukhim, Jason C Chang, Joshua D Campbell, D Neil Hayes, Lixing Yang, Peter W Laird, John N Weinstein, David J Kwiatkowski, Ming S Tsao, William D Travis, Ekta Khurana, Benjamin P Berman, Katherine A Hoadley, Nicolas Robine, Matthew Meyerson, Ramaswamy Govindan, Marcin Imielinski
No abstract text is available yet for this article.
February 23, 2021: Cell Reports
#26
JOURNAL ARTICLE
Jian Carrot-Zhang, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S Damrauer, Tiago Chedraoui Silva, Christopher K Wong, Hyo Young Choi, Ina Felau, A Gordon Robertson, Mauro A A Castro, Lisui Bao, Esther Rheinbay, Eric Minwei Liu, Tuan Trieu, David Haan, Christina Yau, Toshinori Hinoue, Yuexin Liu, Ofer Shapira, Kiran Kumar, Karen L Mungall, Hailei Zhang, Jake June-Koo Lee, Ashton Berger, Galen F Gao, Binyamin Zhitomirsky, Wen-Wei Liang, Meng Zhou, Sitapriya Moorthi, Alice H Berger, Eric A Collisson, Michael C Zody, Li Ding, Andrew D Cherniack, Gad Getz, Olivier Elemento, Christopher C Benz, Josh Stuart, J C Zenklusen, Rameen Beroukhim, Jason C Chang, Joshua D Campbell, D Neil Hayes, Lixing Yang, Peter W Laird, John N Weinstein, David J Kwiatkowski, Ming S Tsao, William D Travis, Ekta Khurana, Benjamin P Berman, Katherine A Hoadley, Nicolas Robine, Matthew Meyerson, Ramaswamy Govindan, Marcin Imielinski
RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to be RPA(-) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of LUADs lacking apparent alterations in this pathway. We show that WGS analysis uncovers RPA(+) in 28 (33%) of the 85 samples. Among the remaining 57 cases, we observe focal deletions targeting the promoter or transcription start site of STK11 (n = 7) or KEAP1 (n = 3), and promoter mutations associated with the increased expression of ILF2 (n = 6)...
February 2, 2021: Cell Reports
#27
JOURNAL ARTICLE
Julia R Naso, James T Topham, Joanna M Karasinska, Michael K C Lee, Steve E Kalloger, Hui-Li Wong, Jessica Nelson, Richard A Moore, Andrew J Mungall, Steven J M Jones, Janessa Laskin, Marco A Marra, Daniel J Renouf, David F Schaeffer
BACKGROUND: RNA-sequencing-based classifiers can stratify pancreatic ductal adenocarcinoma (PDAC) into prognostically significant subgroups but are not practical for use in clinical workflows. Here, we assess whether histomorphological features may be used as surrogate markers for predicting molecular subgroup and overall survival in PDAC. METHODS: Ninety-six tissue samples from 50 patients with non-resectable PDAC were scored for gland formation, stromal maturity, mucin, necrosis, and neutrophil infiltration...
December 28, 2020: Cancer Medicine
#28
JOURNAL ARTICLE
Richard D Corbett, Robert Eveleigh, Joe Whitney, Namrata Barai, Mathieu Bourgey, Eric Chuah, Joanne Johnson, Richard A Moore, Neda Moradin, Karen L Mungall, Sergio Pereira, Miriam S Reuter, Bhooma Thiruvahindrapuram, Richard F Wintle, Jiannis Ragoussis, Lisa J Strug, Jo-Anne Herbrick, Naveed Aziz, Steven J M Jones, Mark Lathrop, Stephen W Scherer, Alfredo Staffa, Andrew J Mungall
Population sequencing often requires collaboration across a distributed network of sequencing centers for the timely processing of thousands of samples. In such massive efforts, it is important that participating scientists can be confident that the accuracy of the sequence data produced is not affected by which center generates the data. A study was conducted across three established sequencing centers, located in Montreal, Toronto, and Vancouver, constituting Canada's Genomics Enterprise (www.cgen.ca). Whole genome sequencing was performed at each center, on three genomic DNA replicates from three well-characterized cell lines...
