Genome-wide association studies articles within Nature Communications

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  • Article
    | Open Access

    Although varicose veins are a common condition, the genetic basis is not well understood. Here, the authors find genetic variants associated with varicose veins and show that a higher polygenic risk score for varicose veins correlates with a greater likelihood of patients undergoing surgical treatment.

    • Waheed-Ul-Rahman Ahmed
    • , Sam Kleeman
    •  & Dominic Furniss

  • Article
    | Open Access

    Inflammation is associated with a variety of diseases. Here, the authors identify 266 genetic loci associated with C-reactive protein levels, a marker of inflammation, in >500,000 Europeans, along with associated pathways, clinical outcomes and potential causal associations with disease.

    • Saredo Said
    • , Raha Pazoki
    •  & Abbas Dehghan

  • Article
    | Open Access

    The Finnish population is enriched for genetic variants which are rare in other populations. Here, the authors find new genetic loci associated with 1391 circulating metabolites in 6136 Finnish men, demonstrating that metabolite genetic associations can help elucidate disease mechanisms.

    • Xianyong Yin
    • , Lap Sum Chan
    •  & Michael Boehnke

  • Article
    | Open Access

    Post-translational modifications are known to diversify protein functions, but the effect of genetic variation on the modifications is not well known. Here, the authors find both shared and protein-specific genetic mechanisms regulating the glycosylation of two different proteins.

    • Arianna Landini
    • , Irena Trbojević-Akmačić
    •  & Lucija Klarić

  • Article
    | Open Access

    Genetic studies of disease-relevant traits have mostly been performed on European populations. Here, the authors perform a genome-wide association study for carotid intima-media thickness, in sub-Saharan African samples, finding population-specific and sex-specific loci.

    • Palwende Romuald Boua
    • , Jean-Tristan Brandenburg
    •  & Michèle Ramsay

  • Article
    | Open Access

    Better understanding of the genetic basis of acne can pave the way to more effective treatments. Here, the authors perform a genome-wide association study meta-analysis of >20,000 cases and identify 29 new acne susceptibility loci, uncovering genetic links to Mendelian hair and skin disorders and other complex traits.

    • Brittany L. Mitchell
    • , Jake R. Saklatvala
    •  & Michael A. Simpson

  • Article
    | Open Access

    Finding the genetic basis of protein expression can elucidate the genetic mechanisms of disease. Here, the authors link low-frequency and common DNA sequence variants to thousands of serum proteins, finding genetic overlap between circulating proteins and a wide range of common diseases.

    • Valur Emilsson
    • , Valborg Gudmundsdottir
    •  & Vilmundur Gudnason

  • Article
    | Open Access

    Numerous disease-associated variants have been described in GWAS for atrial fibrillation. Here the authors integrate omics data to investigate the consequences of genetic variants for transcript and protein levels in the atrium of the human heart. With this multi-omics approach, authors reveal the regulatory network underlying atrial fibrillation and provide a resource for cardiac gene prioritization.

    • Ines Assum
    • , Julia Krause
    •  & Matthias Heinig

  • Article
    | Open Access

    Loneliness and social isolation (LNL-ISO) are associated with schizophrenia. Here the authors demonstrate the role of shared heritability, bidirectional causal relationships and significant differences by sex, illustrating the genomic footprint of social isolation on schizophrenia.

    • Álvaro Andreu-Bernabeu
    • , Covadonga M. Díaz-Caneja
    •  & Javier González-Peñas

  • Article
    | Open Access

    Signals of antimicrobial resistance in pathogen genomes may be detectable before the organism evolves an antimicrobial resistance phenotype. Here, the authors investigate this hypothesis using Mycobacterium tuberculosis data from Peru and identify candidate “pre-resistance” markers.

    • Arturo Torres Ortiz
    • , Jorge Coronel
    •  & Louis Grandjean

  • Article
    | Open Access

    Analyses of summary statistics from GWAS are subject to biases due to errors in the discovery GWAS or linkage disequilibrium reference data set or heterogeneity between data sets. Here, the authors propose a quality control method to be added to analysis of GWAS summary data that can reduce such biases.

    • Wenhan Chen
    • , Yang Wu
    •  & Jian Yang

  • Article
    | Open Access

    Serum proteins are easily accessible biomarkers and drug targets. Here, the authors use whole genome sequencing data to describe the genetic architecture of neurologically-relevant serum proteins and establish causal protein-neurological disease relationships.

    • Grace Png
    • , Andrei Barysenka
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Improving inference in large-scale genetic data linked to electronic medical record data requires the development of novel computationally efficient regression methods. Here, the authors develop a Bayesian approach for association analyses to improve SNP-heritability estimation, discovery, fine-mapping and genomic prediction.

    • Marion Patxot
    • , Daniel Trejo Banos
    •  & Matthew R. Robinson

  • Article
    | Open Access

    Genetic studies of eczema to date have mostly explored common genetic variation. Here, the authors perform a large meta-analysis for common and rare variants and discover 8 loci associated with eczema. Over 20% of the heritability of the condition is attributable to rare variants.

    • Sarah Grosche
    • , Ingo Marenholz
    •  & Young-Ae Lee

  • Article
    | Open Access

    Follistatin promotes in type 2 diabetes (T2D) pathogenesis in model animals and is elevated in patients with T2D. Here the authors report that plasma follistatin associates with increased risk of incident T2D in two longitudinal cohorts, and show that follistatin regulates insulin-induced suppression lipolysis in cultured human adipocytes.

