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JOURNAL ARTICLE
Rebecca J Deyell, Yaoqing Shen, Emma Titmuss, Katherine Dixon, Laura M Williamson, Erin Pleasance, Jessica M T Nelson, Sanna Abbasi, Martin Krzywinski, Linlea Armstrong, Melika Bonakdar, Carolyn Ch'ng, Eric Chuah, Chris Dunham, Alexandra Fok, Martin Jones, Anna F Lee, Yussanne Ma, Richard A Moore, Andrew J Mungall, Karen L Mungall, Paul C Rogers, Kasmintan A Schrader, Alice Virani, Kathleen Wee, Sean S Young, Yongjun Zhao, Steven J M Jones, Janessa Laskin, Marco A Marra, Shahrad R Rassekh
The role for routine whole genome and transcriptome analysis (WGTA) for poor prognosis pediatric cancers remains undetermined. Here, we characterize somatic mutations, structural rearrangements, copy number variants, gene expression, immuno-profiles and germline cancer predisposition variants in children and adolescents with relapsed, refractory or poor prognosis malignancies who underwent somatic WGTA and matched germline sequencing. Seventy-nine participants with a median age at enrollment of 8.8 y (range 6 months to 21...
May 16, 2024: Nature Communications
#2
JOURNAL ARTICLE
Laura K Hilton, Brett J Collinge, Susana Ben-Neriah, Waleed Alduaij, Haya Shaalan, Andrew Weng, Manuela Cruz, Graham W Slack, Pedro Farinha, Tomoko Miyata-Takata, Merrill Boyle, Barbara Meissner, James R Cook, Sarah L Ondrejka, German Ott, Andreas Rosenwald, Elías Campo, Catalina Amador, Timothy C Greiner, Philipp W Raess, Joo Y Song, Giorgio Ga Inghirami, Elaine S Jaffe, Dennis D Weisenburger, Wing C Chan, Klaus Beiske, Kai Fu, Jan Delabie, Stafania Pittaluga, Javeed Iqbal, George Wright, Laurie H Sehn, Kerry J Savage, Andrew J Mungall, Andrew L Feldman, Louis M Staudt, Christian Steidl, Lisa M Rimsza, Ryan D Morin, David W Scott
Rearrangements that place the oncogenes MYC, BCL2, or BCL6 adjacent to superenhancers are common in mature B-cell lymphomas. Lymphomas with diffuse large B-cell lymphoma (DLBCL) or high-grade morphology with both MYC and BCL2 rearrangements are classified as high-grade B-cell lymphoma with MYC and BCL2 rearrangements ("double hit": HGBCL-DH-BCL2) and are associated with aggressive disease and poor outcomes. Although it is established that MYC rearrangements involving immunoglobulin (IG) loci are associated with inferior outcomes relative to those involving other non-IG superenhancers, the frequency of, and mechanisms driving, IG vs non-IG MYC rearrangements have not been elucidated...
May 3, 2024: Blood
#3
JOURNAL ARTICLE
Emma Titmuss, Irene S Yu, Erin D Pleasance, Laura M Williamson, Karen Mungall, Andrew J Mungall, Daniel J Renouf, Richard Moore, Steven J M Jones, Marco A Marra, Janessa J Laskin, Kerry J Savage
Immune checkpoint inhibitors (ICIs) are increasingly used in the treatment of many tumor types, and durable responses can be observed in select populations. However, patients may exhibit significant immune-related adverse events (irAEs) that may lead to morbidity. There is limited information on whether the presence of specific germline mutations may highlight those at elevated risk of irAEs. We evaluated 117 patients with metastatic solid tumors or hematologic malignancies who underwent genomic analysis through the ongoing Personalized OncoGenomics (POG) program at BC Cancer and received an ICI during their treatment history...
