Genetic variation articles within Nature Communications

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  • Article
    | Open Access

    Use of general linear mixed models (GLMMs) in genetic variance analysis can quantify the relative contribution of additive effects from genetic variation on a given trait. Here, Jonathan Mosley and colleagues apply GLMM in a phenome-wide analysis and show that genetic variations in the HLA region are associated with 44 phenotypes, 5 phenotypes which were not previously reported in GWASes.

    • Jonathan D. Mosley
    • , John S. Witte
    •  & Joshua C. Denny

  • Article
    | Open Access

    This report by the Consortium for Refractive Error and Myopia uses gene-environment-wide interaction study (GEWIS) to identify genetic loci that affect environmental influence in myopia development, and identifies ethnic specific genetic loci that attribute to eye refractive errors.

    • Qiao Fan
    • , Virginie J. M. Verhoeven
    •  & Kari Matti Mäkelä

  • Article
    | Open Access

    Understanding the genetic influences on human aging requires a large number of subjects for a study of sufficient power. Here, Jim Wilson and colleagues use information on parental ages at death to show that common variants near the genes for apolipoprotein E and nicotinic acetylcholine receptor subunit alpha 5 are associated with longer lifespan.

    • Peter K. Joshi
    • , Krista Fischer
    •  & James F. Wilson

  • Article
    | Open Access

    Phenome-wide association is a novel method that links sequence variants to a spectrum of phenotypes and diseases. Here the authors generate detailed mouse genetic and phenome data which links their phenome-wide association study (PheWAS) of mouse to corresponding PheWAS in human.

    • Xusheng Wang
    • , Ashutosh K. Pandey
    •  & Robert W. Williams

  • Article
    | Open Access

    Tsai et al. here utilize a multi-stage genome-wide association study in Taiwanese population to show a copy number variation in the intron of potassium interacting channel 1 gene (KCNIP1) to be strongly associated with atrial fibrillation. The study also examines the functionality of KCNIP1 in heart electrophysiological function using cultured myocytes and zebrafish.

    • Chia-Ti Tsai
    • , Chia-Shan Hsieh
    •  & Jiunn-Lee Lin

  • Article
    | Open Access

    Reduced glomerular filtration rate (eGFR) is a hallmark of chronic kidney disease. Here, Pattaro et al. conduct a meta-analysis to discover several new loci associated with variation in eGFR and find that genes associated with eGFR loci often encode proteins potentially related to kidney development.

    • Cristian Pattaro
    • , Alexander Teumer
    •  & Caroline S. Fox

  • Article
    | Open Access

    Based on whole genome resequencing of more than 80 wild and domestic yaks from high-altitude Qinghai-Tibet Plateau, this study recovers demographic and genetic processes underlying the domestication of this animal. Qiu et al.also identify genes and associated pathways as candidates for selection during the domestication process.

    • Qiang Qiu
    • , Lizhong Wang
    •  & Jianquan Liu

  • Article
    | Open Access

    Published sequencing data sets of cancer samples could be used to identify genetic variants associated with the risk of developing cancer. Here, Luet al. analyse over 4,000 tumour-normal pairs to reveal variable frequencies of inherited susceptibilities across 12 cancer types and find enrichment of functionally validated missense variants of unknown significance.

    • Charles Lu
    • , Mingchao Xie
    •  & Li Ding

  • Article
    | Open Access

    The mushroom bodies (MBs) in an insect brain integrate and process sensory information. Using fully sequenced/inbred lines of the Drosophila Genetic Reference Panel, this study performs genome wide association analyses and identifies candidate genes affecting MB size, and uses RNAi to functionally validate the identified loci.

    • Liesbeth Zwarts
    • , Lies Vanden Broeck
    •  & Patrick Callaerts

  • Article
    | Open Access

    DICER1 is required for the maturation of miRNAs which regulate expression of thousands of genes. Here the authors show significantly reduced levels of DICER1in individuals having post-traumatic stress disorder and comorbid depression suggestive of a role in the molecular mechanism of the condition.

    • Aliza P. Wingo
    • , Lynn M. Almli
    •  & Kerry J. Ressler

  • Article
    | Open Access

    One of the key aspects for controlling infectious diseases is understanding how pathogens cross host species. Here the authors conduct a genome-wide analysis of Salmonella and show a high degree of variation, enabling host-adapted colonization among Salmonellaintestinal and systemic serovars.

    • Min Yue
    • , Xiangan Han
    •  & Dieter M. Schifferli

  • Article
    | Open Access

    Imputation uses genotype information from SNP arrays to infer the genotypes of missing markers. Here, the authors show that an imputation reference panel derived from whole-genome sequencing of 3,781 samples from the UK10K project improves the imputation accuracy and coverage of low frequency variants compared to existing methods.

    • Jie Huang
    • , Bryan Howie
    •  & Nicole Soranzo

  • Article
    | Open Access

    The Tohoku Medical Megabank Organization establishes a biobank with detailed patient health care and genome information. Here the authors analyse whole-genome sequences of 1,070 Japanese individuals, allowing them to catalogue 21 million single-nucleotide variants including 12 million novel ones.

    • Masao Nagasaki
    • , Jun Yasuda
    •  & Masayuki Yamamoto

  • Article
    | Open Access

    Kidney stone formation is influenced by genetic factors and recurrent stone formation places a significant burden on health care systems. Here Oddsson et al.perform a large-scale genome-wide association study and uncover new genetic variants associated with kidney stone susceptibility and associated biochemical traits.

