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https://www.readbyqxmd.com/read/28535255/tea-and-coffee-consumption-in-relation-to-dna-methylation-in-four-european-cohorts
#1
Weronica E Ek, Elmar W Tobi, Muhammad Ahsan, Erik Lampa, Erica Ponzi, Soterios A Kyrtopoulos, Panagiotis Georgiadis, L H Lumey, Bastiaan T Heijmans, Maria Botsivali, Ingvar A Bergdahl, Torgny Karlsson, Mathias Rask-Andersen, Domenico Palli, Erik Ingelsson, Åsa K Hedman, Lena M Nilsson, Paolo Vineis, Lars Lind, James M Flanagan, Åsa Johansson
Lifestyle factors, such as food choices and exposure to chemicals, can alter DNA methylation and lead to changes in gene activity. Two such exposures with pharmacologically active components are coffee and tea consumption. Both coffee and tea has been suggested to play an important role in modulating disease-risk in humans by suppressing tumour progression, decreasing inflammation and influencing estrogen metabolism. These mechanisms may be mediated by changes in DNA methylation.To investigate if DNA methylation in blood is associated with coffee and tea consumption we performed a genome-wide DNA methylation study for coffee and tea consumption in four European cohorts (N = 3,096)...
May 23, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28533441/trends-in-dna-methylation-with-age-replicate-across-diverse-human-populations
#2
Shyamalika Gopalan, Oana Carja, Maud Fagny, Etienne Patin, Justin W Myrick, Lisa M McEwen, Sarah M Mah, Michael S Kobor, Alain Froment, Marcus W Feldman, Lluis Quintana-Murci, Brenna M Henn
Aging is associated with widespread changes in genome-wide patterns of DNA methylation. Thousands of CpG sites whose tissue-specific methylation levels are strongly correlated with chronological age have been previously identified. However, the majority of these studies have focused primarily on cosmopolitan populations living in the developed world; it is not known if age-related patterns of DNA methylation at these loci are similar across a broad range of human genetic and ecological diversity. We investigated genome-wide methylation patterns using saliva- and whole blood-derived DNA from two traditionally hunting and gathering African populations: the Baka of the western Central African rainforest and the ≠Khomani San of the South African Kalahari Desert...
May 22, 2017: Genetics
https://www.readbyqxmd.com/read/28533336/a-coding-variant-in-the-gene-bardet-biedl-syndrome-4-bbs4-is-associated-with-a-novel-form-of-canine-progressive-retinal-atrophy
#3
Tracy Chew, Bianca Haase, Roslyn Bathgate, Cali E Willet, Maria K Kaukonen, Lisa J Mascord, Hannes T Lohi, Claire M Wade
Progressive retinal atrophy is a common cause of blindness in the dog and affects over 100 breeds. It is characterized by gradual vision loss that occurs due to the degeneration of photoreceptor cells in the retina. Similar to the human counterpart retinitis pigmentosa, the canine disorder is clinically and genetically heterogeneous and the underlying cause remains unknown for many cases. We use a positional candidate gene approach to identify putative variants in the Hungarian Puli breed using genotyping data of 14 family-based samples (CanineHD BeadChip array, Illumina) and whole genome sequencing data of two proband and two parental samples (Illumina HiSeq 2000)...
May 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28532434/hierarchical-genomic-analysis-of-carried-and-invasive-serogroup-a-neisseria-meningitidis-during-the-2011-epidemic-in-chad
#4
Kanny Diallo, Kadija Gamougam, Doumagoum M Daugla, Odile B Harrison, James E Bray, Dominique A Caugant, Jay Lucidarme, Caroline L Trotter, Musa Hassan-King, James M Stuart, Olivier Manigart, Brian M Greenwood, Martin C J Maiden
BACKGROUND: Serogroup A Neisseria meningitidis (NmA) was the cause of the 2011 meningitis epidemics in Chad. This bacterium, often carried asymptomatically, is considered to be an "accidental pathogen"; however, the transition from carriage to disease phenotype remains poorly understood. This study examined the role genetic diversity might play in this transition by comparing genomes from geographically and temporally matched invasive and carried NmA isolates. RESULTS: All 23 NmA isolates belonged to the ST-5 clonal complex (cc5)...
May 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28531898/plasma-et-1-concentrations-are-elevated-in-patients-with-hypertension-meta-analysis-of-clinical-studies
#5
Mei Xu, Yong-Ping Lu, Ahmed Abdallah Hasan, Berthold Hocher
BACKGROUND/AIMS: A recent study revealed that global overexpression of ET-1 causes a slight reduction in systemic blood pressure. Moreover, heterozygous ET-1 knockout mice are hypertensive. The role of ET-1 in human hypertension was so far not addressed by a strict meta-analysis of published human clinical studies. METHODS: We included studies published between January 1, 1990 and February 28, 2017. We included case control studies analyzing untreated essential hypertension or hypertensive patients where antihypertensive medication was discontinued for at least two weeks...