March 30, 2024: Current Oncology
#4
Vanessa L Porter, Kieran O'Neill, Signe MacLennan, Richard D Corbett, Michelle Ng, Luka Culibrk, Zeid Hamadeh, Marissa Iden, Rachel Schmidt, Shirng-Wern Tsaih, Glenn Chang, Jeremy Fan, Ka Ming Nip, Vahid Akbari, Simon K Chan, James Hopkins, Richard A Moore, Eric Chuah, Karen L Mungall, Andrew J Mungall, Inanc Birol, Steven J M Jones, Janet S Rader, Marco A Marra
Human papillomavirus (HPV) integration has been implicated in transforming HPV infection into cancer, but its genomic consequences have been difficult to study using short-read technologies. To resolve the dysregulation associated with HPV integration, we performed long-read sequencing on 63 cervical cancer genomes. We identified six categories of integration events based on HPV-human genomic structures. Of all HPV integrants, defined as two HPV-human breakpoints bridged by an HPV sequence, 24% contained variable copies of HPV between the breakpoints, a phenomenon we termed heterologous integration...
November 5, 2023: bioRxiv
#5
JOURNAL ARTICLE
Michael A Gargano, Nicolas Matentzoglu, Ben Coleman, Eunice B Addo-Lartey, Anna V Anagnostopoulos, Joel Anderton, Paul Avillach, Anita M Bagley, Eduard Bakštein, James P Balhoff, Gareth Baynam, Susan M Bello, Michael Berk, Holli Bertram, Somer Bishop, Hannah Blau, David F Bodenstein, Pablo Botas, Kaan Boztug, Jolana Čady, Tiffany J Callahan, Rhiannon Cameron, Seth J Carbon, Francisco Castellanos, J Harry Caufield, Lauren E Chan, Christopher G Chute, Jaime Cruz-Rojo, Noémi Dahan-Oliel, Jon R Davids, Maud de Dieuleveult, Vinicius de Souza, Bert B A de Vries, Esther de Vries, J Raymond DePaulo, Beata Derfalvi, Ferdinand Dhombres, Claudia Diaz-Byrd, Alexander J M Dingemans, Bruno Donadille, Michael Duyzend, Reem Elfeky, Shahim Essaid, Carolina Fabrizzi, Giovanna Fico, Helen V Firth, Yun Freudenberg-Hua, Janice M Fullerton, Davera L Gabriel, Kimberly Gilmour, Jessica Giordano, Fernando S Goes, Rachel Gore Moses, Ian Green, Matthias Griese, Tudor Groza, Weihong Gu, Julia Guthrie, Benjamin Gyori, Ada Hamosh, Marc Hanauer, Kateřina Hanušová, Yongqun Oliver He, Harshad Hegde, Ingo Helbig, Kateřina Holasová, Charles Tapley Hoyt, Shangzhi Huang, Eric Hurwitz, Julius O B Jacobsen, Xiaofeng Jiang, Lisa Joseph, Kamyar Keramatian, Bryan King, Katrin Knoflach, David A Koolen, Megan L Kraus, Carlo Kroll, Maaike Kusters, Markus S Ladewig, David Lagorce, Meng-Chuan Lai, Pablo Lapunzina, Bryan Laraway, David Lewis-Smith, Xiarong Li, Caterina Lucano, Marzieh Majd, Mary L Marazita, Victor Martinez-Glez, Toby H McHenry, Melvin G McInnis, Julie A McMurry, Michaela Mihulová, Caitlin E Millett, Philip B Mitchell, Veronika Moslerová, Kenji Narutomi, Shahrzad Nematollahi, Julian Nevado, Andrew A Nierenberg, Nikola Novák Čajbiková, John I Nurnberger, Soichi Ogishima, Daniel Olson, Abigail Ortiz, Harry Pachajoa, Guiomar Perez de Nanclares, Amy Peters, Tim Putman, Christina K Rapp, Ana Rath, Justin Reese, Lauren Rekerle, Angharad M Roberts, Suzy Roy, Stephan J Sanders, Catharina Schuetz, Eva C Schulte, Thomas G Schulze, Martin Schwarz, Katie Scott, Dominik Seelow, Berthold Seitz, Yiping Shen, Morgan N Similuk, Eric S Simon, Balwinder Singh, Damian Smedley, Cynthia L Smith, Jake T Smolinsky, Sarah Sperry, Elizabeth Stafford, Ray Stefancsik, Robin Steinhaus, Rebecca Strawbridge, Jagadish Chandrabose Sundaramurthi, Polina Talapova, Jair A Tenorio Castano, Pavel Tesner, Rhys H Thomas, Audrey Thurm, Marek Turnovec, Marielle E van Gijn, Nicole A Vasilevsky, Markéta Vlčková, Anita Walden, Kai Wang, Ron Wapner, James S Ware, Addo A Wiafe, Samuel A Wiafe, Lisa D Wiggins, Andrew E Williams, Chen Wu, Margot J Wyrwoll, Hui Xiong, Nefize Yalin, Yasunori Yamamoto, Lakshmi N Yatham, Anastasia K Yocum, Allan H Young, Zafer Yüksel, Peter P Zandi, Andreas Zankl, Ignacio Zarante, Miroslav Zvolský, Sabrina Toro, Leigh C Carmody, Nomi L Harris, Monica C Munoz-Torres, Daniel Danis, Christopher J Mungall, Sebastian Köhler, Melissa A Haendel, Peter N Robinson
The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English...
