Epidemiology

  • Article
    | Open Access

    The genetic underpinnings of alcohol use disorder and consumption are incompletely understood. Here, the authors perform GWAS for Alcohol Use Disorder (AUD) Identification Test-Consumption scores and AUD diagnosis from electronic health records of 274,424 individuals and identify a total of 18 associated loci.

    • Henry R. Kranzler
    • , Hang Zhou
    •  & Joel Gelernter
  • Article
    | Open Access

    Lack of knowledge of individual infection history hinders understanding of immunological interactions among DENV serotypes. Here, the authors introduce a framework to infer the relationship between unobserved infection history and subsequent infection and disease risk, and find complex dependencies.

    • Tim K. Tsang
    • , Samson L. Ghebremariam
    •  & Yang Yang
  • Article
    | Open Access

    In 2014 Guangzhou, China experienced its worse dengue epidemic on record. To determine the reasons for this the authors model historical data under combinations of four time-varying factors and find that past epidemics were limited by one or more unfavourable conditions, but the 2014 epidemic faced none of these restraints.

    • Rachel J. Oidtman
    • , Shengjie Lai
    •  & Hongjie Yu
  • Article
    | Open Access

    Oral ulcerations are sores of the mucous membrane of the mouth and highly prevalent in the population. Here, in a genome-wide association study, the authors identify 97 loci associated with mouth ulcers highlighting genes involved in T cell-mediated immunity and TH1 responses.

    • Tom Dudding
    • , Simon Haworth
    •  & Nicholas J. Timpson
  • Article
    | Open Access

    Estimates of the burden of malaria often don't take wider, indirect effects on overall health into consideration. Here, Uyoga et al. estimate the indirect impact of malaria on children’s health in a case-control study, using the sickle cell trait as a proxy indicator for an effective intervention.

    • Sophie Uyoga
    • , Alex W. Macharia
    •  & Thomas N. Williams
  • Article
    | Open Access

    Here, the authors explore the relationship between socioeconomic position (SEP) across the life course and inflammation in a multi-cohort study and show that educational attainment is most strongly related to inflammation, suggesting that socioeconomic disadvantage in young adulthood is independently associated with later life inflammation.

    • Eloïse Berger
    • , Raphaële Castagné
    •  & Michelle Kelly-Irving
  • Article
    | Open Access

    Sex-stratified medicine is an important and understudied field. Here the authors investigate in a systematic study of the Danish population differences in incidence, risk, and several aspects of diagnoses between sexes and find differences across all areas of disease.

    • David Westergaard
    • , Pope Moseley
    •  & Søren Brunak
  • Article
    | Open Access

    It is unclear whether the sequence and timing of early life neurodevelopment varies across human populations, excluding the effects of disease or malnutrition. Here, the authors show that children of healthy, urban, educated mothers show very similar development across five geographically diverse populations.

    • José Villar
    • , Michelle Fernandes
    •  & Stephen Kennedy
  • Article
    | Open Access

    Similarities in cancers can be studied to interrogate their etiology. Here, the authors use genome-wide association study summary statistics from six cancer types based on 296,215 cases and 301,319 controls of European ancestry, showing that solid tumours arising from different tissues share a degree of common germline genetic basis.

    • Xia Jiang
    • , Hilary K. Finucane
    •  & Sara Lindström
  • Article
    | Open Access

    Population structure can bias the results of genetic and epidemiological analysis. Here, Haworth et al. report that fine-scale structure is detectable in apparently homogeneous samples such as ALSPAC when measured very precisely, and remains detectable in UK Biobank despite conventional approaches to account for it.

    • Simon Haworth
    • , Ruth Mitchell
    •  & Nicholas J. Timpson
  • Article
    | Open Access

    Real-time disease surveillance can aid mitigation of outbreaks. Here, Lu et al. combine an approach using Google search and EHR data with an approach leveraging spatiotemporal synchronicities of influenza activity across states to improve state-level influenza activity estimates in the US.

    • Fred S. Lu
    • , Mohammad W. Hattab
    •  & Mauricio Santillana
  • Article
    | Open Access

    Relevance of indirect protection of household members of vaccinees is unclear. Here, Tsang et al. quantify the direct and indirect protection of vaccination in a randomized controlled trial and show that benefits of individual vaccination remain important even when other household members are vaccinated.

    • Tim K. Tsang
    • , Vicky J. Fang
    •  & Simon Cauchemez
  • Article
    | Open Access

    While human lifespan is only moderately heritable, “getting old” runs in families. Here, van den Berg et al. study mortality data from three-generation cohorts to define a threshold for longevity and find that individuals have an increasing survival advantage with each additional relative in the top 10% survivors of their birth cohort.

