27,326 results match your criteria linkage disequilibrium


Contemporary N estimation using temporally-spaced data with linked loci.

Mol Ecol Resour 2021 May 5. Epub 2021 May 5.

Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, United Kingdom.

The contemporary effective population size N is important in many disciplines including population genetics, conservation science and pest management. One of the most popular methods of estimating this quantity uses temporal changes in allele frequency due to genetic drift. A significant assumption of the existing methods is the independence among loci while constructing confidence intervals (C. Read More

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Analysis of Brugada syndrome loci reveals that fine-mapping clustered GWAS hits enhances the annotation of disease-relevant variants.

Cell Rep Med 2021 Apr 20;2(4):100250. Epub 2021 Apr 20.

Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain.

Genome-wide association studies (GWASs) are instrumental in identifying loci harboring common single-nucleotide variants (SNVs) that affect human traits and diseases. GWAS hits emerge in clusters, but the focus is often on the most significant hit in each trait- or disease-associated locus. The remaining hits represent SNVs in linkage disequilibrium (LD) and are considered redundant and thus frequently marginally reported or exploited. Read More

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Genetic factors affect the susceptibility to bacterial infections in diabetes.

Sci Rep 2021 May 4;11(1):9464. Epub 2021 May 4.

Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland.

Diabetes increases the risk of bacterial infections. We investigated whether common genetic variants associate with infection susceptibility in Finnish diabetic individuals. We performed genome-wide association studies and pathway analysis for bacterial infection frequency in Finnish adult diabetic individuals (FinnDiane Study; N = 5092, Diabetes Registry Vaasa; N = 4247) using national register data on antibiotic prescription purchases. Read More

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Evaluation of polygenic prediction methodology within a reference-standardized framework.

PLoS Genet 2021 May 4;17(5):e1009021. Epub 2021 May 4.

Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.

The predictive utility of polygenic scores is increasing, and many polygenic scoring methods are available, but it is unclear which method performs best. This study evaluates the predictive utility of polygenic scoring methods within a reference-standardized framework, which uses a common set of variants and reference-based estimates of linkage disequilibrium and allele frequencies to construct scores. Eight polygenic score methods were tested: p-value thresholding and clumping (pT+clump), SBLUP, lassosum, LDpred1, LDpred2, PRScs, DBSLMM and SBayesR, evaluating their performance to predict outcomes in UK Biobank and the Twins Early Development Study (TEDS). Read More

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A maximum flow-based network approach for identification of stable noncoding biomarkers associated with the multigenic neurological condition, autism.

BioData Min 2021 May 3;14(1):28. Epub 2021 May 3.

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.

Background: Machine learning approaches for predicting disease risk from high-dimensional whole genome sequence (WGS) data often result in unstable models that can be difficult to interpret, limiting the identification of putative sets of biomarkers. Here, we design and validate a graph-based methodology based on maximum flow, which leverages the presence of linkage disequilibrium (LD) to identify stable sets of variants associated with complex multigenic disorders.

Results: We apply our method to a previously published logistic regression model trained to identify variants in simple repeat sequences associated with autism spectrum disorder (ASD); this L-regularized model exhibits high predictive accuracy yet demonstrates great variability in the features selected from over 230,000 possible variants. Read More

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The population of in Brazil is structured by mycelial compatibility groups.

Plant Dis 2021 May 2. Epub 2021 May 2.

Universidade Federal de Viçosa, 28120, Fitopatologia, Vicosa, MG, Brazil;

The genetic structure of the population of was analyzed using 238 individuals collected from different hosts. Individuals were characterized for microsatellite genotypes and mycelial compatibility groups (MCGs). A total of 22 MCGs and 64 multilocus lineages (MLLs) were identified. Read More

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Disparities in COVID-19 severities and casualties across ethnic groups around the globe and patterns of ACE2 and PIR variants.

Infect Genet Evol 2021 Apr 29:104888. Epub 2021 Apr 29.

Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh. Electronic address:

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) mediated Coronavirus disease-19 (COVID-19) has affected millions of individuals around all corners of the globe. Symptoms and severities of infection with this highly contagious virus vary among individuals and there is disparity in the number of COVID-19-related casualties across different ethnic groups. The primary receptor for SARS-CoV-2 entry into the host cells is angiotensin-converting enzyme 2 (ACE2). Read More

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Identification of homozygous haplotypes carrying putative recessive lethal mutations that compromise fertility traits in French Lacaune dairy sheep.

Genet Sel Evol 2021 May 1;53(1):41. Epub 2021 May 1.

GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France.

Background: Homozygous recessive deleterious mutations can cause embryo/fetal or neonatal lethality, or genetic defects that affect female fertility and animal welfare. In livestock populations under selection, the frequency of such lethal mutations may increase due to inbreeding, genetic drift, and/or the positive pleiotropic effects of heterozygous carriers on selected traits.

Results: By scanning the genome of 19,102 Lacaune sheep using 50 k single nucleotide polymorphism (SNP) phased genotypes and pedigree data, we identified 11 Lacaune deficient homozygous haplotypes (LDHH1 to LDHH11) showing a highly significant deficit of homozygous animals ranging from 79 to 100%. Read More

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Multilocus sequence typing (MLST) of Entamoeba histolytica identifies kerp2 as a genetic marker associated with disease outcomes.

Parasitol Int 2021 Apr 28:102370. Epub 2021 Apr 28.

Division of Parasitology, ICMR-National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata 700010, West Bengal, India. Electronic address:

Amoebiasis caused by protozoan parasite Entamoeba histolytica has diverse infection outcomes. The relationship between parasite genotypes and outcome of amoebic infection is still a paradox and needs to be explored. Genome information of infecting strains from endemic areas throughout the world is essential to explore this relation. Read More

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Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution.

Hortic Res 2021 May 1;8(1):98. Epub 2021 May 1.

Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China.

Osmanthus fragrans is a well-known ornamental plant that has been domesticated in China for 2500 years. More than 160 cultivars have been found during this long period of domestication, and they have subsequently been divided into four cultivar groups, including the Yingui, Jingui, Dangui, and Sijigui groups. These groups provide a set of materials to study genetic evolution and variability. Read More

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Whole genome re-sequencing of sweet cherry (Prunus avium L.) yields insights into genomic diversity of a fruit species.

Hortic Res 2020 May 1;7(1):60. Epub 2020 May 1.

Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER. Thermi, Thessaloniki, 570001, Greece.

Sweet cherries, Prunus avium L. (Rosaceae), are gaining importance due to their perenniallity and nutritional attributes beneficial for human health. Interestingly, sweet cherry cultivars exhibit a wide range of phenotypic diversity in important agronomic traits, such as flowering time and defense reactions against pathogens. Read More

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Ongoing controversies and recent insights of the ARMS2-HTRA1 locus in age-related macular degeneration.

Exp Eye Res 2021 Apr 27:108605. Epub 2021 Apr 27.

Age-related macular degeneration (AMD) is the most common cause of central vision loss among elderly populations in industrialized countries. Genome-wide association studies have consistently associated two genomic loci with progression to late-stage AMD: the complement factor H (CFH) locus on chromosome 1q31 and the age-related maculopathy susceptibility 2-HtrA serine peptidase 1 (ARMS2-HTRA1) locus on chromosome 10q26. While the CFH risk variant has been shown to alter complement activity, the ARMS2-HTRA1 risk haplotype remains enigmatic due to high linkage disequilibrium and inconsistent functional findings spanning two genes that are plausibly causative for AMD risk. Read More

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Genetic association with boldness and maternal performance in a free-ranging population of grey seals (Halichoerus grypus).

Heredity (Edinb) 2021 Apr 29. Epub 2021 Apr 29.

Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.

