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https://www.readbyqxmd.com/read/28201737/effectiveness-of-a-screening-programme-in-identifying-individuals-with-increased-risk-of-cardiovascular-disease-in-south-africa
#1
Nasheeta Peer, Yusentha Balakrishna, Anniza de Villiers, Christelle Crickmore, Vash Mungal-Singh
No abstract text is available yet for this article.
February 14, 2017: Journal of Public Health
https://www.readbyqxmd.com/read/27972707/an-updated-cost-effectiveness-analysis-of-synflorix-universal-mass-vaccination-implementation-in-new-zealand
#2
L Varghese, L Talbot, A Govender, B Mungall
No abstract text is available yet for this article.
November 2016: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/27959929/histological-transformation-and-progression-in-follicular-lymphoma-a-clonal-evolution-study
#3
Robert Kridel, Fong Chun Chan, Anja Mottok, Merrill Boyle, Pedro Farinha, King Tan, Barbara Meissner, Ali Bashashati, Andrew McPherson, Andrew Roth, Karey Shumansky, Damian Yap, Susana Ben-Neriah, Jamie Rosner, Maia A Smith, Cydney Nielsen, Eva Giné, Adele Telenius, Daisuke Ennishi, Andrew Mungall, Richard Moore, Ryan D Morin, Nathalie A Johnson, Laurie H Sehn, Thomas Tousseyn, Ahmet Dogan, Joseph M Connors, David W Scott, Christian Steidl, Marco A Marra, Randy D Gascoyne, Sohrab P Shah
BACKGROUND: Follicular lymphoma (FL) is an indolent, yet incurable B cell malignancy. A subset of patients experience an increased mortality rate driven by two distinct clinical end points: histological transformation and early progression after immunochemotherapy. The nature of tumor clonal dynamics leading to these clinical end points is poorly understood, and previously determined genetic alterations do not explain the majority of transformed cases or accurately predict early progressive disease...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27899636/the-monarch-initiative-an-integrative-data-and-analytic-platform-connecting-phenotypes-to-genotypes-across-species
#4
Christopher J Mungall, Julie A McMurry, Sebastian Köhler, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J P Gourdine, Julius O B Jacobsen, Dan Keith, Bryan Laraway, Suzanna E Lewis, Jeremy NguyenXuan, Kent Shefchek, Nicole Vasilevsky, Zhou Yuan, Nicole Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N Robinson, Melissa A Haendel
The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899602/the-human-phenotype-ontology-in-2017
#5
Sebastian Köhler, Nicole A Vasilevsky, Mark Engelstad, Erin Foster, Julie McMurry, Ségolène Aymé, Gareth Baynam, Susan M Bello, Cornelius F Boerkoel, Kym M Boycott, Michael Brudno, Orion J Buske, Patrick F Chinnery, Valentina Cipriani, Laureen E Connell, Hugh J S Dawkins, Laura E DeMare, Andrew D Devereau, Bert B A de Vries, Helen V Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna A Jähn, Roger James, Roland Krause, Stanley J F Laulederkind, Hanns Lochmüller, Gholson J Lyon, Soichi Ogishima, Annie Olry, Willem H Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H Scott, Michael Segal, Panagiotis I Sergouniotis, Richard Sever, Cynthia L Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W M Veltman, Tom Vulliamy, Jing Yu, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O B Jacobsen, Tudor Groza, Damian Smedley, Christopher J Mungall, Melissa Haendel, Peter N Robinson
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27851968/analysis-of-normal-human-mammary-epigenomes-reveals-cell-specific-active-enhancer-states-and-associated-transcription-factor-networks
#6
Davide Pellacani, Misha Bilenky, Nagarajan Kannan, Alireza Heravi-Moussavi, David J H F Knapp, Sitanshu Gakkhar, Michelle Moksa, Annaick Carles, Richard Moore, Andrew J Mungall, Marco A Marra, Steven J M Jones, Samuel Aparicio, Martin Hirst, Connie J Eaves
The normal adult human mammary gland is a continuous bilayered epithelial system. Bipotent and myoepithelial progenitors are prominent and unique components of the outer (basal) layer. The inner (luminal) layer includes both luminal-restricted progenitors and a phenotypically separable fraction that lacks progenitor activity. We now report an epigenomic comparison of these three subsets with one another, with their associated stromal cells, and with three immortalized, non-tumorigenic human mammary cell lines...