    • Niels van den Berg
    • , Mar Rodríguez-Girondo
    •  & P. Eline Slagboom
  • Article
    | Open Access

    Robust surveillance methods are needed for trachoma control and recrudescence monitoring, but existing methods have limitations. Here, Pinsent et al. analyse data from nine trachoma-endemic populations and provide operational thresholds for interpretation of serological data in low transmission and post-elimination settings.

    • Amy Pinsent
    • , Anthony W. Solomon
    •  & Michael. T. White
  • Article
    | Open Access

    Nutritional experience can have phenotypic consequences in subsequent generations, as is evident from studies in animals and plants. Here, Vågerö et al. find in a large three-generation cohort that access to food in the paternal grandfather associates with all-cause and cancer mortality in male grandchildren.

    • Denny Vågerö
    • , Pia R. Pinger
    •  & Gerard J. van den Berg
  • Article
    | Open Access

    Studying the genetic underpinnings of physical activity and sleep duration can be confounded by self-reporting. Here, Doherty et al. use data from 91,105 UK Biobank participants, whose activity had been monitored for a week by a wearable device, for genome-wide association analysis and identify 14 loci.

    • Aiden Doherty
    • , Karl Smith-Byrne
    •  & Cecilia M. Lindgren
  • Article
    | Open Access

    Typhoid fever is caused by the bacterium Salmonella Typhi. Here, Park et al. analyse the genomes of 249 S. Typhi isolates from 11 sub-Saharan African countries, identifying genes and plasmids associated with antibiotic resistance and showing that multi-drug resistance is highly pervasive in sub-Saharan Africa.

    • Se Eun Park
    • , Duy Thanh Pham
    •  & Stephen Baker
  • Article
    | Open Access

    Treatment-seeking for fever is widely used to estimate treatment of childhood infections, but cross-country comparisons are problematic. Here, the authors estimate the probability of seeking treatment for fever at public facilities across 29 countries by quantifying person-level latent variables.

    • Victor A. Alegana
    • , Joseph Maina
    •  & Andrew J. Tatem
  • Article
    | Open Access

    The decision when to stop an intervention is a critical component of parasite elimination programmes, but reliance on surveillance data alone can be inaccurate. Here, Michael et al. combine parasite transmission model predictions with disease survey data to more reliably determine when interventions can be stopped.

    • Edwin Michael
    • , Morgan E. Smith
    •  & Frank O. Richards
  • Article
    | Open Access

    The basis for associations between lung cancer and major histocompatibility complex genes is not completely understood. Here the authors further consider genetic variation within the MHC region in lung cancer patients and identify independent associations within HLA genes that explain MHC lung cancer associations in Europeans and Asian populations.

    • Aida Ferreiro-Iglesias
    • , Corina Lesseur
    •  & Paul Brennan
  • Article
    | Open Access

    There is increasing urgency to understand the spatiotemporal dynamics of dengue in non-endemic regions. Here, the authors reconstruct likely dengue transmission chains in the city of Porto Alegre based on geo-located cases only, and find that most transmission events occur over short-distances.

    • Giorgio Guzzetta
    • , Cecilia A. Marques-Toledo
    •  & Stefano Merler
  • Article
    | Open Access

    Plasmodium vivax incidence in Malaysia has declined markedly over the last decade, despite evidence of chloroquine resistance. Here, Auburn et al. compare population structure of P. vivax in Malaysia to regions with intermediate and high transmission and identify genetic regions under putative selection.

    • Sarah Auburn
    • , Ernest D. Benavente
    •  & Ric N. Price
  • Article
    | Open Access

    The authors examine the role of monkey populations in the sylvatic cycle of chikungunya virus in the Kédougou region, Senegal. The authors show that monkeys are amplification hosts, as opposed to reservoir hosts for infection. These findings expand our knowledge of the transmission dynamics of chikungunya virus in this region of Senegal.

    • Benjamin M. Althouse
    • , Mathilde Guerbois
    •  & Kathryn A. Hanley
  • Article
    | Open Access

    Individuals with different genotypes may respond differently to environmental variation. Here, Favé et al. find substantial impacts of different environment exposures on the transcriptome and clinical endophenotypes when controlling for genetic ancestry by analyzing data from 1000 individuals from a founder population in Quebec.

    • Marie-Julie Favé
    • , Fabien C. Lamaze
    •  & Philip Awadalla
  • Review Article
    | Open Access

    Recall-by-Genotype (RbG) is an approach to recall participants from genetic studies based on their specific genotype for further, more extensive phenotyping. Here, the authors discuss examples of RbG as well as practical and ethical considerations and provide an online tool to aid in designing RbG studies.