Individual variation in quantitative traits clearly influence many ecological and evolutionary processes. Moderate to high heritability estimates of personality and life-history traits suggest some level of genetic control over these traits. Yet, we know very little of the underlying genetic architecture of phenotypic variation in the wild. Read More

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Functional Genomic Analyses of the 21q22.3 Locus Identifying Functional Variants and Candidate Gene for Breast Cancer Risk.

Cancers (Basel) 2021 Apr 23;13(9). Epub 2021 Apr 23.

Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Department of Medicine, Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.

We previously identified a locus at 21q22.3, tagged by the single nucleotide polymorphism (SNP) rs35418111, being associated with breast cancer risk at a genome-wide significance level; however, the underlying causal functional variants and gene(s) responsible for this association are unknown. We performed functional genomic analyses to identify potential functional variants and target genes that may mediate this association. Read More

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Multilocus Sequence Analysis of Selected Housekeeping- and Pathogenicity-Related Genes in .

Pathogens 2021 Apr 8;10(4). Epub 2021 Apr 8.

Department of Plant Protection, The National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland.

The relationship between housekeeping and pathogenicity-related genes and virulence or avirulence towards the primary resistance genes (R) has not been previously studied for fungus, the causal agent of apple scab. In this study, the sequences of two housekeeping genes encoding elongation factor alpha (EF-1α) and β-tubulin and two previously unstudied effector genes of from mannosidase and glucosidase families of 100 strains collected from apple cultivars with , , and and without known scab resistance genes were submitted to the analyses. Based on the phylogenetic and diversity data, as well as recombination analyses of the sequenced regions, we assessed the phylogenetic relationships and genetic structure of the pathogen within the species and the evolutionary forces that are currently acting upon this microorganism. Read More

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Genome-wide association analysis of bean fly resistance and agro-morphological traits in common bean.

PLoS One 2021 29;16(4):e0250729. Epub 2021 Apr 29.

African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa.

The bean fly (Ophiomyia spp) is a key insect pest causing significant crop damage and yield loss in common bean (Phaseolus vulgaris L., 2n = 2x = 22). Development and deployment of agronomic superior and bean fly resistant common bean varieties aredependent on genetic variation and the identification of genes and genomic regions controlling economic traits. Read More

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Adhesion G protein-coupled receptor L3 gene variants: Statistically significant association observed in the male Indo-caucasoid Attention deficit hyperactivity disorder probands.

Mol Biol Rep 2021 Apr 29. Epub 2021 Apr 29.

Manovikas Biomedical Research and Diagnostic Centre, Manovikas Kendra, 482 Madudah, Plot I-24, Sector J, EM Bypass, Kolkata, West Bengal, 700107, India.

Primary symptoms of Attention Deficit Hyperactivity Disorder (ADHD) are age inappropriate inattention, hyperactivity and impulsivity. Caucasoid individuals showed increased susceptibility to ADHD and disruptive behaviour in presence of Adhesion G-protein-coupled receptor L3 (ADGRL3) gene variants. We investigated ADGRL3 rs1868790, rs6551665, rs2345039 in Indo-Caucasoid families with ADHD probands (N = 249) and controls (N = 350). Read More

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Shared genetic etiology and causality between body fat percentage and cardiovascular diseases: a large-scale genome-wide cross-trait analysis.

BMC Med 2021 Apr 29;19(1):100. Epub 2021 Apr 29.

Department of Epidemiology & Biostatistics, School of Public Health, Peking University, China. 38 Xueyuan Road, Beijing, 100191, China.

Background: Accumulating evidences have suggested that high body fat percentage (BF%) often occurs in parallel with cardiovascular diseases (CVDs), implying a common etiology between them. However, the shared genetic etiology underlying BF% and CVDs remains unclear.

Methods: Using large-scale genome-wide association study (GWAS) data, we investigated shared genetics between BF% (N = 100,716) and 10 CVD-related traits (n = 6968-977,323) with linkage disequilibrium score regression, multi-trait analysis of GWAS, and transcriptome-wide association analysis, and evaluated causal associations using Mendelian randomization. Read More

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Variant Intronic Enhancer Controls Expression and Heart Conduction.

