96,521 results match your criteria genome-wide

Prediction of eye, hair and skin colour in Latin Americans.

Forensic Sci Int Genet 2021 Apr 6;53:102517. Epub 2021 Apr 6.

UMR 7268 ADES, CNRS, Aix-Marseille Université, EFS, Faculté de Médecine Timone, Marseille 13005, France; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK; Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China. Electronic address:

Here we evaluate the accuracy of prediction for eye, hair and skin pigmentation in a dataset of > 6500 individuals from Mexico, Colombia, Peru, Chile and Brazil (including genome-wide SNP data and quantitative/categorical pigmentation phenotypes - the CANDELA dataset CAN). We evaluated accuracy in relation to different analytical methods and various phenotypic predictors. As expected from statistical principles, we observe that quantitative traits are more sensitive to changes in the prediction models than categorical traits. Read More

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Genome-wide characterization and expression analysis of TOPP-type protein phosphatases in soybean (Glycine max L.) reveal the role of GmTOPP13 in drought tolerance.

Genes Genomics 2021 Apr 17. Epub 2021 Apr 17.

College of Life Science, Northeast Agricultural University, Harbin, 150030, China.

Background: In response to various abiotic stressors such as drought, many plants engage different protein phosphatases linked to several physiological and developmental processes. However, comprehensive analysis of this gene family is lacking for soybean.

Objective: This study was performed to identify the TOPP-type protein phosphatase family in soybean and investigate the gene's role under drought stress. Read More

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Association of APOE genotype with lipid profiles and type 2 diabetes mellitus in a Korean population.

Genes Genomics 2021 Apr 17. Epub 2021 Apr 17.

Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea.

Background: Type 2 diabetes mellitus (T2DM) is associated with chronic hyperglycemia and lipid metabolism. A previous genome-wide association study revealed the TOMM40-APOE region as novel locus for T2DM susceptibility.

Objective: This association study was conducted to determine the genetic effects of APOE single nucleotide polymorphisms (SNPs) on T2DM susceptibility and lipid profiles in a Korean population. Read More

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New insights into ANGPTL8 in modulating the development of cardio-metabolic disorder diseases.

Mol Biol Rep 2021 Apr 17. Epub 2021 Apr 17.

Department of Cardiology, The Xiamen Cardiovascular Hospital of Xiamen University, No. 2999 Jinshan Road, Xiamen, 361000, Fujian, China.

Dyslipidemia is being identified as the most important factors of several health problems, such as obesity, diabetes mellitus, and cardiovascular diseases (CVD), which are always grouped together as cardio-metabolic disorder diseases. Consistently, dyslipidemia has become one of the most rising crisis of general health. Recently, it is worth noting that both genome-wide association studies (GWAS) and experimental research are being taken advantage to elucidate the potential genetic mechanisms of dyslipidemia and to identify new gene loci which contribute to the development of cardio-metabolic disorder diseases. Read More

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Genome-wide gene-diet interaction analysis in the UK Biobank identifies novel effects on Hemoglobin A1c.

Hum Mol Genet 2021 Apr 16. Epub 2021 Apr 16.

Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.

Diet is a significant modifiable risk factor for type 2 diabetes (T2D), and its effect on disease risk is under partial genetic control. Identification of specific gene-diet interactions (GDIs) influencing risk biomarkers such as glycated hemoglobin (HbA1c) is a critical step towards precision nutrition for T2D prevention, but progress has been slow due to limitations in sample size and accuracy of dietary exposure measurement. We leveraged the large UK Biobank (UKB) cohort and a diverse group of dietary exposures, including 30 individual dietary traits and 8 empirical dietary patterns, to conduct genome-wide interaction studies in ~ 340 000 European-ancestry participants to identify novel GDIs influencing HbA1c. Read More

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Limited Impact of 6-Mercaptopurine on Inflammation-Induced Chemokines Expression Profile in Primary Cultures of Enteric Nervous System.

Neurochem Res 2021 Apr 16. Epub 2021 Apr 16.

Institute of Anatomy, Kiel University, Kiel, Germany.

Increasing evidences indicate that the enteric nervous system (ENS) and enteric glial cells (EGC) play important regulatory roles in intestinal inflammation. Mercaptopurine (6-MP) is a cytostatic compound clinically used for the treatment of inflammatory bowel diseases (IBD), such as ulcerative colitis and Crohn's disease. However, potential impacts of 6-MP on ENS response to inflammation have not been evaluated yet. Read More

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Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts.