    • Laura J. Corbin
    • , Vanessa Y. Tan
    •  & Nicholas J. Timpson
  • Article
    | Open Access

    Vitamin D deficiency is associated with multiple human pathologic conditions. In a genome-wide association study of 79,366 individuals, Jiang et al. replicate four and identify two new genetic loci for serum levels of 25-hydroxyvitamin D and find evidence for a shared genetic basis with autoimmune diseases.

    • Xia Jiang
    • , Paul F. O’Reilly
    •  & Douglas P. Kiel
  • Article
    | Open Access

    Understanding global epidemics spread is crucial for preparedness and response. Here the authors introduce an analytical framework to study epidemic spread on air transport networks, and demonstrate its power to estimate key epidemic parameters by application to the recent influenza pandemic and Ebola outbreak.

    • Lin Wang
    •  & Joseph T. Wu
  • Article
    | Open Access

    Cancer heritability estimates can be obtained via decomposing trait variance into genetic and other factors. Here, the authors obtain the distribution of absolute genetic risk for 15 common cancers, and they use a number of metrics to show that the genetic risk varies considerably across individuals.

    • Mats Julius Stensrud
    •  & Morten Valberg
  • Article
    | Open Access

    Inaccuracy of influenza forecasts based on dynamical models is partly due to nonlinear error growth. Here the authors address the error structure of a compartmental influenza model, and develop a new improved forecast approach combining dynamical error correction and statistical filtering techniques.

    • Sen Pei
    •  & Jeffrey Shaman
  • Article
    | Open Access

    Sleep patterns vary and are associated with health and disease. Here Purcellet alcharacterize sleep spindle activity in 11,630 individuals and describe age-related changes, genetic influences, and possible confounding effects, serving as a resource for further understanding the physiology of sleep.

    • S. M. Purcell
    • , D. S. Manoach
    •  & R. Stickgold
  • Article
    | Open Access

    Genome-wide association studies (GWAS) have become a key tool to discover genetic markers for complex traits; however, environmental factors that interact with genes are rarely considered. Here, the authors conduct a GWAS of obesity traits, and find that smoking may alter genetic susceptibilities.

    • Anne E. Justice
    • , Thomas W. Winkler
    •  & L Adrienne Cupples
  • Article
    | Open Access

    Some argue that health-related behaviours, such as obesity, are contagious, but empirical evidence of health contagion remains inconclusive. Here, using a large scale quasi-experiment in a global network of runners, Aral and Nicolaides show that this type of contagion exists in fitness behaviours.

    • Sinan Aral
    •  & Christos Nicolaides
  • Article
    | Open Access

    DNA methylation is modulated by environmental factors and has a role in many complex diseases. Here, the authors find that methylation at specific DNA sites is associated with all-cause mortality, and a methylation-based risk score may be informative for risk assessment and stratification.

    • Yan Zhang
    • , Rory Wilson
    •  & Hermann Brenner
  • Article
    | Open Access

    The socioeconomic burden of amyotrophic lateral sclerosis (ALS) is high, but the projected number of cases in the upcoming years is unclear. Here, the authors estimate the number and distribution of ALS cases to 2040, and show that cases are projected to increase, particularly in developing nations.

    • Karissa C. Arthur
    • , Andrea Calvo
    •  & Bryan J. Traynor
  • Article
    | Open Access

    The impact of antibiotics on the microbiome and health of children is poorly understood. Here, Korpela et al. study the gut microbiome of 142 children and show that the use of macrolides, but not penicillins, is associated with long-lasting shifts in microbiota composition and increased risk of asthma and overweight.

    • Katri Korpela
    • , Anne Salonen
    •  & Willem M. de Vos
  • Article
    | Open Access

    Mathematical models are used to predict malaria burden to inform disease control efforts. Here, Cameron et al. use Bayesian statistics to calibrate previous models against a data set of age-structured prevalence and incidence, generating stratified forecasts of the prevalence–incidence relationship.

    • Ewan Cameron
    • , Katherine E. Battle
    •  & Peter W. Gething
  • Article |

    African Americans have much higher colon cancer rates than rural South Africans, which is associated with dietary and metabolic differences. Here, O’Keefe et al.show that switching quantities of fat and fibre leads to reciprocal changes in gut microbiota, metabolites and cancer biomarkers.

    • Stephen J. D. O’Keefe
    • , Jia V. Li
    •  & Erwin G. Zoetendal
  • Article |

    Scrapie, a form of prion disease that affects sheep and goats, is believed not to be transmissible to humans. Using transgenic mice expressing human prion protein as a model of cross-species prion transmission, the authors show that ovine scrapie may possess potential to be passed on to humans.

    • Hervé Cassard
    • , Juan-Maria Torres
    •  & Olivier Andréoletti