    • Asmundur Oddsson
    • , Patrick Sulem
    •  & Kari Stefansson

  • Article
    | Open Access

    Previous studies have linked over 100 genomic loci to age-at-menarche but that work was restricted to common autosomal variation. Here, Lunetta et al. identify associations with rare protein-coding and X-linked variants, implicating new mechanisms that regulate puberty timing.

    • Kathryn L. Lunetta
    • , Felix R. Day
    •  & John R. B. Perry

  • Article
    | Open Access

    Cerebral palsy (CP) is a heterogeneous disorder that has been historically attributed to environmental factors with genetic contributions being discovered more recently. Here the authors perform microarray-based analysis of copy number variations in a cohort of children with CP and their parents and find chromosomal abnormalities linked to the disease.

    • Maryam Oskoui
    • , Matthew J. Gazzellone
    •  & Stephen W. Scherer

  • Article
    | Open Access

    How genetic variation contributes to brain morphology is still poorly understood. Here Chenet al. combine brain imaging with single-nucleotide polymorphism data to discover that a substantial degree of cortical variation is derived from underlying genetic differences.

    • Chi-Hua Chen
    • , Qian Peng
    •  & Anders M. Dale

  • Article
    | Open Access

    Schizophrenia is a complex disorder with high heritability but poorly understood genetics. Here Olde Loohuis et al.compare schizophrenia patients to unaffected individuals and identify an increased individual burden of rare deleterious mutations in patients.

    • Loes M. Olde Loohuis
    • , Jacob A. S. Vorstman
    •  & Roel A. Ophoff

  • Article
    | Open Access

    In order to effectively design interventions, it is useful to understand the complex interplay between multiple syndromes. Here, Ahmad et al. use genome-wide association study data and Mendelian randomisation to examine the influence of Type 2 diabetes and fasting glucose levels on coronary heart disease.

    • Omar S. Ahmad
    • , John A. Morris
    •  & J. Brent Richards

  • Article |

    Artifacts caused by whole-genome amplification bias are a recurrent challenge in single-cell sequencing analysis. Here, the authors develop statistical models and demonstrate an efficient strategy for controlling amplification errors by a joint analysis of single cell genomes.

    • Cheng-Zhong Zhang
    • , Viktor A. Adalsteinsson
    •  & J. Christopher Love

  • Article
    | Open Access

    Pulmonary hypertension and congestive right heart failure afflict some cattle living at high altitude in an autosomal dominant pattern, yet no responsible genes have been identified. Here Newman et al.use whole-exome sequencing to identify variants in the hypoxia inducible factor gene, EPAS1.

    • John H. Newman
    • , Timothy N. Holt
    •  & Rizwan Hamid

  • Article
    | Open Access

    Basal cell carcinoma is a common cancer among people of European ancestry, with associated high economic costs to monitor and treat. Here Stacey et al.conduct a genome-wide association study on Icelandic and other European populations, identifying four novel loci associated with cancer susceptibility.

    • Simon N. Stacey
    • , Hannes Helgason
    •  & Kari Stefansson

  • Article
    | Open Access

    H7N9 bird flu viruses cause mild disease in poultry but can occasionally infect humans with fatal consequences. Here, the authors show that viral genetic diversification is low in ferrets and high in chickens, suggesting that a genetic bottleneck limits H7N9 adaptation to mammals

    • Hassan Zaraket
    • , Tatiana Baranovich
    •  & Richard J. Webby

  • Article |

    Pediatric adrenocortical carcinoma is a rare malignancy with poor prognosis. Here the authors analyse the genomes, exomes and transcriptomes of 37 such tumours and identify genetic alterations whose nature, timing and potential interactions are key events with prognostic significance in pediatric adrenocortical tumorigenesis.

    • Emilia M. Pinto
    • , Xiang Chen
    •  & Gerard P. Zambetti

  • Article
    | Open Access

    Levels of circulating thyrotropin and free thyroxine reflect thyroid function, however, their genetic underpinnings remain poorly understood. Taylor et al. take advantage of whole-genome sequence data from cohorts within the UK10K project to identify novel variants associated with these traits.

    • Peter N. Taylor
    • , Eleonora Porcu
    •  & Pingbo Zhang

  • Article |

    Fatty acid amide hydrolase (FAAH) is a key regulator of endocannabinoid signalling. Here, the authors develop a knock-in mouse that recapitulates a common human mutation in the FAAH gene and demonstrate parallel neural and behavioural alterations across species, suggesting a gain-of-function in fear regulation.

    • Iva Dincheva
    • , Andrew T. Drysdale
    •  & Francis S. Lee

  • Article |

    Maternal glucose levels during pregnancy can affect the metabolic health of a developing fetus, both early on and later in life. Here, the authors reveal that genetic variants in several regulatory elements alter glucose homeostasis during pregnancy by reducing the expression of a novel hexokinase gene, HKDC1.

    • Cong Guo
    • , Anton E. Ludvik
    •  & Timothy E. Reddy

  • Article |

    Phenotypic and genetic heterogeneity of cells within a tumour is thought to mediate treatment resistance and contribute to cancer progression. Here the authors show that genetic diversity in pediatric cancers is common after chemotherapy and can be quantified to predict survival.

    • Linda Holmquist Mengelbier
    • , Jenny Karlsson
    •  & David Gisselsson

  • Article
    | Open Access

    The generation of a national pan-genome, a population-specific catalogue of genetic variation, may advance the impact of clinical genetics studies. Here the Besenbacher et al. carry out deep sequencing and de novo assembly of 10 parent–child trios to generate a Danish pan-genome that provides insight into structural variation, de novomutation rates and variant calling.

    • Søren Besenbacher
    • , Siyang Liu
    •  & Simon Rasmussen

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