Genome Res 2021 Apr 16. Epub 2021 Apr 16.

Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany.

Development of complex organisms requires the delicate and dynamic spatiotemporal regulation of gene expression. Central to this are microRNAs (miRNAs). These mobile small RNAs offer specificity in conveying positional information and versatility in patterning the outcomes of gene expression. Read More

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Copy number variation underlies complex phenotypes in domestic dog breeds and other canids.

Genome Res 2021 Apr 16. Epub 2021 Apr 16.

IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain.

Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. Read More

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Type 2 Diabetes Subtype Responsive to ACCORD Intensive Glycemia Treatment.

Diabetes Care 2021 Apr 16. Epub 2021 Apr 16.

Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH

Objective: Current type 2 diabetes (T2D) management contraindicates intensive glycemia treatment in patients with high cardiovascular disease (CVD) risk and is partially motivated by evidence of harms in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial. Heterogeneity in response to intensive glycemia treatment has been observed, suggesting potential benefit for some individuals.

Research Design And Methods: ACCORD was a randomized controlled trial that investigated whether intensively treating glycemia in individuals with T2D would reduce CVD outcomes. Read More

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Genetics of Food Allergy.

Immunol Allergy Clin North Am 2021 May 26;41(2):301-319. Epub 2021 Mar 26.

Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229-3026, USA. Electronic address:

The risk factors for food allergy (FA) include both genetic variants and environmental factors. Advances using both candidate-gene association studies and genome-wide approaches have led to the identification of FA-associated genes involved in immune responses and skin barrier functions. Epigenetic changes have also been associated with the risk of FA. Read More

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Chromatin accessibility landscapes of immune cells in rheumatoid arthritis nominate monocytes in disease pathogenesis.

BMC Biol 2021 Apr 16;19(1):79. Epub 2021 Apr 16.

Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China.

Background: Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease that involves a variety of cell types. However, how the epigenetic dysregulations of peripheral immune cells contribute to the pathogenesis of RA still remains largely unclear.

Results: Here, we analysed the genome-wide active DNA regulatory elements of four major immune cells, namely monocytes, B cells, CD4 T cells and CD8 T cells, in peripheral blood of RA patients, osteoarthritis (OA) patients and healthy donors using Assay of Transposase Accessible Chromatin with sequencing (ATAC-seq). Read More

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Residential surrounding greenness and DNA methylation: An epigenome-wide association study.

Environ Int 2021 Apr 12;154:106556. Epub 2021 Apr 12.

School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia. Electronic address:

Background: DNA methylation is a potential biological mechanism through which residential greenness affects health, but little is known about its association with greenness and whether the association could be modified by genetic background. We aimed to evaluate the association between surrounding greenness and genome-wide DNA methylation and potential gene-greenness interaction effects on DNA methylation.

Methods: We measured blood-derived DNA methylation using the HumanMethylation450 BeadChip array (Illumina) for 479 Australian women, including 66 monozygotic, 66 dizygotic twin pairs, and 215 sisters of these twins. Read More

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A multi-phenotype genome-wide association study of clades causing tuberculosis in a Ghanaian- and South African cohort.

Genomics 2021 Apr 13. Epub 2021 Apr 13.

DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.

Despite decades of research and advancements in diagnostics and treatment, tuberculosis remains a major public health concern. New computational methods are needed to interrogate the intersection of host- and bacterial genomes. Paired host genotype datum and infecting bacterial isolate information were analysed for associations using a multinomial logistic regression framework implemented in SNPTest. Read More

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Genome-wide identification and comparative analysis of the WRKY gene family in aquatic plants and their response to abiotic stresses in giant duckweed (Spirodela polyrhiza).

Genomics 2021 Apr 13. Epub 2021 Apr 13.

The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

WRKY is one of the largest transcription factor families across higher plant species and is involved in important biological processes and plant responses to various biotic/abiotic stresses. However, only a few investigations on WRKYs have been conducted in aquatic plants. This study first systematically analyzed the gene structure, protein properties, and phylogenetic relationship of 693 WRKYs in nine aquatic and two wetland plants at the genome-wide level. Read More

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Draft genome of Korthalsia laciniosa (Griff.) Mart., a climbing rattan elucidates its phylogenetic position.

Genomics 2021 Apr 13. Epub 2021 Apr 13.

Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi P. O, Thrissur, Kerala 680653, India.

