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genome-wide association

Yao-Ting Huang, Jan-Fang Cheng, Shi-Yu Chen, Yu-Kai Hong, Zong-Yen Wu, Po-Yu Liu
OBJECTIVES: Shewanella algae is an environmental marine bacteria and an emerging opportunistic human pathogen. Moreover, there are increasing reports of strains showing multi-drug resistance, particularly carbapenem-resistant isolates. Although S. algae have been found in bivalve shellfish aquaculture, there is very little genome-wide data on resistant determinants in S. algae from shellfish. In the study, we aimed to determine the whole genome sequence of carbapenem-resistant S. algae strain AC isolated from small abalone in Taiwan...
June 19, 2018: Journal of Global Antimicrobial Resistance
Ruifen Miao, Shuran Huang, Chen Li, Songning Ding, Rong Wang, Ke Xu, Chen Yang, Fei Xu, Haibo Ge
OBJECTIVE: Genome-wide association study (GWAS) in Icelanders identified HLA class II sequence variants on chromosome 6p21 as tuberculosis (TB) susceptibility loci. To evaluate the role of these loci in other populations with different ancestry, we conducted a case-control study in Chinese population. METHODS: We genotyped two genetic variants (rs9272461 and rs9271300) on the reported chromosome 6p21 in 739 pulmonary tuberculosis (PTB) cases and 749 healthy controls from Chinese Han population using TaqMan allelic discrimination assay...
June 19, 2018: Infection, Genetics and Evolution
Kritarth Singh, Lakshmi Sripada, AnastasiaLipatova, Milton Roy, Paresh Prajapati, Dhruv Gohil, Khyati Bhatelia, Peter M Chumakov, Rajesh Singh
The role of mitochondria is emerging in regulation of innate immunity, inflammation and cell death beyond its primary role in energy metabolism. Mitochondria act as molecular platform for immune adaptor protein complexes, which participate in innate immune signaling. The mitochondrial localized immune adaptors are widely expressed in non-immune cells, however their role in regulation of mitochondrial function and metabolic adaption is not well understood. NLRX1, a member of NOD family receptor proteins, localizes to mitochondria and is a negative regulator of anti-viral signaling...
June 19, 2018: Biochimica et Biophysica Acta
Maria Keller, Matthias Klös, Kerstin Rohde, Jacqueline Krüger, Tabea Kurze, Arne Dietrich, Michael R Schön, Daniel Gärtner, Tobias Lohmann, Miriam Dreßler, Michael Stumvoll, Matthias Blüher, Peter Kovacs, Yvonne Böttcher
DNA methylation is a crucial epigenetic mechanism in obesity and fat distribution. We explored the Sarcospan ( SSPN) gene locus by using genome-wide data sets comprising methylation and expression data, pyrosequencing analysis in the promoter region, and genetic analysis of an SNP variant rs718314, which was previously reported to associate with waist-to-hip ratio. We found that DNA methylation influences several clinical variables related to fat distribution and glucose metabolism, while SSPN mRNA levels showed directionally opposite effects on these traits...
June 22, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
N Dürig, A Letko, V Lepori, S Hadji Rasouliha, R Loechel, A Kehl, M K Hytönen, H Lohi, N Mauri, J Dietrich, M Wiedmer, M Drögemüller, V Jagannathan, S M Schmutz, T Leeb
Loss-of-function variants in the MC1R gene cause recessive red or yellow coat-colour phenotypes in many species. The canine MC1R:c.916C>T (p.Arg306Ter) variant is widespread and found in a homozygous state in many uniformly yellow- or red-coloured dogs. We investigated cream-coloured Australian Cattle Dogs whose coat colour could not be explained by this variant. A genome-wide association study with 10 cream and 123 red Australian Cattle Dogs confirmed that the cream locus indeed maps to MC1R. Whole-genome sequencing of cream dogs revealed a single nucleotide variant within the MITF binding site of the canine MC1R promoter...
June 22, 2018: Animal Genetics
T Chang, J Xia, L Xu, X Wang, B Zhu, L Zhang, X Gao, Y Chen, J Li, H Gao
A genome-wide association study (GWAS) was conducted for two carcass traits in Chinese Simmental beef cattle. The experimental population consisted of 1301 individuals genotyped with the Illumina BovineHD SNP BeadChip (770K). After quality control, 671 990 SNPs and 1217 individuals were retained for the GWAS. The phenotypic traits included carcass weight and bone weight, which were measured after the cattle were slaughtered at 16 to 18 months of age. Three statistical models-a fixed polygene model, a random polygene model and a composite interval mapping polygene model-were used for the GWAS...