November 15, 2016: Cell Reports
https://www.readbyqxmd.com/read/27824051/genomic-analyses-identify-recurrent-mef2d-fusions-in-acute-lymphoblastic-leukaemia
#7
Zhaohui Gu, Michelle Churchman, Kathryn Roberts, Yongjin Li, Yu Liu, Richard C Harvey, Kelly McCastlain, Shalini C Reshmi, Debbie Payne-Turner, Ilaria Iacobucci, Ying Shao, I-Ming Chen, Marcus Valentine, Deqing Pei, Karen L Mungall, Andrew J Mungall, Yussanne Ma, Richard Moore, Marco Marra, Eileen Stonerock, Julie M Gastier-Foster, Meenakshi Devidas, Yunfeng Dai, Brent Wood, Michael Borowitz, Eric E Larsen, Kelly Maloney, Leonard A Mattano, Anne Angiolillo, Wanda L Salzer, Michael J Burke, Francesca Gianni, Orietta Spinelli, Jerald P Radich, Mark D Minden, Anthony V Moorman, Bella Patel, Adele K Fielding, Jacob M Rowe, Selina M Luger, Ravi Bhatia, Ibrahim Aldoss, Stephen J Forman, Jessica Kohlschmidt, Krzysztof Mrózek, Guido Marcucci, Clara D Bloomfield, Wendy Stock, Steven Kornblau, Hagop M Kantarjian, Marina Konopleva, Elisabeth Paietta, Cheryl L Willman, Mignon L Loh, Stephen P Hunger, Charles G Mullighan
Chromosomal rearrangements are initiating events in acute lymphoblastic leukaemia (ALL). Here using RNA sequencing of 560 ALL cases, we identify rearrangements between MEF2D (myocyte enhancer factor 2D) and five genes (BCL9, CSF1R, DAZAP1, HNRNPUL1 and SS18) in 22 B progenitor ALL (B-ALL) cases with a distinct gene expression profile, the most common of which is MEF2D-BCL9. Examination of an extended cohort of 1,164 B-ALL cases identified 30 cases with MEF2D rearrangements, which include an additional fusion partner, FOXJ2; thus, MEF2D-rearranged cases comprise 5...
November 8, 2016: Nature Communications
https://www.readbyqxmd.com/read/27794045/update-of-the-fantom-web-resource-high-resolution-transcriptome-of-diverse-cell-types-in-mammals
#8
Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David Arenillas, Anthony Mathelier, Yulia A Medvedeva, Andreas Lennartsson, Finn Drabløs, Jordan A Ramilowski, Owen Rackham, Julian Gough, Robin Andersson, Albin Sandelin, Hans Ienasescu, Hiromasa Ono, Hidemasa Bono, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest, Takeya Kasukawa, Hideya Kawaji
Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27785453/distributed-cognition-and-process-management-enabling-individualized-translational-research-the-nih-undiagnosed-diseases-program-experience
#9
Amanda E Links, David Draper, Elizabeth Lee, Jessica Guzman, Zaheer Valivullah, Valerie Maduro, Vlad Lebedev, Maxim Didenko, Garrick Tomlin, Michael Brudno, Marta Girdea, Sergiu Dumitriu, Melissa A Haendel, Christopher J Mungall, Damian Smedley, Harry Hochheiser, Andrew M Arnold, Bert Coessens, Steven Verhoeven, William Bone, David Adams, Cornelius F Boerkoel, William A Gahl, Murat Sincan
The National Institutes of Health Undiagnosed Diseases Program (NIH UDP) applies translational research systematically to diagnose patients with undiagnosed diseases. The challenge is to implement an information system enabling scalable translational research. The authors hypothesized that similar complex problems are resolvable through process management and the distributed cognition of communities. The team, therefore, built the NIH UDP integrated collaboration system (UDPICS) to form virtual collaborative multidisciplinary research networks or communities...