2020: Frontiers in Genetics
#29
JOURNAL ARTICLE
Erica S Tsang, Cameron J Grisdale, Erin Pleasance, James T Topham, Karen Mungall, Caralyn Reisle, Caleb Choo, Marcus Carreira, Reanne Bowlby, Joanna M Karasinska, Daniel MacMillan, Laura M Williamson, Eric Chuah, Richard A Moore, Andrew J Mungall, Yongjun Zhao, Basile Tessier-Cloutier, Tony Ng, Sophie Sun, Howard J Lim, David F Schaeffer, Daniel J Renouf, Stephen Yip, Janessa Laskin, Marco A Marra, Steven J M Jones, Jonathan M Loree
PURPOSE: Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions. EXPERIMENTAL DESIGN: Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches...
January 15, 2021: Clinical Cancer Research
#30
COMPARATIVE STUDY
Robin Jn Coope, Colin Schlosser, Richard D Corbett, Stephen Pleasance, Basile Tessier-Cloutier, Pawan Pandoh, Heather Kirk, Simon Haile, Yongjun Zhao, Andrew J Mungall, Marco A Marra
The practical application of genome-scale technologies to precision oncology research requires flexible tissue processing strategies that can be used to differentially select both tumour and normal cell populations from formalin-fixed, paraffin-embedded tissues. As tumour sequencing scales towards clinical implementation, practical difficulties in scheduling and obtaining fresh tissue biopsies at scale, including blood samples as surrogates for matched 'normal' DNA, have focused attention on the use of formalin-preserved clinical samples collected routinely for diagnostic purposes...
February 2021: Journal of Pathology
#31
JOURNAL ARTICLE
Brett Collinge, Susana Ben-Neriah, Lauren Chong, Merrill Boyle, Aixiang Jiang, Tomoko Miyata-Takata, Pedro Farinha, Jeffrey W Craig, Graham W Slack, Daisuke Ennishi, Anja Mottok, Barbara Meissner, Elizabeth A Chavez, Alina S Gerrie, Diego Villa, Ciara Freeman, Kerry J Savage, Laurie H Sehn, Ryan D Morin, Andrew J Mungall, Randy D Gascoyne, Marco A Marra, Joseph M Connors, Christian Steidl, David W Scott
When the World Health Organization defined high-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/TH) as a clinical category, rearrangements were the only structural variant (SV) incorporated. An "atypical double-hit" category has been proposed, encompassing tumors with concurrent MYC and BCL2 SVs other than cooccurring translocations (ie, copy number variations [CNVs]). Although the identification of a gene expression signature (DHITsig) shared among tumors harboring MYC and BCL2 rearrangements (HGBL-DH/TH-BCL2) has confirmed a common underlying biology, the biological implication of MYC and BCL2 CNVs requires further elucidation...
April 22, 2021: Blood
#32
JOURNAL ARTICLE
James T Topham, Joanna M Karasinska, Michael K C Lee, Veronika Csizmok, Laura M Williamson, Gun Ho Jang, Robert E Denroche, Erica S Tsang, Steve E Kalloger, Hui-Li Wong, Grainne M O'Kane, Richard A Moore, Andrew J Mungall, Faiyaz Notta, Jonathan M Loree, Julie M Wilson, Oliver Bathe, Patricia A Tang, Rachel Goodwin, Jennifer J Knox, Steven Gallinger, Janessa Laskin, Marco A Marra, Steven J M Jones, Daniel J Renouf, David F Schaeffer
PURPOSE: RNA-sequencing-based subtyping of pancreatic ductal adenocarcinoma (PDAC) has been reported by multiple research groups, each using different methodologies and patient cohorts. "Classical" and "basal-like" PDAC subtypes are associated with survival differences, with basal-like tumors associated with worse prognosis. We amalgamated various PDAC subtyping tools to evaluate the potential of such tools to be reliable in clinical practice. EXPERIMENTAL DESIGN: Sequencing data for 574 PDAC tumors was obtained from prospective trials and retrospective public databases...