June 22, 2018: Animal Genetics
Cosmika Goswami, Stephen Fox, Matthew Holden, Martin Connor, Alistair Leanord, Thomas J Evans
Bacteraemia caused by Escherichia coli is a growing problem with a significant mortality. The factors that influence the acquisition and outcome of these infections are not clear. Here, we have linked detailed genetic data from the whole-genome sequencing of 162 bacteraemic isolates collected in Scotland, UK, in 2013-2015, with clinical data in order to delineate bacterial and host factors that influence the acquisition in hospital or the community, outcome and antibiotic resistance. We identified four major sequence types (STs) in these isolates: ST131, ST69, ST73 and ST95...
June 22, 2018: Microbial Genomics
Andreas Wanninger, Tim Wollesen
Molluscs are extremely diverse invertebrate animals with a rich fossil record, highly divergent life cycles, and considerable economical and ecological importance. Key representatives include worm-like aplacophorans, armoured groups (e.g. polyplacophorans, gastropods, bivalves) and the highly complex cephalopods. Molluscan origins and evolution of their different phenotypes have largely remained unresolved, but significant progress has been made over recent years. Phylogenomic studies revealed a dichotomy of the phylum, resulting in Aculifera (shell-less aplacophorans and multi-shelled polyplacophorans) and Conchifera (all other, primarily uni-shelled groups)...
June 21, 2018: Biological Reviews of the Cambridge Philosophical Society
Thao P Ho-Le, Hanh M Pham, Jacqueline R Center, John A Eisman, Hung T Nguyen, Tuan V Nguyen
The contribution of genetic variants to longitudinal bone loss has not been well documented. We constructed an "osteogenomic profile" based on 62 BMD-associated genetic variants and showed that the profile was significantly associated with bone loss, independently from baseline BMD and age. The osteogenomic profile can help predict bone loss in an individual. INTRODUCTION: The rate of longitudinal bone loss (ΔBMD) is a risk factor for fracture. The variation in ΔBMD is partly determined by genetic factors...
June 21, 2018: Archives of Osteoporosis
A Jabrocka-Hybel, A Skalniak, J Piątkowski, R Turek-Jabrocka, P Vyhouskaya, A Ludwig-Słomczyńska, J Machlowska, P Kapusta, M Małecki, D Pach, M Trofimiuk-Müldner, K Lizis-Kolus, A Hubalewska-Dydejczyk
PURPOSE: Our insight in the genetics of Hashimoto's thyroiditis (HT) has become clearer through information provided by genome-wide association studies and candidate gene studies, but remains still not fully understood. Our aim was to assess how many different genetic risk variants contribute to the development of HT. METHODS: 147 HT cases (10.2% men) and 147 controls (13.6% men) were qualified for the analysis. Intrinsic and environmental factors were controlled for...
June 21, 2018: Journal of Endocrinological Investigation
Chloé Sarnowski, Marie-France Hivert
PURPOSE OF REVIEW: Glycated hemoglobin (A1c) is used to diagnose type 2 diabetes and monitor glycemic control. Specific genetic variants interfere with A1c and effects/frequencies of some variants vary by ancestry. In this review, we summarize findings from large trans-ethnic meta-analyses of genome-wide association studies (GWAS) of A1c and describe some variants influencing erythrocyte biology and interfering with A1c. RECENT FINDINGS: Recent GWAS meta-analyses have revealed 60 loci associated with A1c in multi-ethnic populations...
June 21, 2018: Current Diabetes Reports
Jennifer N Todd, Shylaja Srinivasan, Toni I Pollin
PURPOSE OF REVIEW: To provide an update on knowledge the role of genetics in youth-onset type 2 diabetes (T2D). RECENT FINDINGS: The prevalence in youth of T2D, once thought to be exclusively a disease of adults, has increased by over 35% since 2001. Youth with T2D tend to have higher rates of complications, more aggressive disease, with more rapid loss of beta-cell function and a less favorable response to treatment than adults. Obesity is the most important risk factor for T2D, and the rise in childhood overweight and obesity appears responsible for the dramatic increase in T2D in youth...
June 22, 2018: Current Diabetes Reports
Simon Haworth, Dmitry Shungin, Justin T van der Tas, Strahinja Vucic, Carolina Medina-Gomez, Victor Yakimov, Bjarke Feenstra, John R Shaffer, Myoung Keun Lee, Marie Standl, Elisabeth Thiering, Carol Wang, Klaus Bønnelykke, Johannes Waage, Leon Eyrich Jessen, Pia Elisabeth Nørrisgaard, Raimo Joro, Ilkka Seppälä, Olli Raitakari, Tom Dudding, Olja Grgic, Edwin Ongkosuwito, Anu Vierola, Aino-Maija Eloranta, Nicola X West, Steven J Thomas, Daniel W McNeil, Steven M Levy, Rebecca Slayton, Ellen A Nohr, Terho Lehtimäki, Timo Lakka, Hans Bisgaard, Craig Pennell, Jan Kühnisch, Mary L Marazita, Mads Melbye, Frank Geller, Fernando Rivadeneira, Eppo B Wolvius, Paul W Franks, Ingegerd Johansson, Nicholas J Timpson
Prior studies suggest dental caries traits in children and adolescents are partially heritable, but there has been no large-scale consortium genome-wide association study (GWAS) to date. We therefore performed GWAS for caries in participants aged 2.5-18.0 years from 9 contributing centres. Phenotype definitions were created for the presence or absence of treated or untreated caries, stratified by primary and permanent dentition. All studies tested for association between caries and genotype dosage and results were combined using fixed-effects meta-analysis...
