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https://www.readbyqxmd.com/read/28650483/disease-model-discovery-from-3-328-gene-knockouts-by-the-international-mouse-phenotyping-consortium
#1
Terrence F Meehan, Nathalie Conte, David B West, Julius O Jacobsen, Jeremy Mason, Jonathan Warren, Chao-Kung Chen, Ilinca Tudose, Mike Relac, Peter Matthews, Natasha Karp, Luis Santos, Tanja Fiegel, Natalie Ring, Henrik Westerberg, Simon Greenaway, Duncan Sneddon, Hugh Morgan, Gemma F Codner, Michelle E Stewart, James Brown, Neil Horner, Melissa Haendel, Nicole Washington, Christopher J Mungall, Corey L Reynolds, Juan Gallegos, Valerie Gailus-Durner, Tania Sorg, Guillaume Pavlovic, Lynette R Bower, Mark Moore, Iva Morse, Xiang Gao, Glauco P Tocchini-Valentini, Yuichi Obata, Soo Young Cho, Je Kyung Seong, John Seavitt, Arthur L Beaudet, Mary E Dickinson, Yann Herault, Wolfgang Wurst, Martin Hrabe de Angelis, K C Kent Lloyd, Ann M Flenniken, Lauryl M J Nutter, Susan Newbigging, Colin McKerlie, Monica J Justice, Stephen A Murray, Karen L Svenson, Robert E Braun, Jacqueline K White, Allan Bradley, Paul Flicek, Sara Wells, William C Skarnes, David J Adams, Helen Parkinson, Ann-Marie Mallon, Steve D M Brown, Damian Smedley
Although next-generation sequencing has revolutionized the ability to associate variants with human diseases, diagnostic rates and development of new therapies are still limited by a lack of knowledge of the functions and pathobiological mechanisms of most genes. To address this challenge, the International Mouse Phenotyping Consortium is creating a genome- and phenome-wide catalog of gene function by characterizing new knockout-mouse strains across diverse biological systems through a broad set of standardized phenotyping tests...
June 26, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28583177/dead-simple-owl-design-patterns
#2
David Osumi-Sutherland, Melanie Courtot, James P Balhoff, Christopher Mungall
BACKGROUND: Bio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automate classification via consistent patterns of axiomatization. Many bio-ontologies originating in OBO or OWL follow this approach. These patterns need to be documented in a form that requires minimal expertise to understand and edit and that can be validated and applied using any of the various programmatic approaches to working with OWL ontologies...
June 5, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28570594/automated-high-throughput-nucleic-acid-purification-from-formalin-fixed-paraffin-embedded-tissue-samples-for-next-generation-sequence-analysis
#3
Simon Haile, Pawan Pandoh, Helen McDonald, Richard D Corbett, Philip Tsao, Heather Kirk, Tina MacLeod, Martin Jones, Steve Bilobram, Denise Brooks, Duane Smailus, Christian Steidl, David W Scott, Miruna Bala, Martin Hirst, Diane Miller, Richard A Moore, Andrew J Mungall, Robin J Coope, Yussanne Ma, Yongjun Zhao, Rob A Holt, Steven J Jones, Marco A Marra
Curation and storage of formalin-fixed, paraffin-embedded (FFPE) samples are standard procedures in hospital pathology laboratories around the world. Many thousands of such samples exist and could be used for next generation sequencing analysis. Retrospective analyses of such samples are important for identifying molecular correlates of carcinogenesis, treatment history and disease outcomes. Two major hurdles in using FFPE material for sequencing are the damaged nature of the nucleic acids and the labor-intensive nature of nucleic acid purification...
2017: PloS One
https://www.readbyqxmd.com/read/28559340/microlayer-source-of-oxygenated-volatile-organic-compounds-in-the-summertime-marine-arctic-boundary-layer
#4
Emma L Mungall, Jonathan P D Abbatt, Jeremy J B Wentzell, Alex K Y Lee, Jennie L Thomas, Marjolaine Blais, Michel Gosselin, Lisa A Miller, Tim Papakyriakou, Megan D Willis, John Liggio
Summertime Arctic shipboard observations of oxygenated volatile organic compounds (OVOCs) such as organic acids, key precursors of climatically active secondary organic aerosol (SOA), are consistent with a novel source of OVOCs to the marine boundary layer via chemistry at the sea surface microlayer. Although this source has been studied in a laboratory setting, organic acid emissions from the sea surface microlayer have not previously been observed in ambient marine environments. Correlations between measurements of OVOCs, including high levels of formic acid, in the atmosphere (measured by an online high-resolution time-of-flight mass spectrometer) and dissolved organic matter in the ocean point to a marine source for the measured OVOCs...