January 5, 2024: Nucleic Acids Research
#6
REVIEW
Mark A Colijn, Prescilla Carrion, Guillaume Poirier-Morency, Sanja Rogic, Ivan Torres, Mahesh Menon, Michelle Lisonek, Courtney Cook, Ashley DeGraaf, Subramanya Ponnachana Thammaiah, Harish Neelakant, Veerle Willaeys, Olga Leonova, Randall F White, Stephen Yip, Andrew J Mungall, Patrick M MacLeod, William T Gibson, Patrick F Sullivan, William G Honer, Paul Pavlidis, Robert M Stowe
OBJECTIVE: SETD1A encodes a histone methyltransferase involved in various cell cycle regulatory processes. Loss-of-function SETD1A variants have been associated with numerous neurodevelopmental phenotypes, including intellectual disability and schizophrenia. While the association between rare coding variants in SETD1A and schizophrenia has achieved genome-wide significance by rare variant burden testing, only a few studies have described the psychiatric phenomenology of such individuals in detail...
October 31, 2023: Progress in Neuro-psychopharmacology & Biological Psychiatry
#7
JOURNAL ARTICLE
Karamarie Fecho, Chris Bizon, Tursynay Issabekova, Sierra Moxon, Anne E Thessen, Shervin Abdollahi, Sergio E Baranzini, Basazin Belhu, William E Byrd, Lawrence Chung, Andrew Crouse, Marc P Duby, Stephen Ferguson, Aleksandra Foksinska, Laura Forero, Jennifer Friedman, Vicki Gardner, Gwênlyn Glusman, Jennifer Hadlock, Kristina Hanspers, Eugene Hinderer, Charlotte Hobbs, Gregory Hyde, Sui Huang, David Koslicki, Philip Mease, Sandrine Muller, Christopher J Mungall, Stephen A Ramsey, Jared Roach, Irit Rubin, Shepherd H Schurman, Anath Shalev, Brett Smith, Karthik Soman, Sarah Stemann, Andrew I Su, Casey Ta, Paul B Watkins, Mark D Williams, Chunlei Wu, Colleen H Xu
Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder efforts to harmonize and integrate across these diverse sources. As part of The Biomedical Translator Consortium, we have developed a knowledge graph-based question-answering system designed to augment human reasoning and accelerate translational scientific discovery: the Translator system...
2023: Journal of Clinical and Translational Science
#8
JOURNAL ARTICLE
Theodora Lo, Lauren Coombe, Kristina K Gagalova, Alex Marr, René L Warren, Heather Kirk, Pawan Pandoh, Yongjun Zhao, Richard A Moore, Andrew J Mungall, Carol Ritland, Nathalie Pavy, Steven J M Jones, Joerg Bohlmann, Jean Bousquet, Inanç Birol, Ashley Thomson
Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and five other spruces for which complete nuclear and organelle genome sequences were available...
October 24, 2023: G3: Genes—Genomes—Genetics
#9
JOURNAL ARTICLE
Jing Xu, Pawan K Pandoh, Richard D Corbett, Duane Smailus, Reanne Bowlby, Denise Brooks, Helen McDonald, Simon Haile, Sundeep Chahal, Steve Bilobram, Karen L Mungall, Andrew J Mungall, Robin Coope, Richard A Moore, Yongjun Zhao, Steven Jm Jones, Marco A Marra
High-throughput total nucleic acid (TNA) purification methods based on solid-phase reversible immobilization (SPRI) beads produce TNA suitable for both genomic and transcriptomic applications. Even so, small RNA species, including miRNA, bind weakly to SPRI beads under standard TNA purification conditions, necessitating a separate workflow using column-based methods that are difficult to automate. Here, an SPRI-based high-throughput TNA purification protocol that recovers DNA, RNA and small RNA, called GSC-modified RLT+ Aline bead-based protocol (GRAB-ALL), which incorporates modifications to enhance small RNA recovery is presented...