Korthalsia laciniosa (Griff.) Mart. is a climbing rattan used as a source of durable and flexible cane. Read More

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Association of metabolites with obesity based on two gene variants, MC4R and BDNF.

Biochim Biophys Acta Mol Basis Dis 2021 Apr 13:166144. Epub 2021 Apr 13.

H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan; Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan. Electronic address:

Previous genome-wide association analyses for obesity related genes demonstrated the association of BDNF variant rs6265 and MC4R gene variant rs17782313 with body mass index (BMI). However, the associated metabolite pathways are still behind the curtain. The aimed of current study is to investigate the associations of metabolic changes in obesity with MC4R gene variant rs17782313 and BDNF variant rs6265. Read More

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Prediction of genomic breeding values of milk traits in Brazilian Saanen goats.

J Anim Breed Genet 2021 Apr 16. Epub 2021 Apr 16.

Animal Sciences Department, Federal University of Ceará, Fortaleza, Brazil.

The study's objective was to compare the genomic prediction ability methods for the traits milk yield, milk composition and somatic cell count of Saanen Brazilian goats. Nine hundred forty goats, genotyped with an Axiom_OviCap (Caprine) panel, Affimetrix customized array with 62,557 single nucleotide polymorphisms (SNPs), were used for the genomic selection analyses. The genomic methods studied to estimate the effects of SNPs and direct genomic values (DGV) were as follows: (a) genomic BLUP (GBLUP), (b) Bayes Cπ and (c) Bayesian Lasso (BLASSO). Read More

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The Impact of Removing Former Drinkers from Genome-wide Association Studies of AUDIT-C.

Addiction 2021 Apr 16. Epub 2021 Apr 16.

Yale University School of Public Health, New Haven, CT, USA.

Background And Aims: The Alcohol Use Disorders Identification Test-Consumption (AUDIT-C) questionnaire screens for harmful drinking using a 12-month timeframe. A score of 0 is assigned to individuals who report abstaining from alcohol in the past year. However, many middle-aged individuals reporting current abstinence are former drinkers (FDs). Read More

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Impact of variant-level batch effects on identification of genetic risk factors in large sequencing studies.

PLoS One 2021 16;16(4):e0249305. Epub 2021 Apr 16.

Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, Florida, United States of America.

Genetic studies have shifted to sequencing-based rare variants discovery after decades of success in identifying common disease variants by Genome-Wide Association Studies using Single Nucleotide Polymorphism chips. Sequencing-based studies require large sample sizes for statistical power and therefore often inadvertently introduce batch effects because samples are typically collected, processed, and sequenced at multiple centers. Conventionally, batch effects are first detected and visualized using Principal Components Analysis and then controlled by including batch covariates in the disease association models. Read More

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CSNK1G2 differently sensitizes tamoxifen-induced decrease in PI3K/AKT/mTOR/S6K and ERK signaling according to the estrogen receptor existence in breast cancer cells.

PLoS One 2021 16;16(4):e0246264. Epub 2021 Apr 16.

Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeollabuk-do, Republic of Korea.

Tamoxifen (TAM) is a selective estrogen receptor modulator used for breast cancer patients. Prolonged use of tamoxifen is not recommended for some patients. In this study, we aimed to identify molecular targets sensitive to TAM using a genome-wide gene deletion library screening of fission yeast heterozygous mutants. Read More

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Genome-wide analysis of lncRNA stability in human.

PLoS Comput Biol 2021 Apr 16;17(4):e1008918. Epub 2021 Apr 16.

Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.

Transcript stability is associated with many biological processes, and the factors affecting mRNA stability have been extensively studied. However, little is known about the features related to human long noncoding RNA (lncRNA) stability. By inhibiting transcription and collecting samples in 10 time points, genome-wide RNA-seq studies was performed in human lung adenocarcinoma cells (A549) and RNA half-life datasets were constructed. Read More

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Hedgehog signaling pathway gene variant influences bronchopulmonary dysplasia in extremely low birth weight infants.

World J Pediatr 2021 Apr 16. Epub 2021 Apr 16.

Newborn Medicine Division, The Regional Neonatal Intensive Care Unit, Maria Fareri Children's Hospital At Westchester Medical Center, Valhalla, NY, USA.