May 26, 2017: Kidney & Blood Pressure Research
https://www.readbyqxmd.com/read/28530654/allele-specific-expression-reveals-interactions-between-genetic-variation-and-environment
#6
David A Knowles, Joe R Davis, Hilary Edgington, Anil Raj, Marie-Julie Favé, Xiaowei Zhu, James B Potash, Myrna M Weissman, Jianxin Shi, Douglas F Levinson, Philip Awadalla, Sara Mostafavi, Stephen B Montgomery, Alexis Battle
Identifying interactions between genetics and the environment (GxE) remains challenging. We have developed EAGLE, a hierarchical Bayesian model for identifying GxE interactions based on associations between environmental variables and allele-specific expression. Combining whole-blood RNA-seq with extensive environmental annotations collected from 922 human individuals, we identified 35 GxE interactions, compared with only four using standard GxE interaction testing. EAGLE provides new opportunities for researchers to identify GxE interactions using functional genomic data...
May 22, 2017: Nature Methods
https://www.readbyqxmd.com/read/28526730/a-targeted-capture-linkage-map-anchors-the-genome-of-the-schistosomiasis-vector-snail-biomphalaria-glabrata
#7
Jacob A Tennessen, Stephanie R Bollmann, Michael S Blouin
The aquatic planorbid snail Biomphalaria glabrate is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here we used targeted capture markers to map over 10,000 B. glabrate scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups. We added additional scaffolds to these linkage groups based on linkage disequilibrium analysis of targeted capture and whole-genome sequences of 96 unrelated snails...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526032/multiplex-dnase-free-one-step-reverse-transcription-pcr-for-plasmodium-18s-rrna-and-spliced-gametocyte-specific-mrnas
#8
Amelia E Hanron, Zachary P Billman, Annette M Seilie, Tayla M Olsen, Matthew Fishbaugher, Ming Chang, Thomas Rueckle, Nicole Andenmatten, Bryan Greenhouse, Emmanuel Arinaitwe, John Rek, Smita Das, Gonzalo J Domingo, Kelly Shipman, Stefan H Kappe, James G Kublin, Sean C Murphy
BACKGROUND: Plasmodium gametocytes are sexual stages transmitted to female Anopheles mosquitoes. While Plasmodium parasites can be differentiated microscopically on Giemsa-stained blood smears, molecular methods are increasingly used because of their increased sensitivity. Molecular detection of gametocytes requires methods that discriminate between asexual and sexual stage parasites. Commonly tested gametocyte-specific mRNAs are pfs25 and pfs230 detected by reverse transcription polymerase chain reaction (RT-PCR)...
May 19, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28525288/inference-of-the-genetic-polymorphisms-of-cyp2d6-in-six-subtribes-of-the-malaysian-orang-asli-from-whole-genome-sequencing-data
#9
Choo Yee Yu, Geik Yong Ang, Vinothini Subramaniam, Richard Johari James, Aminuddin Ahmad, Thuhairah Abdul Rahman, Fadzilah Mohd Nor, Syahrul Azlin Shaari, Lay Kek Teh, Mohd Zaki Salleh
AIMS: CYP2D6 is one of the major enzymes in the cytochrome P450 monooxygenase system. It metabolizes ∼25% of prescribed drugs and hence, the genetic diversity of CYP2D6 gene has continued to be of great interest to the medical and pharmaceutical industries. This study aims to perform a systematic analysis of the CYP2D6 gene in six subtribes of the Malaysian Orang Asli. METHODS: Genomic DNAs were extracted from the blood samples followed by whole-genome sequencing...