August 8, 2023: BioTechniques
#10
JOURNAL ARTICLE
Kostiantyn Dreval, Laura K Hilton, Manuela Cruz, Haya Shaalan, Susana Ben-Neriah, Merrill Boyle, Brett J Collinge, Krysta Mila Coyle, Gerben Duns, Pedro Farinha, Bruno Grande, Barbara Meissner, Prasath Pararajalingam, Christopher K Rushton, Graham W Slack, Jasper Chun Hei Wong, Andrew J Mungall, Marco A Marra, Joseph M Connors, Christian Steidl, David W Scott, Ryan D Morin
Follicular lymphoma (FL) accounts for approximately 20% of all new lymphoma cases. Increases in cytological grade are a feature of the clinical progression of this malignancy, and eventual histologic transformation (HT) to the aggressive diffuse large B-cell lymphoma (DLBCL) occurs in up to 15% of patients. Clinical or genetic features to predict the risk and timing of HT have not been comprehensively described. In this study, we analyzed whole genome sequencing data from 423 patients to compare the protein coding and non-coding mutation landscapes of untransformed FL, transformed FL and de novo DLBCL...
April 21, 2023: Blood
#11
JOURNAL ARTICLE
Katherine Dixon, Yaoqing Shen, Kieran O'Neill, Karen L Mungall, Simon Chan, Steve Bilobram, Wei Zhang, Marjorie Bezeau, Alshanee Sharma, Alexandra Fok, Andrew J Mungall, Richard Moore, Ian Bosdet, My Linh Thibodeau, Sophie Sun, Stephen Yip, Kasmintan A Schrader, Steven J M Jones
Germline structural variants (SVs) are challenging to resolve by conventional genetic testing assays. Long-read sequencing has improved the global characterization of SVs, but its sensitivity at cancer susceptibility loci has not been reported. Nanopore long-read genome sequencing was performed for nineteen individuals with pathogenic copy number alterations in BRCA1, BRCA2, CHEK2 and PALB2 identified by prior clinical testing. Fourteen variants, which spanned single exons to whole genes and included a tandem duplication, were accurately represented...
February 16, 2023: European Journal of Human Genetics: EJHG
#12
JOURNAL ARTICLE
Waleed Alduaij, Brett Collinge, Susana Ben-Neriah, Aixiang Jiang, Laura K Hilton, Merrill Boyle, Barbara Meissner, Lauren Chong, Tomoko Miyata-Takata, Graham W Slack, Pedro Farinha, Jeffrey W Craig, Andrew Lytle, Kerry J Savage, Diego Villa, Alina S Gerrie, Ciara L Freeman, Randy D Gascoyne, Joseph M Connors, Ryan D Morin, Laurie H Sehn, Andrew J Mungall, Christian Steidl, David W Scott
Molecular heterogeneity of diffuse large B-cell lymphoma (DLBCL) underlies the variable outcomes achieved with immunochemotherapy. However, outcomes of gene expression profiling (GEP)-defined molecular subgroups in a real-world DLBCL population remain unknown. Here we examined the prevalence and outcomes of molecular subgroups in an unselected population of 1149 patients with de novo DLBCL in British Columbia, Canada. Evaluable biopsies were profiled by fluorescence in situ hybridization (FISH), immunohistochemistry, and digital GEP to assign cell-of-origin and the so-called "double-hit signature" (DHITsig)-a signature originally described as being characteristic for high-grade B-cell lymphoma with MYC and BCL2 rearrangements (HGBCL-DH-BCL2)...