January 1, 2021: Clinical Cancer Research
#33
JOURNAL ARTICLE
Alexandra Pender, Emma Titmuss, Erin D Pleasance, Kevin Y Fan, Hillary Pearson, Scott D Brown, Cameron J Grisdale, James T Topham, Yaoqing Shen, Melika Bonakdar, Greg Taylor, Laura M Williamson, Karen L Mungall, Eric Chuah, Andrew J Mungall, Richard A Moore, Jean-Michel Lavoie, Stephen Yip, Howard Lim, Daniel J Renouf, Sophie Sun, Robert A Holt, Steven Jm Jones, Marco A Marra, Janessa Laskin
PURPOSE: Immune checkpoint inhibitors (ICIs) have revolutionised the treatment of solid tumours with dramatic and durable responses seen across multiple tumour types. However, identifying patients who will respond to these drugs remains challenging, particularly in the context of advanced and previously treated cancers. EXPERIMENTAL DESIGN: We characterised fresh tumour biopsies from a heterogeneous pan-cancer cohort of 98 patients with metastatic predominantly pre-treated disease through the Personalized OncoGenomics (POG) program at BC Cancer using whole genome and transcriptome analysis (WGTA)...
October 5, 2020: Clinical Cancer Research
#34
JOURNAL ARTICLE
Theodora Lo, Lauren Coombe, Diana Lin, René L Warren, Heather Kirk, Pawan Pandoh, Yongjun Zhao, Richard A Moore, Andrew J Mungall, Carol Ritland, Jean Bousquet, Steven J M Jones, Joerg Bohlmann, Ashley Thomson, Inanc Birol
Here, we present the chloroplast genome sequence of black spruce ( Picea mariana ), a conifer widely distributed throughout North American boreal forests. This complete and annotated chloroplast sequence is 123,961 bp long and will contribute to future studies on the genetic basis of evolutionary change in spruce and adaptation in conifers.
September 24, 2020: Microbiology Resource Announcements
#35
COMMENT
Erica S Tsang, James T Topham, Joanna M Karasinska, Michael K C Lee, Laura M Williamson, Shehara Mendis, Robert E Denroche, Gun Ho Jang, Steve E Kalloger, Richard A Moore, Andrew J Mungall, Oliver F Bathe, Patricia A Tang, Faiyaz Notta, Julie M Wilson, Janessa Laskin, Grainne M O'Kane, Jennifer J Knox, Rachel A Goodwin, Jonathan M Loree, Steven J M Jones, Marco A Marra, Steven Gallinger, David F Schaeffer, Daniel J Renouf
PURPOSE: With the rising incidence of early-onset pancreatic cancer (EOPC), molecular characteristics that distinguish early-onset pancreatic ductal adenocarcinoma (PDAC) tumors from those arising at a later age are not well understood. EXPERIMENTAL DESIGN: We performed bioinformatic analysis of genomic and transcriptomic data generated from 269 advanced (metastatic or locally advanced) and 277 resectable PDAC tumor samples. Patient samples were stratified into EOPC (age of onset ≤55 years; n = 117), intermediate (age of onset 55-70 years; n = 264), and average (age of onset ≥70 years; n = 165) groups...
January 1, 2021: Clinical Cancer Research
#36
JOURNAL ARTICLE
Mark G MacAskill, Agne Stadulyte, Lewis Williams, Timaeus E F Morgan, Nikki L Sloan, Carlos J Alcaide-Corral, Tashfeen Walton, Catriona Wimberley, Chris-Anne McKenzie, Nick B Spath, William Mungall, Ralph BouHaidar, Marc R Dweck, Gillian A Gray, David E Newby, Christophe Lucatelli, Andrew Sutherland, Sally Pimlott, Adriana A S Tavares
Rationale: Myocardial infarction (MI) is one of the leading causes of death worldwide and inflammation is central to the tissue response and patient outcomes. The 18kDa translocator protein (TSPO) has been utilized in positron emission tomography (PET) as an inflammatory biomarker. The aims of this study were to: 1) screen novel, fluorinated, TSPO radiotracers for susceptibility to the rs6971 genetic polymorphism using in vitro competition binding assays in human brain and heart, 2) assess whether the in vivo characteristics of our lead radiotracer, 18 F-LW223, are suitable for clinical translation and 3) validate whether 18 F-LW223 can detect macrophage driven inflammation in a rat myocardial infarction model...