June 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28539120/comprehensive-whole-genome-sequence-analyses-yields-novel-genetic-and-structural-insights-for-intellectual-disability
#5
Farah R Zahir, Jill C Mwenifumbo, Hye-Jung E Chun, Emilia L Lim, Clara D M Van Karnebeek, Madeline Couse, Karen L Mungall, Leora Lee, Nancy Makela, Linlea Armstrong, Cornelius F Boerkoel, Sylvie L Langlois, Barbara M McGillivray, Steven J M Jones, Jan M Friedman, Marco A Marra
BACKGROUND: Intellectual Disability (ID) is among the most common global disorders, yet etiology is unknown in ~30% of patients despite clinical assessment. Whole genome sequencing (WGS) is able to interrogate the entire genome, providing potential to diagnose idiopathic patients. METHODS: We conducted WGS on eight children with idiopathic ID and brain structural defects, and their normal parents; carrying out an extensive data analyses, using standard and discovery approaches...
May 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28532962/from-snomed-ct-to-uberon-transferability-of-evaluation-methodology-between-similarly-structured-ontologies
#6
Gai Elhanan, Christopher Ochs, Jose L V Mejino, Hao Liu, Christopher J Mungall, Yehoshua Perl
OBJECTIVE: To examine whether disjoint partial-area taxonomy, a semantically-based evaluation methodology that has been successfully tested in SNOMED CT, will perform with similar effectiveness on Uberon, an anatomical ontology that belongs to a structurally similar family of ontologies as SNOMED CT. METHOD: A disjoint partial-area taxonomy was generated for Uberon. One hundred randomly selected test concepts that overlap between partial-areas were matched to a same size control sample of non-overlapping concepts...
May 19, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28515149/pyruvate-kinase-inhibits-proliferation-during-postnatal-cerebellar-neurogenesis-and-suppresses-medulloblastoma-formation
#7
Katherine Tech, Andrey P Tikunov, Hamza Farooq, A Sorana Morrissy, Jessica Meidinger, Taylor Fish, Sarah C Green, Hedi Liu, Yisu Li, Andrew J Mungall, Richard A Moore, Yussanne Ma, Steven J M Jones, Marco A Marra, Matthew G Vander Heiden, Michael D Taylor, Jeffrey M Macdonald, Timothy R Gershon
Aerobic glycolysis supports proliferation through unresolved mechanisms. We have previously shown that aerobic glycolysis is required for the regulated proliferation of cerebellar granule neuron progenitors (CGNP) and for the growth of CGNP-derived medulloblastoma. Blocking the initiation of glycolysis via deletion of hexokinase-2 (Hk2) disrupts CGNP proliferation and restricts medulloblastoma growth. Here, we assessed whether disrupting pyruvate kinase-M (Pkm), an enzyme that acts in the terminal steps of glycolysis, would alter CGNP metabolism, proliferation, and tumorigenesis...
June 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28514723/genomic-profiling-of-pelvic-genital-type-leiomyosarcoma-in-a-woman-with-a-germline-chek2-c-1100delc-mutation-and-a-concomitant-diagnosis-of-metastatic-invasive-ductal-breast-carcinoma
#8
My Linh Thibodeau, Caralyn Reisle, Eric Zhao, Lee Ann Martin, Yazeed Alwelaie, Karen L Mungall, Carolyn Ch'ng, Ruth Thomas, Tony Ng, Stephen Yip, Howard Lim, Sophie Sun, Sean S Young, Aly Karsan, Yongjun Zhao, Andrew J Mungall, Richard A Moore, Daniel Renouf, Karen Gelmon, Yussanne P Ma, Malcolm Hayes, Janessa Laskin, Marco A Marra, Kasmintan A Schrader, Steven J M Jones
INTRODUCTION: We describe a woman with the known pathogenic germline variant CHEK2:c.1100delC and synchronous diagnoses of both pelvic genital type leiomyosarcoma and metastatic invasive ductal breast carcinoma. CHEK2 (checkpoint kinase 2) is a tumour suppressor gene encoding a serine/threonine-protein kinase (CHEK2) involved in double-strand DNA break repair and cell cycle arrest. The CHEK2:c.1100delC variant is a moderate penetrance allele resulting in an approximate 2-fold increase in breast cancer risk...
