Genome-wide association studies articles within Nature Communications

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  • Article
    | Open Access

    Ageing phenotypes are of great interest but are difficult to study genetically, partly due to the sample sizes required. Here, the authors present a multivariate framework to combine GWAS summary statistics and increase statistical power, identifying additional loci enriched for aging.

    • Paul R. H. J. Timmers
    • , James F. Wilson
    •  & Joris Deelen

  • Article
    | Open Access

    Regional brain morphology has a complex genetic architecture. Here the authors present MOSTest, a multivariate statistical framework, apply it to UK Biobank data, and discover hundreds of loci associated with regional brain morphology.

    • Dennis van der Meer
    • , Oleksandr Frei
    •  & Anders M. Dale

  • Article
    | Open Access

    The association between blood pressure (BP) and migraine is poorly understood. Here, the authors explore this relationship using summary-level GWAS data for BP and migraine. Cross-trait meta-analysis reveals shared loci between BP and migraine, while Mendelian randomization suggests that diastolic BP specifically plays a key role in migraine susceptibility.

    • Yanjun Guo
    • , Pamela M. Rist
    •  & Daniel I. Chasman

  • Article
    | Open Access

    Reduction of pollen grain number is widespread in selfing plants, but the determining gene is unknown. Here, the authors show that a ribosome-biogenesis factor encoding gene RDP1 is responsible for adaptive reduction of male gamete number in Arabidopsis thaliana.

    • Takashi Tsuchimatsu
    • , Hiroyuki Kakui
    •  & Kentaro K. Shimizu

  • Article
    | Open Access

    Methods to integrate association evidence across multiple traits often focus on individual common variants GWAS. Here the authors present multi-trait analysis of rare-variant associations (MTAR), a framework for joint analysis of association summary statistics between multiple rare variants and different traits.

    • Lan Luo
    • , Judong Shen
    •  & Zheng-Zheng Tang

  • Article
    | Open Access

    On the electrocardiogram, the PR interval reflects conduction from the atria to ventricles and also serves as risk indicator of cardiovascular morbidity and mortality. Here, the authors perform genome-wide meta-analyses for PR interval in multiple ancestries and identify 141 previously unreported genetic loci.

    • Ioanna Ntalla
    • , Lu-Chen Weng
    •  & Patricia B. Munroe

  • Article
    | Open Access

    Depression is correlated with many brain-related traits. Here, Shen et al. perform phenome-wide association studies of a depression polygenic risk score (PRS) and find associations with 51 behavioural and 26 neuroimaging traits which are further followed up on using Mendelian randomization and mediation analyses.

    • Xueyi Shen
    • , David M. Howard
    •  & Andrew M. McIntosh

  • Article
    | Open Access

    Structural changes to the left ventricle are characteristic of dilated cardiomyopathy (DCM), a disease for which many rare genetic variants are known. Here, Pirruccello et al. report GWAS of seven cardiac MRI measurements in the left ventricle and describe shared loci and polygenic association with DCM.

    • James P. Pirruccello
    • , Alexander Bick
    •  & Krishna G. Aragam

  • Article
    | Open Access

    Immune infiltration provides critical information for health and disease, yet it is unclear what factors influence infiltration levels. Here, the authors analyze human tissue transcriptomes from the Genotype-Tissue Expression project to find infiltration patterns regulated by age, sex and host genetic information.

    • Andrew R. Marderstein
    • , Manik Uppal
    •  & Olivier Elemento

  • Article
    | Open Access

    Epidemiological studies have shown an association between sedentary behaviours and cardiovascular disease risk. Here, van de Vegte et al. perform GWAS for self-reported sedentary behaviours (TV watching, computer use, driving) and Mendelian randomization analyses to explore potential causal relationships with coronary artery disease.

    • Yordi J. van de Vegte
    • , M. Abdullah Said
    •  & Niek Verweij

  • Article
    | Open Access

    Asthma is a common disease of the airways for which numerous genetic loci have been identified. Here, Han et al. carry out a genome-wide analysis for asthma to identify additional loci, report sex-stratified and genetic risk score analyses, and functionally follow-up one locus using a murine model of airway hyperreactivity.