2016: Frontiers in Medicine
https://www.readbyqxmd.com/read/27733503/ontobee-a-linked-ontology-data-server-to-support-ontology-term-dereferencing-linkage-query-and-integration
#10
Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He
Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27702824/significance-of-tp53-mutation-in-wilms-tumors-with-diffuse-anaplasia-a-report-from-the-children-s-oncology-group
#11
Ariadne H A G Ooms, Samantha Gadd, Daniela S Gerhard, Malcolm A Smith, Jaime M Guidry Auvil, Daoud Meerzaman, Qing-Rong Chen, Chih Hao Hsu, Chunhua Yan, Cu Nguyen, Ying Hu, Yussanne Ma, Zusheng Zong, Andrew J Mungall, Richard A Moore, Marco A Marra, Vicki Huff, Jeffrey S Dome, Yueh-Yun Chi, Jing Tian, James I Geller, Charles G Mullighan, Jing Ma, David A Wheeler, Oliver A Hampton, Amy L Walz, Marry M van den Heuvel-Eibrink, Ronald R de Krijger, Nicole Ross, Julie M Gastier-Foster, Elizabeth J Perlman
PURPOSE: To investigate the role and significance of TP53 mutation in diffusely anaplastic Wilms tumors (DAWTs). EXPERIMENTAL DESIGN: All DAWTs registered on National Wilms Tumor Study-5 (n = 118) with available samples were analyzed for TP53 mutations and copy loss. Integrative genomic analysis was performed on 39 selected DAWTs. RESULTS: Following analysis of a single random sample, 57 DAWTs (48%) demonstrated TP53 mutations, 13 (11%) copy loss without mutation, and 48 (41%) lacked both [defined as TP53-wild-type (wt)]...
November 15, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27664130/the-environment-ontology-in-2016-bridging-domains-with-increased-scope-semantic-density-and-interoperation
#12
Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E Lewis, Mark P Schildhauer, Ramona L Walls, Christopher J Mungall
BACKGROUND: The Environment Ontology (ENVO; http://www.environmentontology.org/ ), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description...
September 23, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27602295/the-health-care-and-life-sciences-community-profile-for-dataset-descriptions
#13
Michel Dumontier, Alasdair J G Gray, M Scott Marshall, Vladimir Alexiev, Peter Ansell, Gary Bader, Joachim Baran, Jerven T Bolleman, Alison Callahan, José Cruz-Toledo, Pascale Gaudet, Erich A Gombocz, Alejandra N Gonzalez-Beltran, Paul Groth, Melissa Haendel, Maori Ito, Simon Jupp, Nick Juty, Toshiaki Katayama, Norio Kobayashi, Kalpana Krishnaswami, Camille Laibe, Nicolas Le Novère, Simon Lin, James Malone, Michael Miller, Christopher J Mungall, Laurens Rietveld, Sarala M Wimalaratne, Atsuko Yamaguchi
Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets...
2016: PeerJ
https://www.readbyqxmd.com/read/27589964/modeling-biochemical-pathways-in-the-gene-ontology
#14
David P Hill, Peter D'Eustachio, Tanya Z Berardini, Christopher J Mungall, Nikolai Renedo, Judith A Blake
The concept of a biological pathway, an ordered sequence of molecular transformations, is used to collect and represent molecular knowledge for a broad span of organismal biology. Representations of biomedical pathways typically are rich but idiosyncratic presentations of organized knowledge about individual pathways. Meanwhile, biomedical ontologies and associated annotation files are powerful tools that organize molecular information in a logically rigorous form to support computational analysis. The Gene Ontology (GO), representing Molecular Functions, Biological Processes and Cellular Components, incorporates many aspects of biological pathways within its ontological representations...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27569544/a-whole-genome-analysis-framework-for-effective-identification-of-pathogenic-regulatory-variants-in-mendelian-disease
#15
Damian Smedley, Max Schubach, Julius O B Jacobsen, Sebastian Köhler, Tomasz Zemojtel, Malte Spielmann, Marten Jäger, Harry Hochheiser, Nicole L Washington, Julie A McMurry, Melissa A Haendel, Christopher J Mungall, Suzanna E Lewis, Tudor Groza, Giorgio Valentini, Peter N Robinson
The interpretation of non-coding variants still constitutes a major challenge in the application of whole-genome sequencing in Mendelian disease, especially for single-nucleotide and other small non-coding variants. Here we present Genomiser, an analysis framework that is able not only to score the relevance of variation in the non-coding genome, but also to associate regulatory variants to specific Mendelian diseases. Genomiser scores variants through either existing methods such as CADD or a bespoke machine learning method and combines these with allele frequency, regulatory sequences, chromosomal topological domains, and phenotypic relevance to discover variants associated to specific Mendelian disorders...