May 18, 2023: Blood
#13
JOURNAL ARTICLE
James T Topham, Erica S Tsang, Joanna M Karasinska, Andrew Metcalfe, Hassan Ali, Steve E Kalloger, Veronika Csizmok, Laura M Williamson, Emma Titmuss, Karina Nielsen, Gian Luca Negri, Sandra E Spencer Miko, Gun Ho Jang, Robert E Denroche, Hui-Li Wong, Grainne M O'Kane, Richard A Moore, Andrew J Mungall, Jonathan M Loree, Faiyaz Notta, Julie M Wilson, Oliver F Bathe, Patricia A Tang, Rachel Goodwin, Gregg B Morin, Jennifer J Knox, Steven Gallinger, Janessa Laskin, Marco A Marra, Steven J M Jones, David F Schaeffer, Daniel J Renouf
Oncogenic KRAS mutations are absent in approximately 10% of patients with metastatic pancreatic ductal adenocarcinoma (mPDAC) and may represent a subgroup of mPDAC with therapeutic options beyond standard-of-care cytotoxic chemotherapy. While distinct gene fusions have been implicated in KRAS wildtype mPDAC, information regarding other types of mutations remain limited, and gene expression patterns associated with KRAS wildtype mPDAC have not been reported. Here, we leverage sequencing data from the PanGen trial to perform comprehensive characterization of the molecular landscape of KRAS wildtype mPDAC and reveal increased frequency of chr1q amplification encompassing transcription factors PROX1 and NR5A2...
October 8, 2022: Nature Communications
#14
JOURNAL ARTICLE
Nicole Thomas, Kostiantyn Dreval, Daniela S Gerhard, Laura K Hilton, Jeremy S Abramson, Richard F Ambinder, Stefan Barta, Nancy L Bartlett, Jeffrey Bethony, Kishor Bhatia, Jay Bowen, Anthony C Bryan, Ethel Cesarman, Corey Casper, Amy Chadburn, Manuela Cruz, Dirk P Dittmer, Maureen A Dyer, Pedro Farinha, Julie M Gastier-Foster, Alina S Gerrie, Bruno M Grande, Timothy Greiner, Nicholas B Griner, Thomas G Gross, Nancy L Harris, John D Irvin, Elaine S Jaffe, David Henry, Rebecca Huppi, Fabio E Leal, Michael S Lee, Jean Paul Martin, Marie-Reine Martin, Sam M Mbulaiteye, Ronald Mitsuyasu, Vivian Morris, Charles G Mullighan, Andrew J Mungall, Karen Mungall, Innocent Mutyaba, Mostafa Nokta, Constance Namirembe, Ariela Noy, Martin D Ogwang, Abraham Omoding, Jackson Orem, German Ott, Hilary Petrello, Stefania Pittaluga, James D Phelan, Juan Carlos Ramos, Lee Ratner, Steven J Reynolds, Paul G Rubinstein, Gerhard Sissolak, Graham Slack, Shaghayegh Soudi, Steven H Swerdlow, Alexandra Traverse-Glehen, Wyndham H Wilson, Jasper Wong, Robert Yarchoan, Jean C ZenKlusen, Marco A Marra, Louis M Staudt, David W Scott, Ryan D Morin
Burkitt lymphoma (BL) accounts for most pediatric non-Hodgkin lymphomas, being less common but significantly more lethal when diagnosed in adults. Much of the knowledge of the genetics of BL thus far has originated from the study of pediatric BL (pBL), leaving its relationship to adult BL (aBL) and other adult lymphomas not fully explored. We sought to more thoroughly identify the somatic changes that underlie lymphomagenesis in aBL and any molecular features that associate with clinical disparities within and between pBL and aBL...
February 23, 2023: Blood
#15
JOURNAL ARTICLE
Kristina K Gagalova, René L Warren, Lauren Coombe, Johnathan Wong, Ka Ming Nip, Macaire Man Saint Yuen, Justin Ga Whitehill, Jose M Celedon, Carol Ritland, Greg A Taylor, Dean Cheng, Patrick Plettner, S Austin Hammond, Hamid Mohamadi, Yongjun Zhao, Richard A Moore, Andrew J Mungall, Brian Boyle, Jérôme Laroche, Joan Cottrell, John J Mackay, Manuel Lamothe, Sébastien Gérardi, Nathalie Isabel, Nathalie Pavy, Steven Jm Jones, Joerg Bohlmann, Jean Bousquet, Inanc Birol
Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (P. sitchensis) together with improved and more contiguous genome assemblies for white spruce (P...