    • Yi Han
    • , Qiong Jia
    •  & Hooman Allayee

  • Article
    | Open Access

    Vitamin D is a precursor of the steroid hormone 1,25-dihydroxyvitamin D3, and its deficiency is associated with many adverse health outcomes. Here, Revez et al. perform a genome-wide association study for circulating 25-hydroxyvitamin D in 417,580 individuals and test for potential causal relationships with other traits using Mendelian randomization.

    • Joana A. Revez
    • , Tian Lin
    •  & John J. McGrath

  • Article
    | Open Access

    Membranous nephropathy (MN) is a rare autoimmune disease of podocyte-directed antibodies, such as anti-phospholipase A2 receptor. Here, the authors report a genome-wide association study for MN and identify two previously unreported loci encompassing the NFKB1 and IRF4 genes and additional ancestry-specific effects.

    • Jingyuan Xie
    • , Lili Liu
    •  & Krzysztof Kiryluk

  • Article
    | Open Access

    Age at voice-breaking is used to determine puberty timing in men, recall of which is considered less accurate than age at first menarche in women. Here, the authors perform multi-trait GWAS for male puberty timing by including both age at voice breaking and age of first facial hair for improved phenotype definition and power.

    • Ben Hollis
    • , Felix R. Day
    •  & John R. B. Perry

  • Article
    | Open Access

    The choice of food intake is at least partially influenced by genetics, even though the effect sizes appear rather modest. Here, Cole et al. perform GWAS for food intake (85 individual food items and 85 derived dietary patterns) and test potential causal relationships with cardiometabolic traits using Mendelian randomization.

    • Joanne B. Cole
    • , Jose C. Florez
    •  & Joel N. Hirschhorn

  • Article
    | Open Access

    Heart failure has a heterogeneous etiology and the genetic underpinnings are not well understood. Here, Arvanitis et al. perform GWAS meta-analysis including 10,976 heart failure cases and 437,573 controls, identify new loci near ABO and ACTN2 and show that deletion of a ACTN2 enhancer leads to reduced ACTN2 expression in differentiating cardiomyocytes.

    • Marios Arvanitis
    • , Emmanouil Tampakakis
    •  & Alexis Battle

  • Article
    | Open Access

    GWAS analysis currently relies mostly on linear mixed models, which do not account for linkage disequilibrium (LD) between tested variants. Here, Sesia et al. propose KnockoffZoom, a non-parametric statistical method for the simultaneous discovery and fine-mapping of causal variants, assuming only that LD is described by hidden Markov models (HMMs).

    • Matteo Sesia
    • , Eugene Katsevich
    •  & Chiara Sabatti

  • Article
    | Open Access

    In this study the authors identify a possible link between the gene FAM222A and brain atrophy. The protein it encodes is found to accumulate in plaques seen in Alzheimer’s disease, and functional analysis suggests it interacts with amyloid-beta.

    • Tingxiang Yan
    • , Jingjing Liang
    •  & Xinglong Wang

  • Article
    | Open Access

    Asthma is a common allergic airway disease with significant inter-individual heterogeneity. Here, Olafsdottir et al. report a genome-wide meta-analysis of two large population-based cohorts to identify sequence variants that associate with asthma risk and perform follow-up functional analyses on a protective loss-of-function variant in TNFRSF8.

    • Thorunn A. Olafsdottir
    • , Fannar Theodors
    •  & Kari Stefansson

  • Article
    | Open Access

    Local adaptation contributes to plant colonization across extreme environmental gradients. Here, the authors reconstruct the colonization history of Lotus japonicus in Japan and identify extreme genetic signatures of local adaptation to a cold climate using genome resequencing and common garden experiments.