May 19, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28521008/gemstone-orchestrated-prioritization-of-human-germline-mutations-in-the-cloud
#10
Siwei Chen, Juan F Beltrán, Clara Esteban-Jurado, Sebastià Franch-Expósito, Sergi Castellví-Bel, Steven Lipkin, Xiaomu Wei, Haiyuan Yu
Integrative analysis of whole-genome/exome-sequencing data has been challenging, especially for the non-programming research community, as it requires simultaneously managing a large number of computational tools. Even computational biologists find it unexpectedly difficult to reproduce results from others or optimize their strategies in an end-to-end workflow. We introduce Germline Mutation Scoring Tool fOr Next-generation sEquencing data (GeMSTONE), a cloud-based variant prioritization tool with high-level customization and a comprehensive collection of bioinformatics tools and data libraries (http://gemstone...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28518168/using-high-resolution-variant-frequencies-to-empower-clinical-genome-interpretation
#11
Nicola Whiffin, Eric Minikel, Roddy Walsh, Anne H O'Donnell-Luria, Konrad Karczewski, Alexander Y Ing, Paul J R Barton, Birgit Funke, Stuart A Cook, Daniel MacArthur, James S Ware
PurposeWhole-exome and whole-genome sequencing have transformed the discovery of genetic variants that cause human Mendelian disease, but discriminating pathogenic from benign variants remains a daunting challenge. Rarity is recognized as a necessary, although not sufficient, criterion for pathogenicity, but frequency cutoffs used in Mendelian analysis are often arbitrary and overly lenient. Recent very large reference datasets, such as the Exome Aggregation Consortium (ExAC), provide an unprecedented opportunity to obtain robust frequency estimates even for very rare variants...
May 18, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28516971/salivary-biomarkers-and-proteomics-future-diagnostic-and-clinical-utilities
#12
M Castagnola, E Scarano, G C Passali, I Messana, T Cabras, F Iavarone, G Di Cintio, A Fiorita, E De Corso, G Paludetti
Saliva testing is a non-invasive and inexpensive test that can serve as a source of information useful for diagnosis of disease. As we enter the era of genomic technologies and -omic research, collection of saliva has increased. Recent proteomic platforms have analysed the human salivary proteome and characterised about 3000 differentially expressed proteins and peptides: in saliva, more than 90% of proteins in weight are derived from the secretion of three couples of "major" glands; all the other components are derived from minor glands, gingival crevicular fluid, mucosal exudates and oral microflora...
April 2017: Acta Otorhinolaryngologica Italica
https://www.readbyqxmd.com/read/28516864/genomic-analysis-of-salmonella-enterica-serovar-typhimurium-dt160-associated-with-a-14-year-outbreak-new-zealand-1998-2012
#13
Samuel J Bloomfield, Jackie Benschop, Patrick J Biggs, Jonathan C Marshall, David T S Hayman, Philip E Carter, Anne C Midwinter, Alison E Mather, Nigel P French
During 1998-2012, an extended outbreak of Salmonella enterica serovar Typhimurium definitive type 160 (DT160) affected >3,000 humans and killed wild birds in New Zealand. However, the relationship between DT160 within these 2 host groups and the origin of the outbreak are unknown. Whole-genome sequencing was used to compare 109 Salmonella Typhimurium DT160 isolates from sources throughout New Zealand. We provide evidence that DT160 was introduced into New Zealand around 1997 and rapidly propagated throughout the country, becoming more genetically diverse over time...
June 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28515134/identification-of-novel-seroreactive-antigens-in-johne-s-disease-cattle-using-the-mycobacterium-tuberculosis-protein-array
#14
John P Bannantine, Joseph J Campo, Lingling Li, Arlo Randall, Jozelyn Pablo, Craig A Praul, Juan Antonio Raygoza Garay, Judith R Stabel, Vivek Kapur
Johne's Disease, a chronic gastrointestinal inflammatory disease caused by Mycobacterium avium subspecies paratuberculosis (Map), is endemic in dairy cattle and other ruminants worldwide and remains a challenge to diagnose using traditional serological methods. Given the close phylogenetic relationship between Map and the human pathogen, Mycobacterium tuberculosis (Mtb), we here applied a whole proteome Mtb protein array to identify seroreactive and diagnostic Map antigens. A genome-scale pairwise analysis of amino acid identity between orthologous proteins in Map and Mtb showed an average of 62% identity, with more than half the orthologous proteins sharing > 75% identity...
May 17, 2017: Clinical and Vaccine Immunology: CVI
https://www.readbyqxmd.com/read/28514307/exome-sequencing-identifies-a-de-novo-mutation-of-ctnnb1-gene-in-a-patient-mainly-presented-with-retinal-detachment-lens-and-vitreous-opacities-microcephaly-and-developmental-delay-case-report-and-literature-review
#15
Niu Li, Yufei Xu, Guoqiang Li, Tingting Yu, Ru-En Yao, Xiumin Wang, Jian Wang
RATIONALE: The CTNNB1 (β-catenin) gene is well known for its crucial role in cell adhesion and the Wnt-signaling pathway. Previous studies have shown that gain-of-function mutations in the CTNNB1 gene contribute to the occurrence and development of a variety of carcinomas in humans. Recently, de novo, heterozygous, loss-of-function mutations of the CTNNB1 gene were found that partially explain intellectual disability in some patients. Other major clinical symptoms in these patients included microcephaly, abnormal facial features, motor delays, speech impairments, and deformities of the hands and feet...