July 4, 2022: Plant Journal
#16
MULTICENTER STUDY
Justin T Reese, Ben Coleman, Lauren Chan, Hannah Blau, Tiffany J Callahan, Luca Cappelletti, Tommaso Fontana, Katie R 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 A 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...
May 15, 2022: Virology Journal
#17
JOURNAL ARTICLE
Alexandra Garancher, Hiromichi Suzuki, Svasti Haricharan, Lianne Q Chau, Meher Beigi Masihi, Jessica M Rusert, Paula S Norris, Florent Carrette, Megan M Romero, Sorana A Morrissy, Patryk Skowron, Florence M G Cavalli, Hamza Farooq, Vijay Ramaswamy, Steven J M Jones, Richard A Moore, Andrew J Mungall, Yussanne Ma, Nina Thiessen, Yisu Li, Alaide Morcavallo, Lin Qi, Mari Kogiso, Yuchen Du, Patricia Baxter, Jacob J Henderson, John R Crawford, Michael L Levy, James M Olson, Yoon-Jae Cho, Aniruddha J Deshpande, Xiao-Nan Li, Louis Chesler, Marco A Marra, Harald Wajant, Oren J Becher, Linda M Bradley, Carl F Ware, Michael D Taylor, Robert J Wechsler-Reya
No abstract text is available yet for this article.
January 2022: Nature Neuroscience
#18
JOURNAL ARTICLE
Cody A Despins, Scott D Brown, Avery V Robinson, Andrew J Mungall, Emma Allen-Vercoe, Robert A Holt
Fusobacterium nucleatum is a ubiquitous opportunistic pathogen with an emerging role as an oncomicrobe in colorectal cancer and other cancer settings. F. nucleatum can adhere to and invade host cells in a manner that varies across F. nucleatum strains and host cell phenotypes. Here, we performed pairwise cocultures between three F. nucleatum strains and two immortalized primary host cell types (human colonic epithelial [HCE] cells and human carotid artery endothelial [HCAE] cells) followed by transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to investigate transcriptional and epigenetic host cell responses...
October 26, 2021: MBio
#19
JOURNAL ARTICLE
Simon Haile, Aidan M Nikiforuk, Pawan K Pandoh, David D W Twa, Duane E Smailus, Jason Nguyen, Stephen Pleasance, Angus Wong, Yongjun Zhao, Diane Eisler, Michelle Moksa, Qi Cao, Marcus Wong, Edmund Su, Martin Krzywinski, Jessica Nelson, Andrew J Mungall, Frankie Tsang, Leah M Prentice, Agatha Jassem, Amee R Manges, Steven J M Jones, Robin J Coope, Natalie Prystajecky, Marco A Marra, Mel Krajden, Martin Hirst
The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagnostic testing. Magnetic bead-based nucleic acid extraction protocols using 96-well plates on open liquid handlers are readily amenable to meet this need. Here, one such approach is rigorously optimized to minimize cross-well contamination while maintaining sensitivity.
October 20, 2021: Journal of Virological Methods
#20
JOURNAL ARTICLE
Kevin C Yang, Steve E Kalloger, John J Aird, Michael K C Lee, Christopher Rushton, Karen L Mungall, Andrew J Mungall, Dongxia Gao, Christine Chow, Jing Xu, Joanna M Karasinska, Shane Colborne, Steven J M Jones, Jörg Schrader, Ryan D Morin, Jonathan M Loree, Marco A Marra, Daniel J Renouf, Gregg B Morin, David F Schaeffer, Sharon M Gorski
Pancreatic neuroendocrine neoplasms (PNENs) are biologically and clinically heterogeneous. Here, we use a multi-omics approach to uncover the molecular factors underlying this heterogeneity. Transcriptomic analysis of 84 PNEN specimens, drawn from two cohorts, is substantiated with proteomic profiling and identifies four subgroups: Proliferative, PDX1-high, Alpha cell-like and Stromal/Mesenchymal. The Proliferative subgroup, consisting of both well- and poorly differentiated specimens, is associated with inferior overall survival probability...
October 12, 2021: Cell Reports
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