August 28, 2020: Journal of Nuclear Medicine
#37
JOURNAL ARTICLE
Keren Isaev, Daisuke Ennishi, Laura Hilton, Brian Skinnider, Karen L Mungall, Andrew J Mungall, Mehran Bakhtiari, Rosemarie Tremblay-LeMay, Anjali Silva, Susana Ben-Neriah, Merrill Boyle, Diego Villa, Marco A Marra, Christian Steidl, Randy D Gascoyne, Ryan Morin, Kerry J Savage, David W Scott, Robert Kridel
No abstract text is available yet for this article.
August 13, 2020: Haematologica
#38
JOURNAL ARTICLE
Alessia Gagliardi, Vanessa L Porter, Zusheng Zong, Reanne Bowlby, Emma Titmuss, Constance Namirembe, Nicholas B Griner, Hilary Petrello, Jay Bowen, Simon K Chan, Luka Culibrk, Teresa M Darragh, Mark H Stoler, Thomas C Wright, Patee Gesuwan, Maureen A Dyer, Yussanne Ma, Karen L Mungall, Steven J M Jones, Carolyn Nakisige, Karen Novik, Jackson Orem, Martin Origa, Julie M Gastier-Foster, Robert Yarchoan, Corey Casper, Gordon B Mills, Janet S Rader, Akinyemi I Ojesina, Daniela S Gerhard, Andrew J Mungall, Marco A Marra
Cervical cancer is the most common cancer affecting sub-Saharan African women and is prevalent among HIV-positive (HIV+ ) individuals. No comprehensive profiling of cancer genomes, transcriptomes or epigenomes has been performed in this population thus far. We characterized 118 tumors from Ugandan patients, of whom 72 were HIV+ , and performed extended mutation analysis on an additional 89 tumors. We detected human papillomavirus (HPV)-clade-specific differences in tumor DNA methylation, promoter- and enhancer-associated histone marks, gene expression and pathway dysregulation...
August 2020: Nature Genetics
#39
JOURNAL ARTICLE
Luolan Li, Cecile L Maire, Misha Bilenky, Annaïck Carles, Alireza Heravi-Moussavi, Chibo Hong, Angela Tam, Baljit Kamoh, Stephanie Cho, Dorothy Cheung, Irene Li, Tina Wong, Raman P Nagarajan, Andrew J Mungall, Richard Moore, Ting Wang, Claudia L Kleinman, Nada Jabado, Steven Jm Jones, Marco A Marra, Keith L Ligon, Joseph F Costello, Martin Hirst
Aim: To provide a comprehensive understanding of gene regulatory networks in the developing human brain and a foundation for interpreting pathogenic deregulation. Materials & methods: We generated reference epigenomes and transcriptomes of dissected brain regions and primary neural progenitor cells (NPCs) derived from cortical and ganglionic eminence tissues of four normal human fetuses. Results: Integration of these data across developmental stages revealed a directional increase in active regulatory states, transcription factor activities and gene transcription with developmental stage...
July 17, 2020: Epigenomics
#40
JOURNAL ARTICLE
My Linh Thibodeau, Kieran O'Neill, Katherine Dixon, Caralyn Reisle, Karen L Mungall, Martin Krzywinski, Yaoqing Shen, Howard J Lim, Dean Cheng, Kane Tse, Tina Wong, Eric Chuah, Alexandra Fok, Sophie Sun, Daniel Renouf, David F Schaeffer, Carol Cremin, Stephen Chia, Sean Young, Pawan Pandoh, Stephen Pleasance, Erin Pleasance, Andrew J Mungall, Richard Moore, Stephen Yip, Aly Karsan, Janessa Laskin, Marco A Marra, Kasmintan A Schrader, Steven J M Jones
PURPOSE: Structural variants (SVs) may be an underestimated cause of hereditary cancer syndromes given the current limitations of short-read next-generation sequencing. Here we investigated the utility of long-read sequencing in resolving germline SVs in cancer susceptibility genes detected through short-read genome sequencing. METHODS: Known or suspected deleterious germline SVs were identified using Illumina genome sequencing across a cohort of 669 advanced cancer patients with paired tumor genome and transcriptome sequencing...
July 6, 2020: Genetics in Medicine: Official Journal of the American College of Medical Genetics
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