May 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28512778/cagi4-crohn-s-exome-challenge-marker-snp-versus-exome-variant-models-for-assigning-risk-of-crohn-disease
#16
Lipika R Pal, Kunal Kundu, Yizhou Yin, John Moult
Understanding the basis of complex trait disease is a fundamental problem in human genetics. The CAGI Crohn's Exome challenges are providing insight into the adequacy of current disease models by requiring participants to identify which of a set of individuals has been diagnosed with the disease, given exome data. For the CAGI4 round, we developed a method that used the genotypes from exome sequencing data only to impute the status of Genome Wide Association Studies (GWAS) marker single nucleotide polymorphisms (SNPs)...
May 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/28512358/delayed-epidural-transplantation-of-human-induced-pluripotent-stem-cell-derived-neural-progenitors-enhances-functional-recovery-after-stroke
#17
I-Hui Lee, Shiang-Suo Huang, Ching-Yu Chuang, Ko-Hsun Liao, Li-Hsin Chang, Chia-Chi Chuang, Yu-Shih Su, Hung-Jui Lin, Jui-Yu Hsieh, Shu-Han Su, Oscar Kuang-Sheng Lee, Hung-Chih Kuo
Induced pluripotent stem cell-derived neural progenitor cells (iPSC-NPCs) are a promising source of tailor-made cell therapy for neurological diseases. However, major obstacles to clinical use still exist. To circumvent complications related to intracerebral administration, we implanted human iPSC-NPCs epidurally over the peri-infarct cortex 7 days after permanent middle cerebral artery occlusion in adult rats. Compared to controls, cell-treated rats showed significant improvements in paretic forelimb usage and grip strength from 10 days post-transplantation (dpt) onwards, as well as reductions in lesion volumes, inflammatory infiltration and astrogliosis at 21 dpt...
May 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28512093/population-genomic-analysis-of-1-777-extended-spectrum-beta-lactamase-producing-klebsiella-pneumoniae-isolates-houston-texas-unexpected-abundance-of-clonal-group-307
#18
S Wesley Long, Randall J Olsen, Todd N Eagar, Stephen B Beres, Picheng Zhao, James J Davis, Thomas Brettin, Fangfang Xia, James M Musser
Klebsiella pneumoniae is a major human pathogen responsible for high morbidity and mortality rates. The emergence and spread of strains resistant to multiple antimicrobial agents and documented large nosocomial outbreaks are especially concerning. To develop new therapeutic strategies for K. pneumoniae, it is imperative to understand the population genomic structure of strains causing human infections. To address this knowledge gap, we sequenced the genomes of 1,777 extended-spectrum beta-lactamase-producing K...
May 16, 2017: MBio
https://www.readbyqxmd.com/read/28511110/determination-of-regional-relationships-among-salmonella-spp-isolated-from-retail-pork-circulating-in-the-chiang-mai-municipality-area-using-a-wgs-data-approach
#19
Prapas Patchanee, Thanaporn Eiamsam-Ang, Juntakarn Vanaseang, Phacharaporn Boonkhot, Pakpoom Tadee
Salmonella is recognized as a significant zoonotic foodborne pathogen, and pork products are involved in one-fifth of infections. Whole genome sequencing data of Salmonella isolated from retail's pork circulating in the Chiang Mai Municipality area between April 2013 and September 2014, were used to focus on genetic diversity and proven in pig-human transmission based on Multilocus Sequence Typing (MLST). Additionally, WGS data were used to investigate virulence genes, to assess the hazard or pathogenic potential transferred into the food production chain...
May 10, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28510608/the-biomphalaria-glabrata-dna-methylation-machinery-displays-spatial-tissue-expression-is-differentially-active-in-distinct-snail-populations-and-is-modulated-by-interactions-with-schistosoma-mansoni
#20
Kathrin K Geyer, Umar H Niazi, David Duval, Céline Cosseau, Chad Tomlinson, Iain W Chalmers, Martin T Swain, David J Cutress, Utibe Bickham-Wright, Sabrina E Munshi, Christoph Grunau, Timothy P Yoshino, Karl F Hoffmann
BACKGROUND: The debilitating human disease schistosomiasis is caused by infection with schistosome parasites that maintain a complex lifecycle alternating between definitive (human) and intermediate (snail) hosts. While much is known about how the definitive host responds to schistosome infection, there is comparably less information available describing the snail's response to infection. METHODOLOGY/PRINCIPLE FINDINGS: Here, using information recently revealed by sequencing of the Biomphalaria glabrata intermediate host genome, we provide evidence that the predicted core snail DNA methylation machinery components are associated with both intra-species reproduction processes and inter-species interactions...
May 2017: PLoS Neglected Tropical Diseases
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