May 16, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28486579/biomake-a-gnu-make-compatible-utility-for-declarative-workflow-management
#9
Ian H Holmes, Christopher J Mungall
. The Unix "make" program is widely used in bioinformatics pipelines, but suffers from problems that limit its application to large analysis datasets. These include reliance on file modification times to determine whether a target is stale, lack of support for parallel execution on clusters, and restricted flexibility to extend the underlying logic program. . We present BioMake, a make-like utility that is compatible with most features ofGNUMake and adds support for popular cluster-based job-queue engines, MD5 signatures as an alternative to timestamps, and logic programming extensions in Prolog...
May 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28436987/genomic-consequences-of-aberrant-dna-repair-mechanisms-stratify-ovarian-cancer-histotypes
#10
Yi Kan Wang, Ali Bashashati, Michael S Anglesio, Dawn R Cochrane, Diljot S Grewal, Gavin Ha, Andrew McPherson, Hugo M Horlings, Janine Senz, Leah M Prentice, Anthony N Karnezis, Daniel Lai, Mohamed R Aniba, Allen W Zhang, Karey Shumansky, Celia Siu, Adrian Wan, Melissa K McConechy, Hector Li-Chang, Alicia Tone, Diane Provencher, Manon de Ladurantaye, Hubert Fleury, Aikou Okamoto, Satoshi Yanagida, Nozomu Yanaihara, Misato Saito, Andrew J Mungall, Richard Moore, Marco A Marra, C Blake Gilks, Anne-Marie Mes-Masson, Jessica N McAlpine, Samuel Aparicio, David G Huntsman, Sohrab P Shah
We studied the whole-genome point mutation and structural variation patterns of 133 tumors (59 high-grade serous (HGSC), 35 clear cell (CCOC), 29 endometrioid (ENOC), and 10 adult granulosa cell (GCT)) as a substrate for class discovery in ovarian cancer. Ab initio clustering of integrated point mutation and structural variation signatures identified seven subgroups both between and within histotypes. Prevalence of foldback inversions identified a prognostically significant HGSC group associated with inferior survival...
June 2017: Nature Genetics
https://www.readbyqxmd.com/read/28403581/correction-mir-509-3p-is-clinically-significant-and-strongly-attenuates-cellular-migration-and-multi-cellular-spheroids-in-ovarian-cancer
#11
Yinghong Pan, Gordon Robertson, Lykke Pedersen, Emilia Lim, Anadulce Hernandez-Herrera, Amy C Rowat, Sagar L Patil, Clara K Chan, Yunfei Wen, Xinna Zhang, Upal Basu-Roy, Alka Mansukhani, Andy Chu, Payal Sipahimalani, Reanne Bowlby, Denise Brooks, Nina Thiessen, Cristian Coarfa, Yussanne Ma, Richard A Moore, Jacquie E Schein, Andrew J Mungall, Jinsong Liu, Chad V Pecot, Anil K Sood, Steven J M Jones, Marco A Marra, Preethi H Gunaratne
No abstract text is available yet for this article.