Background: Genome wide association study identified hedgehog interacting protein gene (HHIP) variants with chronic obstructive pulmonary disease and asthma. Loss of HHIP, a key regulator of the hedgehog signaling pathway, leads to impaired lung morphogenesis and lethality in animal models, through unimpeded sonic hedgehog expression blocking mesenchymal-expressed fibroblast growth factor 10 (FGF10). Since bronchopulmonary dysplasia (BPD) is also associated with altered lung development and worsens with stimuli including mechanical ventilation, reactive oxygen species, and inflammation, HHIP and FGF10 may be candidate genes. Read More

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An integrated epigenomic-transcriptomic landscape of lung cancer reveals novel methylation driver genes of diagnostic and therapeutic relevance.

Theranostics 2021 11;11(11):5346-5364. Epub 2021 Mar 11.

Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China.

Aberrant DNA methylation occurs commonly during carcinogenesis and is of clinical value in human cancers. However, knowledge of the impact of DNA methylation changes on lung carcinogenesis and progression remains limited. Genome-wide DNA methylation profiles were surveyed in 18 pairs of tumors and adjacent normal tissues from non-small cell lung cancer (NSCLC) patients using Reduced Representation Bisulfite Sequencing (RRBS). Read More

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Identification of Major Loci and Candidate Genes for Meat Production-Related Traits in Broilers.

Front Genet 2021 30;12:645107. Epub 2021 Mar 30.

State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.

Background: Carcass traits are crucial characteristics of broilers. However, the underlying genetic mechanisms are not well understood. In the current study, significant loci and major-effect candidate genes affecting nine carcass traits related to meat production were analyzed in 873 purebred broilers using an imputation-based genome-wide association study. Read More

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Integrated Genome-Wide Analysis of MicroRNA Expression Quantitative Trait Loci in Pig Longissimus Dorsi Muscle.

Front Genet 2021 30;12:644091. Epub 2021 Mar 30.

Department of Animal Science, Michigan State University, East Lansing, MI, United States.

Determining mechanisms regulating complex traits in pigs is essential to improve the production efficiency of this globally important protein source. MicroRNAs (miRNAs) are a class of non-coding RNAs known to post-transcriptionally regulate gene expression affecting numerous phenotypes, including those important to the pig industry. To facilitate a more comprehensive understanding of the regulatory mechanisms controlling growth, carcass composition, and meat quality phenotypes in pigs, we integrated miRNA and gene expression data from muscle samples with genotypic and phenotypic data from the same animals. Read More

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A Vernalization Response in a Winter Safflower () Involves the Upregulation of Homologs of , , and .

Front Plant Sci 2021 30;12:639014. Epub 2021 Mar 30.

Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia.

Safflower () is a member of the Asteraceae family that is grown in temperate climates as an oil seed crop. Most commercially grown safflower varieties can be sown in late winter or early spring and flower rapidly in the absence of overwintering. There are winter-hardy safflower accessions that can be sown in autumn and survive over-wintering. Read More

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Estrogen Receptor Beta Influences the Inflammatory p65 Cistrome in Colon Cancer Cells.

Front Endocrinol (Lausanne) 2021 30;12:650625. Epub 2021 Mar 30.

Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden.

Inflammation is a primary component of both initiation and promotion of colorectal cancer (CRC). Cytokines secreted by macrophages, including tumor necrosis factor alpha (TNFα), activates the pro-survival transcription factor complex NFκB. The precise mechanism of NFκB in CRC is not well studied, but we recently reported the genome-wide transcriptional impact of TNFα in two CRC cell lines. Read More

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A genome-wide atlas of co-essential modules assigns function to uncharacterized genes.

Nat Genet 2021 Apr 15. Epub 2021 Apr 15.

Department of Genetics, Stanford University, Stanford, CA, USA.

A central question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into 'co-essential' pathways, but this approach has been limited by ubiquitous false positives. In the present study, we develop a statistical method that enables robust identification of gene co-essentiality and yields a genome-wide set of functional modules. Read More

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Genome-wide specificity of prime editors in plants.

Nat Biotechnol 2021 Apr 15. Epub 2021 Apr 15.

State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.

Although prime editors (PEs) have the potential to facilitate precise genome editing in therapeutic, agricultural and research applications, their specificity has not been comprehensively evaluated. To provide a systematic assessment in plants, we first examined the mismatch tolerance of PEs in plant cells and found that the editing frequency was influenced by the number and location of mismatches in the primer binding site and spacer of the prime editing guide RNA (pegRNA). Assessing the activity of 12 pegRNAs at 179 predicted off-target sites, we detected only low frequencies of off-target edits (0. Read More

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