    • Niraj Shah
    • , Tomomi Wakabayashi
    •  & Stig Uggerhøj Andersen

  • Article
    | Open Access

    Associations of copy number variations (CNVs) with complex traits are challenging to study because of their low frequency. Here, the authors analyse SNP array and array comparative genomic hybridization data of 100,028 individuals and report their associations with immune-related, cardiometabolic and neuropsychiatric diseases as well as cancer.

    • Yun Rose Li
    • , Joseph T. Glessner
    •  & Hakon Hakonarson

  • Article
    | Open Access

    Heart failure is a complex syndrome that is associated with many different underlying risk factors. Here, to increase power, the authors jointly analyse cases of heart failure of different aetiologies in a genome-wide association study and identify 11 loci of which ten had not been previously reported.

    • Sonia Shah
    • , Albert Henry
    •  & R. Thomas Lumbers

  • Article
    | Open Access

    Blood metabolite levels are under the influence of environmental and genetic factors. Here, Hagenbeek et al. perform heritability estimations for metabolite measures and determine the contribution of known metabolite loci to metabolite levels using data from 40 genome-wide association studies.

    • Fiona A. Hagenbeek
    • , René Pool
    •  & Dorret I. Boomsma

  • Article
    | Open Access

    Multivariable Mendelian randomization (MR) extends the standard MR framework to consider multiple risk factors in a single model. Here, Zuber et al. propose MR-BMA, a Bayesian variable selection approach to identify the likely causal determinants of a disease from many candidate risk factors as for example high-throughput data sets.

    • Verena Zuber
    • , Johanna Maria Colijn
    •  & Stephen Burgess

  • Article
    | Open Access

    Stroke risk is influenced by genetic and lifestyle factors and previously a genomic risk score (GRS) for stroke was proposed, albeit with limited predictive power. Here, Abraham et al. develop a metaGRS that is composed of several stroke-related GRSs and demonstrate improved predictive power compared with individual GRS or classic risk factors.

    • Gad Abraham
    • , Rainer Malik
    •  & Martin Dichgans

  • Article
    | Open Access

    Four genome-wide associated loci are currently known for malaria susceptibility. Here, the authors expand on earlier work by combining data from 11 malaria-endemic countries and additional population sequencing informing an African-enriched imputation reference panel, with findings including a previously unreported association on chromosome 6.

    • Gavin Band
    • , Quang Si Le
    •  & Dominic P. Kwiatkowski

  • Article
    | Open Access

    Household income is used as a marker of socioeconomic position, a trait that is associated with better physical and mental health. Here, Hill et al. report a genome-wide association study for household income in the UK and explore its relationship with intelligence in post-GWAS analyses including Mendelian randomization.

    • W. David Hill
    • , Neil M. Davies
    •  & Ian J. Deary

  • Article
    | Open Access

    Machine learning algorithms can be trained to estimate age from brain structural MRI. Here, the authors introduce a new deep-learning-based age prediction approach, and then carry out a GWAS of the difference between predicted and chronological age, revealing two associated variants.

    • B. A. Jonsson
    • , G. Bjornsdottir
    •  & M. O. Ulfarsson

  • Article
    | Open Access

    B-cell acute lymphoblastic leukaemia (B-ALL) is a common childhood cancer. Here, the authors conducted a meta-analysis with four genome-wide association studies, totalling 5,321 cases and 16,666 controls of European descent, identifying B-ALL risk loci, whose integration with epigenomic profiling indicates cell-cycle and B-cell development deregulation as central mechanisms in B-ALL susceptibility, often in a subtype-specific fashion.

    • Jayaram Vijayakrishnan
    • , Maoxiang Qian
    •  & Jun J. Yang

  • Article
    | Open Access

    Kidney stones form in the presence of overabundance of crystal-forming substances such as Ca2+ and oxalate. Here, the authors report genome-wide association analyses for kidney stone disease, report seven previously unknown loci and find that some of these loci also associate with Ca2+ concentration and excretion.