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28394352/spatial-heterogeneity-in-medulloblastoma
#12
A Sorana Morrissy, Florence M G Cavalli, Marc Remke, Vijay Ramaswamy, David J H Shih, Borja L Holgado, Hamza Farooq, Laura K Donovan, Livia Garzia, Sameer Agnihotri, Erin N Kiehna, Eloi Mercier, Chelsea Mayoh, Simon Papillon-Cavanagh, Hamid Nikbakht, Tenzin Gayden, Jonathon Torchia, Daniel Picard, Diana M Merino, Maria Vladoiu, Betty Luu, Xiaochong Wu, Craig Daniels, Stuart Horswell, Yuan Yao Thompson, Volker Hovestadt, Paul A Northcott, David T W Jones, John Peacock, Xin Wang, Stephen C Mack, Jüri Reimand, Steffen Albrecht, Adam M Fontebasso, Nina Thiessen, Yisu Li, Jacqueline E Schein, Darlene Lee, Rebecca Carlsen, Michael Mayo, Kane Tse, Angela Tam, Noreen Dhalla, Adrian Ally, Eric Chuah, Young Cheng, Patrick Plettner, Haiyan I Li, Richard D Corbett, Tina Wong, William Long, James Loukides, Pawel Buczkowicz, Cynthia E Hawkins, Uri Tabori, Brian R Rood, John S Myseros, Roger J Packer, Andrey Korshunov, Peter Lichter, Marcel Kool, Stefan M Pfister, Ulrich Schüller, Peter Dirks, Annie Huang, Eric Bouffet, James T Rutka, Gary D Bader, Charles Swanton, Yusanne Ma, Richard A Moore, Andrew J Mungall, Jacek Majewski, Steven J M Jones, Sunit Das, David Malkin, Nada Jabado, Marco A Marra, Michael D Taylor
Spatial heterogeneity of transcriptional and genetic markers between physically isolated biopsies of a single tumor poses major barriers to the identification of biomarkers and the development of targeted therapies that will be effective against the entire tumor. We analyzed the spatial heterogeneity of multiregional biopsies from 35 patients, using a combination of transcriptomic and genomic profiles. Medulloblastomas (MBs), but not high-grade gliomas (HGGs), demonstrated spatially homogeneous transcriptomes, which allowed for accurate subgrouping of tumors from a single biopsy...
May 2017: Nature Genetics
https://www.readbyqxmd.com/read/28245243/serelaxin-as-a-potential-treatment-for-renal-dysfunction-in-cirrhosis-preclinical-evaluation-and-results-of-a-randomized-phase-2-trial
#13
Victoria K Snowdon, Neil J Lachlan, Anna M Hoy, Patrick W F Hadoke, Scott I Semple, Dilip Patel, Will Mungall, Timothy J Kendall, Adrian Thomson, Ross J Lennen, Maurits A Jansen, Carmel M Moran, Antonella Pellicoro, Prakash Ramachandran, Isaac Shaw, Rebecca L Aucott, Thomas Severin, Rajnish Saini, Judy Pak, Denise Yates, Neelesh Dongre, Jeremy S Duffield, David J Webb, John P Iredale, Peter C Hayes, Jonathan A Fallowfield
BACKGROUND: Chronic liver scarring from any cause leads to cirrhosis, portal hypertension, and a progressive decline in renal blood flow and renal function. Extreme renal vasoconstriction characterizes hepatorenal syndrome, a functional and potentially reversible form of acute kidney injury in patients with advanced cirrhosis, but current therapy with systemic vasoconstrictors is ineffective in a substantial proportion of patients and is limited by ischemic adverse events. Serelaxin (recombinant human relaxin-2) is a peptide molecule with anti-fibrotic and vasoprotective properties that binds to relaxin family peptide receptor-1 (RXFP1) and has been shown to increase renal perfusion in healthy human volunteers...
February 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28223492/role-of-degassing-of-the-noril-sk-nickel-deposits-in-the-permian-triassic-mass-extinction-event
#14
Margaux Le Vaillant, Stephen J Barnes, James E Mungall, Emma L Mungall
The largest mass extinction event in Earth's history marks the boundary between the Permian and Triassic Periods at circa 252 Ma and has been linked with the eruption of the basaltic Siberian Traps large igneous province (SLIP). One of the kill mechanisms that has been suggested is a biogenic methane burst triggered by the release of vast amounts of nickel into the atmosphere. A proposed Ni source lies within the huge Noril'sk nickel ore deposits, which formed in magmatic conduits widely believed to have fed the eruption of the SLIP basalts...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28201737/effectiveness-of-a-screening-programme-in-identifying-individuals-with-increased-risk-of-cardiovascular-disease-in-south-africa
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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