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genomic epidemiology

David G Cox, Elsa Curtit, Gilles Romieu, Pierre Fumoleau, Maria Rios, Hervé Bonnefoi, Thomas Bachelot, Patrick Soulié, Christelle Jouannaud, Hugues Bourgeois, Thierry Petit, Isabelle Tennevet, David Assouline, Marie-Christine Mathieu, Jean-Philippe Jacquin, Sandrine Lavau-Denes, Ariane Darut-Jouve, Jean-Marc Ferrero, Carole Tarpin, Christelle Lévy, Valérie Delecroix, Véronique Trillet-Lenoir, Oana Cojocarasu, Jérôme Meunier, Jean-Yves Pierga, Céline Faure-Mercier, Hélène Blanché, Mourad Sahbatou, Anne Boland, Delphine Bacq, Céline Besse, Jean-François Deleuze, Iris Pauporté, Gilles Thomas, Xavier Pivot
Genetic polymorphisms are associated with breast cancer risk. Clinical and epidemiological observations suggest that clinical characteristics of breast cancer, such as estrogen receptor or HER2 status, are also influenced by hereditary factors. To identify genetic variants associated with pathological characteristics of breast cancer patients, a Genome Wide Association Study was performed in a cohort of 9365 women from the French nationwide SIGNAL/PHARE studies (NCT00381901/RECF1098). Strong association between the FGFR2 locus and ER status of breast cancer patients was observed (ER-positive n=6211, ER-negative n=2516; rs3135718 OR=1...
October 14, 2016: Oncotarget
Johanna Jakobsdottir, Sven J van der Lee, Joshua C Bis, Vincent Chouraki, David Li-Kroeger, Shinya Yamamoto, Megan L Grove, Adam Naj, Maria Vronskaya, Jose L Salazar, Anita L DeStefano, Jennifer A Brody, Albert V Smith, Najaf Amin, Rebecca Sims, Carla A Ibrahim-Verbaas, Seung-Hoan Choi, Claudia L Satizabal, Oscar L Lopez, Alexa Beiser, M Arfan Ikram, Melissa E Garcia, Caroline Hayward, Tibor V Varga, Samuli Ripatti, Paul W Franks, Göran Hallmans, Olov Rolandsson, Jan-Håkon Jansson, David J Porteous, Veikko Salomaa, Gudny Eiriksdottir, Kenneth M Rice, Hugo J Bellen, Daniel Levy, Andre G Uitterlinden, Valur Emilsson, Jerome I Rotter, Thor Aspelund, Christopher J O'Donnell, Annette L Fitzpatrick, Lenore J Launer, Albert Hofman, Li-San Wang, Julie Williams, Gerard D Schellenberg, Eric Boerwinkle, Bruce M Psaty, Sudha Seshadri, Joshua M Shulman, Vilmundur Gudnason, Cornelia M van Duijn
We performed an exome-wide association analysis in 1393 late-onset Alzheimer's disease (LOAD) cases and 8141 controls from the CHARGE consortium. We found that a rare variant (P155L) in TM2D3 was enriched in Icelanders (~0.5% versus <0.05% in other European populations). In 433 LOAD cases and 3903 controls from the Icelandic AGES sub-study, P155L was associated with increased risk and earlier onset of LOAD [odds ratio (95% CI) = 7.5 (3.5-15.9), p = 6.6x10-9]. Mutation in the Drosophila TM2D3 homolog, almondex, causes a phenotype similar to loss of Notch/Presenilin signaling...
October 2016: PLoS Genetics
Thomas J Hoffmann, Bronya J Keats, Noriko Yoshikawa, Catherine Schaefer, Neil Risch, Lawrence R Lustig
Age-related hearing impairment (ARHI), one of the most common sensory disorders, can be mitigated, but not cured or eliminated. To identify genetic influences underlying ARHI, we conducted a genome-wide association study of ARHI in 6,527 cases and 45,882 controls among the non-Hispanic whites from the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. We identified two novel genome-wide significant SNPs: rs4932196 (odds ratio = 1.185, p = 4.0x10-11), 52Kb 3' of ISG20, which replicated in a meta-analysis of the other GERA race/ethnicity groups (1,025 cases, 12,388 controls, p = 0...
October 2016: PLoS Genetics
Maria Stefania Latrofa, Alessio Giannelli, Maria Flaminia Persichetti, Maria Grazia Pennisi, Laia Solano-Gallego, Emanuele Brianti, Antonio Parisi, Richard Wall, Filipe Dantas-Torres, Domenico Otranto
Despite their medical and veterinary importance, some tick species are so poorly studied, that their role within pathogen vector transmission cycles is difficult to assess. The tick Ixodes ventalloi is one such species, and its biology and phylogenetic status remain an issue of debate. In the present study, specimens of adult I. ventalloi (n = 65 females; n = 31 males) infesting cats in the Lipari Island (Aeolian archipelago, Sicily, southern Italy) were characterized morphologically and molecularly, the latter based on mitochondrial 16S rRNA and cytochrome c oxidase subunit 1 (cox1) genes...