    • Chuanyan Wu
    • , Yan Borné
    •  & Yang De Marinis

  • Article
    | Open Access

    Genetic signals from quantitative traits could be a challenge to finemap. Flashfm uses summary-level data in a Bayesian framework to favour shared causal variants and capitalises on information between traits, providing an accurate and efficient joint fine-mapping tool for up to six traits.

    • N. Hernández
    • , J. Soenksen
    •  & J. L. Asimit

  • Article
    | Open Access

    Fibromuscular dysplasia is a cardiovascular disease affecting mostly women with a mostly unknown genetic basis. Here the authors have performed a genome-wide association meta-analysis of Fibromuscular dysplasia to identify genetic loci, some of which are shared with common cardiovascular disease and traits.

    • Adrien Georges
    • , Min-Lee Yang
    •  & Nabila Bouatia-Naji

  • Article
    | Open Access

    Genetic susceptibility loci for oropharyngeal cancer have been reported but these studies have not always examined human papillomavirus (HPV) status. Here, the authors perform genome-wide analysis taking into account HPV16 serology status and report two independent loci in the HLA region, suggesting the protective role of HLA variants against HPV infection.

    • Aida Ferreiro-Iglesias
    • , James D. McKay
    •  & Paul Brennan

  • Article
    | Open Access

    Perilla is a young allotetraploid species within the mint family Lamiaceae. Here, the authors assemble the genomes of a tetraploid species and its diploid progenitor, characterize the incipient diploidization of the tetraploid, conduct population genetics analyses, and identify loci associate with pigmentation and oil content.

    • Yujun Zhang
    • , Qi Shen
    •  & Shilin Chen

  • Article
    | Open Access

    Estimating direct and indirect effects of genotypes on phenotypes is important for genetic analyses such as Mendelian randomization. Here the authors compare five different methods to estimate direct and indirect genetic effects using summary results statistics that account for sample overlap.

    • Nicole M. Warrington
    • , Liang-Dar Hwang
    •  & David M. Evans

  • Article
    | Open Access

    While polygenic risk scores have been shown to be correlated with disease risk, there is little agreement on how the score should be calculated. Here the authors investigate risk scores for Alzheimer’s disease, finding that the most effective approach includes an APOE score and a polygenic score excluding APOE.

    • Ganna Leonenko
    • , Emily Baker
    •  & Valentina Escott-Price

  • Article
    | Open Access

    We lack a comprehensive understanding of how Neanderthal ancestry influences human traits. This study finds that regions with Neanderthal ancestry are broadly depleted of trait-associated variation; yet, introgressed variants likely contributed to human adaptation in a few traits, like skin color and immune response modulation.

    • Evonne McArthur
    • , David C. Rinker
    •  & John A. Capra

  • Article
    | Open Access

    Identifying causal variants and genes in genome-wide association studies remains a challenge, an issue that is ameliorated with larger sample sizes. Here the authors meta-analyze kidney function genome-wide association studies to identify new loci and fine-map loci to home in on variants and genes involved in kidney function.

    • Kira J. Stanzick
    • , Yong Li
    •  & Thomas W. Winkler

  • Article
    | Open Access

    Mosaic loss of chromosome Y (LOY) is a common form of clonal mosaicism in leukocytes. Here, the authors extend genetic association analyses to rare variation using exome-sequence data from 82,277 males, finding that loss-of-function alleles in GIGYF1 are associated with six-fold higher susceptibility to both LOY and Type 2 Diabetes.

    • Yajie Zhao
    • , Stasa Stankovic
    •  & John R. B. Perry

  • Article
    | Open Access

    Pernicious anemia shows co-incidence with autoimmune disorders, yet the genetic basis for this condition is understudied. Here, the authors perform a genome-wide association study meta-analysis on pernicious anemia, identifying five susceptibility loci that map to genes with known roles in autoimmune disease.

    • Triin Laisk
    • , Maarja Lepamets
    •  & Reedik Mägi

  • Article
    | Open Access

    Platelet aggregation is associated with myocardial infarction and stroke. Here, the authors have conducted a whole genome sequencing association study on platelet aggregation, discovering a locus in RGS18, where enhancer assays suggest an effect on activity of haematopoeitic lineage transcription factors.

    • Ali R. Keramati
    • , Ming-Huei Chen
    •  & Andrew D. Johnson

  • Article
    | Open Access

    Age at onset of X-linked dystonia-parkinsonism is 50% explained by the length of a repeat in an SVA insert. The authors perform a GWAS for genetic modifiers and discover three more loci, accounting for another 13% of variability in age at onset with the protective alleles delaying onset by seven years.

    • Björn-Hergen Laabs
    • , Christine Klein
    •  & Ana Westenberger

  • Article
    | Open Access

    Quantifying the effects of individual loci on the human phenome is a challenging task. Here, the authors introduce a modelling technique, TGCA, that assesses total genetic contribution per locus and apply this to UK Biobank phenotype domains, revealing top loci and links to tissue-specific gene expression.

    • Ting Li
    • , Zheng Ning
    •  & Xia Shen

  • Article
    | Open Access

    While coffee and tea consumption has been associated with risk of diseases, their mechanisms of action remain elusive. Here the authors present a large EWAS on coffee and tea consumption in cohorts of European and African-American ancestries, finding that coffee consumption is associated with differential DNA methylation levels at multiple CpGs.

    • Irma Karabegović
    • , Eliana Portilla-Fernandez
    •  & Mohsen Ghanbari

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