Circulation 2021 Apr 29. Epub 2021 Apr 29.

Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam UMC, University of Amsterdam, location AMC, Amsterdam, The Netherlands.

Genetic variants in , encoding the neural voltage-gated sodium channel NaV1.8, are strongly associated with atrial fibrillation, Brugada syndrome, cardiac conduction velocities and heart rate. The cardiac function of has not been resolved, however, and diverging mechanisms have been proposed. Read More

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Genetic evidence suggests posttraumatic stress disorder as a subtype of major depressive disorder.

J Clin Invest 2021 Apr 27. Epub 2021 Apr 27.

School of Systems Biology, George Mason University, Fairfax, United States of America.

Background: Major depressive disorder (MDD) and posttraumatic stress disorder (PTSD) are highly comorbid and exhibit strong correlations with one another. We aimed to investigate mechanisms of underlying relationships between PTSD and three kinds of depressive phenotypes, namely, MDD, depressed affect (DAF), and depression (DEP, including both MDD and the broad definition of depression).

Methods: Genetic correlations between PTSD and the depressive phenotypes were tested using linkage disequilibrium score regression. Read More

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The evolution of sex along an environmental gradient.

Evolution 2021 Apr 26. Epub 2021 Apr 26.

IRL 3614 Evolutionary Biology and Ecology of Algae, CNRS, Roscoff, 29688, France.

While temporally changing environments generally favor sex and recombination, the effects of spatial environmental heterogeneity have been less explored. In this paper, we use a classical model of adaptation along an environmental gradient to study the selective forces acting on reproductive mode evolution in the central and marginal parts of the distribution range of a species. The model considers a polygenic trait under stabilizing selection (the optimal trait value changing across space) and includes a demographic component imposing range limits. Read More

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Virus-derived variation in diverse human genomes.

PLoS Genet 2021 Apr 26;17(4):e1009324. Epub 2021 Apr 26.

Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Center for Integrative Medical Sciences and RIKEN Cluster for Pioneering Research, Yokohama, Japan.

Acquisition of genetic material from viruses by their hosts can generate inter-host structural genome variation. We developed computational tools enabling us to study virus-derived structural variants (SVs) in population-scale whole genome sequencing (WGS) datasets and applied them to 3,332 humans. Although SVs had already been cataloged in these subjects, we found previously-overlooked virus-derived SVs. Read More

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Modification of Heritability for Educational Attainment and Fluid Intelligence by Socioeconomic Deprivation in the UK Biobank.

Am J Psychiatry 2021 Apr 26:appiajp202020040462. Epub 2021 Apr 26.

Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

Objective: Socioeconomic factors have been suggested to influence the effect of education- and intelligence-associated genetic variants. However, results from previous studies on the interaction between socioeconomic status and education or intelligence have been inconsistent. The authors sought to assess these interactions in the UK Biobank cohort of 500,000 participants. Read More

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Genome-wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose.

Plant Genome 2021 Apr 26:e20097. Epub 2021 Apr 26.

Dep. of Plant Pathology & Microbiology, Texas A&M Univ., College Station, TX, 77843, USA.

Anthracnose disease of sorghum is caused by Colletotrichum sublineola, a filamentous fungus. The genetic basis of resistance to anthracnose in sorghum is largely unclear, especially in Senegalese sorghum germplasm. In this study, 163 Senegalese sorghum accessions were evaluated for response to C. Read More

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G6PD Polymorphisms and Hemolysis After Antimalarial Treatment With Low Single-Dose Primaquine: A Pooled Analysis of Six African Clinical Trials.

Front Genet 2021 9;12:645688. Epub 2021 Apr 9.

Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.