September 1, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27516611/navigating-the-phenotype-frontier-the-monarch-initiative
#16
Julie A McMurry, Sebastian Köhler, Nicole L Washington, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, Jean-Philippe Gourdine, Julius O B Jacobsen, Daniel Keith, Bryan Laraway, Jeremy Nguyen Xuan, Kent Shefchek, Nicole A Vasilevsky, Zhou Yuan, Suzanna E Lewis, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N Robinson, Christopher J Mungall, Melissa A Haendel
The principles of genetics apply across the entire tree of life. At the cellular level we share biological mechanisms with species from which we diverged millions, even billions of years ago. We can exploit this common ancestry to learn about health and disease, by analyzing DNA and protein sequences, but also through the observable outcomes of genetic differences, i.e. phenotypes. To solve challenging disease problems we need to unify the heterogeneous data that relates genomics to disease traits. Without a big-picture view of phenotypic data, many questions in genetics are difficult or impossible to answer...
August 2016: Genetics
https://www.readbyqxmd.com/read/27459265/response-to-wu-et%C3%A2-al-cost-effectiveness-analysis-of-infant-pneumococcal-vaccination-in-malaysia-and-hong-kong
#17
Lijoy Varghese, Bruce Mungall, Xu-Hao Zhang, Bernard Hoet
A recently published paper that assessed the comparative cost-effectiveness of the 2 pneumococcal conjugate vaccines (PCVs) in Malaysia and Hong Kong reported that the 13-valent PCV vaccine (PCV13) is a better choice compared to the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV or PCV10) from both a payer and societal perspective as well as under various scenarios. However, the analysis relied on a large number of assumptions that were either erroneous or did not take into account the most recent body of evidence available...
October 2, 2016: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/27377652/the-cell-ontology-2016-enhanced-content-modularization-and-ontology-interoperability
#18
Alexander D Diehl, Terrence F Meehan, Yvonne M Bradford, Matthew H Brush, Wasila M Dahdul, David S Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E Van Slyke, Nicole A Vasilevsky, Melissa A Haendel, Judith A Blake, Christopher J Mungall
BACKGROUND: The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. CONSTRUCTION AND CONTENT: Recent work on the CL has focused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologies in coordination with the CL...
July 4, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27296299/faldo-a-semantic-standard-for-describing-the-location-of-nucleotide-and-protein-feature-annotation
#19
Jerven T Bolleman, Christopher J Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul J P Bonnal, Robert Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama, Peter J A Cock
BACKGROUND: Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. DESCRIPTION: We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27268263/comprehensive-characterization-of-programmed-death-ligand-structural-rearrangements-in-b-cell-non-hodgkin-lymphomas
#20
Lauren C Chong, David D W Twa, Anja Mottok, Susana Ben-Neriah, Bruce W Woolcock, Yongjun Zhao, Kerry J Savage, Marco A Marra, David W Scott, Randy D Gascoyne, Ryan D Morin, Andrew J Mungall, Christian Steidl
Programmed death ligands (PDLs) are immune-regulatory molecules that are frequently affected by chromosomal alterations in B-cell lymphomas. Although PDL copy-number variations are well characterized, a detailed and comprehensive analysis of structural rearrangements (SRs) and associated phenotypic consequences is largely lacking. Here, we used oligonucleotide capture sequencing of 67 formalin-fixed paraffin-embedded tissues derived from primary B-cell lymphomas and 1 cell line to detect and characterize, at base-pair resolution, SRs of the PDL locus (9p24...
September 1, 2016: Blood
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