    • Sarah A. Howles
    • , Akira Wiberg
    •  & Dominic Furniss

  • Article
    | Open Access

    Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare inflammatory disorder characterised by asthma, eosinophilia and vasculitis. Here, the authors describe a genome-wide association study of EGPA that reveals clinical and genetic differences between subgroups stratified by autoantibody status (ANCA).

    • Paul A Lyons
    • , James E Peters
    •  & Kenneth G. C. Smith

  • Article
    | Open Access

    Systemic sclerosis (SSc) is a heterogeneous chronic autoimmune disease that affects the connective tissue. Here, López-Isac et al. identify 13 new risk loci for SSc as well as loci specific for limited cutaneous and diffuse SSc and, defining credible sets and performing functional annotation, highlight key pathways and cell types for SSc.

    • Elena López-Isac
    • , Marialbert Acosta-Herrera
    •  & Javier Martin

  • Article
    | Open Access

    Uterine leiomyomata (UL) or fibroids are neoplasms of the uterine smooth muscle associated with heavy menstrual bleeding and other female reproductive tract morbidity. Here, the authors identify eight previously undescribed genetic loci for UL and further look into genetic overlap with heavy menstrual bleeding and endometriosis.

    • C. S. Gallagher
    • , N. Mäkinen
    •  & C. C. Morton

  • Article
    | Open Access

    Aberrant morphology of the QRS complex in an electrocardiogram can be associated with cardiac morbidity and mortality. Here, the authors perform genome-wide association studies for ten measures of the QRS complex in 81,192 individuals and find 86 previously unreported loci that associate with at least one parameter.

    • Kristjan Norland
    • , Gardar Sveinbjornsson
    •  & Kari Stefansson

  • Article
    | Open Access

    Genome-wide association studies of metabolites have revealed hundreds of genetic associations using univariate analyses. Here, the authors use a multivariate approach to perform association analyses for 158 serum metabolites, followed by fine mapping and GxE interaction tests with statin use and age.

    • Apolline Gallois
    • , Joel Mefford
    •  & Hugues Aschard

  • Article
    | Open Access

    Mosaic loss of chromosome Y (mLOY) is associated with age and smoking but also genetic factors play a role. Here, Terao et al. perform GWAS for mLOY in 95,380 Japanese men and identify 46 loci that overlap with hematopoietic stem cell enhancers and transcription factor binding sites critical for hematopoiesis.

    • Chikashi Terao
    • , Yukihide Momozawa
    •  & Yoichiro Kamatani

  • Article
    | Open Access

    Post-traumatic stress disorder (PTSD) is a common mental health problem. Here, the authors report a GWAS from the Psychiatric Genomics Consortium in which they identify two risk loci in European ancestry and one locus in African ancestry individuals and find that PTSD is genetically correlated with several other psychiatric traits.

    • Caroline M. Nievergelt
    • , Adam X. Maihofer
    •  & Karestan C. Koenen

  • Article
    | Open Access

    Thousands of genetic loci are known to associate with human height, but these are mainly based on studies in European ancestry populations. Here, Akiyama et al. construct a genotype reference panel for the Japanese population followed by GWAS and report 573 height associated variants in 191,787 Japanese.

    • Masato Akiyama
    • , Kazuyoshi Ishigaki
    •  & Yoichiro Kamatani

  • Article
    | Open Access

    Cardiovascular diseases (CVD) are associated with plasma lipid levels. Here, Tabassum et al. perform genome-wide association studies for lipidomic profiles with 141 (non-standard) lipid species which highlights shared genetic loci with CVD and that traditional lipids have low genetic correlation with other lipids.

    • Rubina Tabassum
    • , Joel T. Rämö
    •  & Samuli Ripatti

  • Article
    | Open Access

    The majority of published GWAS was performed in European ancestry populations. Here, Kuchenbaecker et al., test to which extent lipid loci are shared and find that the major lipid loci are mostly transferrable between Europeans and Asians while there are notable exceptions for African populations.

    • Karoline Kuchenbaecker
    • , Nikita Telkar
    •  & Dieter Wolke

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