June 20, 2018: Human Molecular Genetics
J L Min, G Hemani, G Davey Smith, C Relton, M Suderman
Motivation: DNA methylation datasets are growing ever larger both in sample size and genome coverage. Novel computational solutions are required to efficiently handle these data. Results: We have developed meffil, an R package designed for efficient quality control, normalization and epigenome-wide association studies of large samples of Illumina Methylation BeadChip microarrays. A complete reimplementation of functional normalization minimizes computational memory without increasing running time...
June 21, 2018: Bioinformatics
Julian M Rozenberg, Joan M Taylor, Christopher P Mack
Given our previous demonstration that RBPJ binds a methylated repressor element and regulates smooth muscle cell (SMC)-specific gene expression, we used genome-wide approaches to identify RBPJ binding regions in human aortic SMC and to assess RBPJ's effects on chromatin structure and gene expression. RBPJ bound to consensus cis elements, but also to TCmGGGA sequences within Alu repeats that were less transcriptionally active as assessed by DNAse hypersensitivity, H3K9 acetylation, and Notch3 and RNA Pol II binding...
June 21, 2018: Nucleic Acids Research
Peilin Jia, Xiangning Chen, Wei Xie, Kenneth S Kendler, Zhongming Zhao
Numerous high-throughput omics studies have been conducted in schizophrenia, providing an accumulated catalog of susceptible variants and genes. The results from these studies, however, are highly heterogeneous. The variants and genes nominated by different omics studies often have limited overlap with each other. There is thus a pressing need for integrative analysis to unify the different types of data and provide a convergent view of schizophrenia candidate genes (SZgenes). In this study, we collected a comprehensive, multidimensional dataset, including 7819 brain-expressed genes...
June 20, 2018: Schizophrenia Bulletin
Nilotpal Sanyal, Min-Tzu Lo, Karolina Kauppi, Srdjan Djurovic, Ole A Andreassen, Valen E Johnson, Chi-Hua Chen
Motivation: Multiple marker analysis of the genome-wide association study (GWAS) data has gained ample attention in recent years. However, because of the ultra high-dimensionality of GWAS data, such analysis is challenging. Frequently used penalized regression methods often lead to large number of false positives, whereas Bayesian methods are computationally very expensive. Motivated to ameliorate these issues simultaneously, we consider the novel approach of using nonlocal priors in an iterative variable selection framework...
June 19, 2018: Bioinformatics
Wolfgang Lieb, Ramachandran S Vasan
Longitudinal, well phenotyped, population-based cohort studies offer unique research opportunities in the context of genome-wide association studies (GWAS), including GWAS for new-onset (incident) cardiovascular disease (CVD) events, the assessment of gene x lifestyle interactions, and evaluating the incremental predictive utility of genetic information in apparently healthy individuals. Furthermore, comprehensively phenotyped community-dwelling samples have contributed to GWAS of numerous traits that reflect normal organ function (e...
2018: Frontiers in Cardiovascular Medicine
Yoshiji Yamada, Kimihiko Kato, Mitsutoshi Oguri, Hideki Horibe, Tetsuo Fujimaki, Yoshiki Yasukochi, Ichiro Takeuchi, Jun Sakuma
Given that early-onset type 2 diabetes mellitus (T2DM), metabolic syndrome (MetS), and hyperuricemia have been shown to have strong genetic components, the statistical power of a genetic association study may be increased by focusing on early-onset subjects with these conditions. Although genome-wide association studies have identified various genes and loci significantly associated with T2DM, MetS, and hyperuricemia, genetic variants that contribute to predisposition to these conditions in Japanese subjects remain to be identified definitively...
July 2018: Biomedical Reports
Yoshiji Yamada, Kimihiko Kato, Mitsutoshi Oguri, Hideki Horibe, Tetsuo Fujimaki, Yoshiki Yasukochi, Ichiro Takeuchi, Jun Sakuma
Given that substantial genetic components have been shown in ischemic stroke, intracerebral hemorrhage (ICH), and subarachnoid hemorrhage (SAH), heritability may be higher in early-onset than late-onset individuals with these conditions. Although genome-wide association studies (GWASs) have identified various genes and loci significantly associated with ischemic stroke, ICH, or intracranial aneurysm mainly in European ancestry populations, genetic variants that contribute to susceptibility to these disorders remain to be identified definitively...
July 2018: Biomedical Reports
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