October 20, 2016: Parasitology Research
N C Knox, K A Weedmark, J Conly, A W Ensminger, F S Hosein, S J Drews
An outbreak of Legionnaires' disease occurred in an inner city district in Calgary, Canada. This outbreak spanned a 3-week period in November-December 2012, and a total of eight cases were identified. Four of these cases were critically ill requiring intensive care admission but there was no associated mortality. All cases tested positive for Legionella pneumophila serogroup 1 (LP1) by urinary antigen testing. Five of the eight patients were culture positive for LP1 from respiratory specimens. These isolates were further identified as Knoxville monoclonal subtype and sequence subtype ST222...
October 20, 2016: Epidemiology and Infection
Sarah A Weiss, Joseph Han, Farbod Darvishian, Jeremy Tchack, Sung Won Han, Karolina Malecek, Michelle Krogsgaard, Iman Osman, Judy Zhong
BACKGROUND: Age has been reported as an independent prognostic factor for melanoma-specific survival (MSS). We tested the hypothesis that age impacts the host anti-tumor immune response, accounting for age-specific survival outcomes in three unique melanoma patient cohorts. METHODS: We queried the U.S. population-based Surveillance, Epidemiology, and End Results Program (SEER), the prospective tertiary care hospital-based Interdisciplinary Melanoma Cooperative Group (IMCG) biorepository, and the Cancer Genome Atlas (TCGA) biospecimen database to test the association of patient age at time of melanoma diagnosis with clinicopathologic features and survival outcomes...
October 19, 2016: Journal of Translational Medicine
Soledad Sagastume, Raquel Martín-Hernández, Mariano Higes, Nuno Henriques-Gil
BACKGROUND: There is great controversy as to whether Microsporidia undergo a sexual cycle. In the paradigmatic case of Nosema ceranae, although there is no morphological evidence of sex, some meiosis-specific genes are present in its reduced genome and there is also high intraspecific variability, with incongruent phylogenies having been systematically obtained. The possibility of sexual recombination is important from an epidemiological standpoint, particularly as N. ceranae is considered to be a major factor in the current disquieting epidemic of widespread bee colony losses...
October 18, 2016: BMC Evolutionary Biology
Hyung Tak Lee, Jinho Shin Shin, Jin-Kyu Park, Young-Hyo Lim
OBJECTIVE: The aim of this study is to evaluate the effect of visit-to-visit variability (VVV) of blood pressure (BP) on development of metabolic syndrome (Mets) in general population without cardiovascular disease, diabetes mellitus, MetS, and BP medication. DESIGN AND METHOD: We used data from the Korean Genome Epidemiology Study (KoGES) conducted by the Korean Centers for Disease Control and Prevention (KCDC). All cohorts who were followed first 3 periods without omission, formed the basis of the study sample, which consisted of 7195 people...
September 2016: Journal of Hypertension
Tien Wong
The vasculature in the retina can be viewed directly and non-invasively in vivo, offers a unique perspective of the human microvasculature, and therefore the ability to understand early changes, processes, pathways and consequences of hypertension. In the past 15 years, advances in high resolution digital retinal photography and automated or semi-automated computer image software have been applied to measure and quantify a variety of retinal microvascular parameter, including retinal arteriolar and venular caliber, tortuosity, branching patterns and fractal dimensions...
September 2016: Journal of Hypertension
Qian Wang, Renato Polimanti, Henry R Kranzler, Lindsay A Farrer, Hongyu Zhao, Joel Gelernter
Schizophrenia (SZ) and HIV infection are serious disorders with a complex phenotypic relationship. Observational studies have described their comorbidity; their genetic correlation is not well studied. We performed extensive analysis in search of common genetic factors for SZ and HIV, and their relationship with risky sexual behavior (RSB). Summary statistics from genome-wide association studies of HIV infection and schizophrenia were obtained and 2379 European Americans were genotyped and assessed for RSB score...
October 17, 2016: Human Genetics
Yoonjin Shin, Yangha Kim
The aim of this study was to investigate the association of CD36, a class B scavenger receptor, rs6969989 polymorphism with the serum lipid profiles in Korean women, together with their modulation by oily fish consumption. Subjects were participants from the Korean Genome Epidemiology Study (KoGES), which was initiated in 2001 as a large-scale. A total of 4,210 women aged 39 to 70 were included in this study. Data were collected using self-administered questionnaires, anthropometric measurements, and blood chemical analysis...