Primaquine (PQ) is an antimalarial drug with the potential to reduce malaria transmission due to its capacity to clear mature gametocytes in the human host. However, the large-scale roll-out of PQ has to be counterbalanced by the additional risk of drug-induced hemolysis in individuals suffering from Glucose-6-phospate dehydrogenase (G6PD) deficiency, a genetic condition determined by polymorphisms on the X-linked gene. Most studies on G6PD deficiency and PQ-associated hemolysis focused on the G6PD A- variant, a combination of the two single nucleotide changes G202A (rs1050828) and A376G (rs1050829), although other polymorphisms may play a role. Read More

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Isolation and characterization of microsatellites for the endangered endemic tree Nothofagus alessandrii (Nothofagaceae).

Mol Biol Rep 2021 Apr 24. Epub 2021 Apr 24.

Instituto de Ciencias Biológicas, Universidad de Talca, Avenida Lircay S/N, 3460000, Talca, Chile.

Nothofagus alessandrii (Nothofagaceae) is one of the most endangered trees from Chile due to high rates of habitat disturbance caused by human activities. Despite its conservation status, few molecular markers are available to study its population genetic, connectivity and to assist reproduction programs. Thus, the species needs urgent actions to restore its original distribution. Read More

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Peroxisome Proliferator-Activated Receptor Gamma Pro12Ala/C161T Genotypes and Risky Haplotype Altering Risk of Breast Cancer: A Turkish Case-Control Study.

Biochem Genet 2021 Apr 24. Epub 2021 Apr 24.

Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Vakıf Gureba c. Çapa 34093, Istanbul, Turkey.

Breast cancer (BC) has a high incidence rate among women worldwide, and the mechanisms and etiology of this disease are not yet fully understood. The peroxisome proliferator-activated receptor gamma (PPARgamma), a nuclear hormone receptor that plays important roles in energy metabolism and cellular differentiation, is also suggested to be effective in cancer development. However, the results of studies investigating the cancer association with PPARgamma are inconsistent, creating a need for further investigation of the effects of this transcription factor on BC risk. Read More

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Effects of kinship correction on inflation of genetic interaction statistics in commonly used mouse populations.

G3 (Bethesda) 2021 Apr 23. Epub 2021 Apr 23.

The Jackson Laboratory, 600 Main St. Bar Harbor, ME, 04609, USA.

It is well understood that variation in relatedness among individuals, or kinship, can lead to false genetic associations. Multiple methods have been developed to adjust for kinship while maintaining power to detect true associations. However, relatively unstudied, are the effects of kinship on genetic interaction test statistics. Read More

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Cross-ancestry genome-wide association studies identified heterogeneous loci associated with differences of allele frequency and regulome tagging between participants of European descent and other ancestry groups from the UK Biobank.

Hum Mol Genet 2021 Apr 22. Epub 2021 Apr 22.

Department of Psychiatry, Yale University School of Medicine, West Haven, CT, USA.

To investigate cross-ancestry genetics of complex traits, we conducted a phenome-wide analysis of loci with heterogeneous effects across African, Admixed-American, Central/South Asian, East Asian, European, and Middle Eastern participants of UK Biobank (N = 441 331). Testing 843 phenotypes, we identified 82 independent genomic regions mapping variants showing genome-wide significant (GWS) associations (P < 5 × 10-8) in the trans-ancestry meta-analysis and GWS heterogeneity among the ancestry-specific effects. These included: i) loci with GWS association in one ancestry and concordant but heterogeneous effects among the other ancestries; ii) loci with a GWS association in one ancestry group and an experiment-wide significant discordant effect (P < 6. Read More

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Linkage and linkage disequilibrium among the markers in the forensic MPS panels.

J Forensic Sci 2021 Apr 22. Epub 2021 Apr 22.

Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.

For the past two to three decades, forensic DNA evidence has been analyzed with a limited number of short tandem repeats (STRs), and these STRs are usually assumed to be independent for statistical calculations. With the development and implementation of the MPS technologies, more autosomal markers, both single nucleotide polymorphisms (SNPs) and STRs, can be analyzed. A number of these markers are physically very close to each other, and it may not be appropriate to assume all these markers are genetically unlinked or in linkage equilibrium. Read More

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