September 2016: Preventive Nutrition and Food Science
H Harvala, E Alm, T Åkerlund, K Rizzardi
An aggregation of moxifloxacin-resistant Clostridium difficile ribotype 231 (RT231) isolates was first identified in the county of Stockholm in 2008, and by the end of 2015 isolates of RT231 had spread to 13 of 21 Swedish counties. We investigated the epidemiology of C. difficile RT231 in Sweden between 2006 and 2015 using whole genome sequencing (WGS) and evaluated whether its emergence could be associated with extended moxifloxacin use. We performed WGS and phylogenetic analysis of 51 C. difficile RT231 strains isolated in Sweden over a 10-year period...
November 2016: New Microbes and New Infections
Edson R A Oliveira, Ronaldo Mohana-Borges, Ricardo B de Alencastro, Bruno A C Horta
Flaviviruses, such as dengue and zika viruses, are etiologic agents transmitted to humans mainly by arthropods and are of great epidemiological interest. The flavivirus capsid protein is a structural element required for the viral nucleocapsid assembly that presents the classical function of sheltering the viral genome. After decades of research, many reports have shown its different functionalities and influence over cell normal functioning. The subcellular distribution of this protein, which involves accumulation around lipid droplets and nuclear localization, also corroborates with its multi-functional characteristic...
October 14, 2016: Virus Research
Paul J Planet, Apurva Narechania, Liang Chen, Barun Mathema, Sam Boundy, Gordon Archer, Barry Kreiswirth
A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions...
October 14, 2016: Trends in Microbiology
José E Belizário, Beatriz A Sangiuliano, Marcela Perez-Sosa, Jennifer M Neyra, Dayson F Moreira
With multiple omics strategies being applied to several cancer genomics projects, researchers have the opportunity to develop a rational planning of targeted cancer therapy. The investigation of such numerous and diverse pharmacogenomic datasets is a complex task. It requires biological knowledge and skills on a set of tools to accurately predict signaling network and clinical outcomes. Herein, we describe Web-based in silico approaches user friendly for exploring integrative studies on cancer biology and pharmacogenomics...
2016: Frontiers in Pharmacology
Laura Pérez-Lago, Santiago Izco, Marta Herranz, Griselda Tudó, María Carcelén, Iñaki Comas, Olalla Sierra, Juliá González, María Jesús Ruiz-Serrano, Juan Eyene, Emilio Bouza, Darío García-de-Viedma
OBJECTIVE: Molecular epidemiology techniques in tuberculosis (TB) can identify high-risk strains that are actively transmitted. We aimed to implement a novel strategy to optimize the identification and control of MDR-TB in a specific population. METHODS: We developed a strain-specific-PCR tailored from whole-genome-sequencing (WGS) data to track a specific multidrug-resistant prevalent strain in Equatorial Guinea (EG-MDR). RESULTS: The PCR was applied prospectively on remnants of GeneXpert reaction mixtures owing to the lack of culture facilities in EG...
October 13, 2016: Clinical Microbiology and Infection
G Kim, Y-H Lee, J Y Jeon, H Bang, B-W Lee, E S Kang, I-K Lee, B-S Cha, C S Kim
OBJECTIVE: The association between resting heart rate (RHR) and the development of diabetes has yet to be fully elucidated, and the relationship between changes in RHR and incidence of diabetes also remains unclear. Our study aimed to investigate the association between changes in RHR over 2 years and the risk of diabetes. METHODS: A total of 7416 adults without diabetes were included. All had participated in the Korean Genome and Epidemiology Study, a community-based, 10-year prospective study in which RHR was measured at baseline and 2 years later...
October 10, 2016: Diabetes & Metabolism
Kelly L Wyres, Kathryn E Holt
Antimicrobial-resistant Klebsiella pneumoniae (Kp) has emerged as a major global public health problem. While resistance can occur across a broad range of Kp clones, a small number have become globally distributed and commonly cause outbreaks in hospital settings. Here we describe recent comparative genomics investigations that have shed light on Kp population structure and the evolution of antimicrobial-resistant clones. These studies provide the basic framework within which genomic epidemiology and evolution can be understood, but have merely scratched the surface of what can and should be explored...
October 11, 2016: Trends in Microbiology
Tsai-Wen Wan, Olga E Khokhlova, Yasuhisa Iwao, Wataru Higuchi, Wei-Chun Hung, Ivan V Reva, Olga A Singur, Vladimir V Gostev, Sergey V Sidorenko, Olga V Peryanova, Alla B Salmina, Galina V Reva, Lee-Jene Teng, Tatsuo Yamamoto
ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaβ split...
2016: PloS One
Mary E Torrence
This introductory article provides an overview of preharvest food safety activities and initiatives for the past 15 years. The section on traditional areas of preharvest food safety focuses on significant scientific advancements that are a culmination of collaborative efforts (both public health and agriculture) and significant research results. The highlighted advancements provide the foundation for exploring future preharvest areas and for improving and focusing on more specific intervention/control/prevention strategies...
October 2016: Microbiology Spectrum
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