Genetic variation articles within Nature Communications

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  • 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

  • Article
    | Open Access

    Common variants account for only a small amount of the heritable risk for developing asthma. Using a meta-analysis approach, Igartua et al. identify one low-frequency missense mutation and two genes with functional variants that are associated with asthma, but only in specific ethnic groups.

    • Catherine Igartua
    • , Rachel A. Myers
    •  & Carole Ober

  • Article
    | Open Access

    The microbial RNA-guided CRISPR/Cas9 system has robust genome-editing activities, but the off-target effects of the Cas9 nuclease have only recently begun to be analysed. Here the authors provide evidence for high specificity of the Cas9 nuclease on targeting of the Tafazzin gene in human-induced pluripotent stem cells and demonstrate the impact of single-nucleotide variations of the human genome on Cas9 specificity.

    • Luhan Yang
    • , Dennis Grishin
    •  & George Church

  • Article |

    The functional relevance of age-related variation in DNA methylation is unclear. Here, Reynolds et al. analyze how patterns of genome-wide gene expression and DNA methylation data vary with age in circulating monocytes and T cells, and report age-associated methylation signals that are correlated with cis-gene expression and vascular aging.

    • Lindsay M. Reynolds
    • , Jackson R. Taylor
    •  & Yongmei Liu

  • Article
    | Open Access

    Isolated populations can increase power to detect low frequency and rare risk variants associated with complex phenotypes. Here, the authors identify variants associated with haematological traits in two isolated Greek populations that would be difficult to detect in the general population, due to their low frequency.

    • Kalliope Panoutsopoulou
    • , Konstantinos Hatzikotoulas
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Previous studies identified genetic variants associated with colorectal cancer (CRC), but the functional consequences of these genetic risk factors remain poorly understood. Here, the authors report that CRC risk variants reside in promoters and enhancers and could increase colon cancer risk through gene expression regulation.

    • Lijing Yao
    • , Yu Gyoung Tak
    •  & Peggy J. Farnham

  • Article
    | Open Access

    The genetic basis of expressive vocabulary in children around 2 years old is poorly understood. Here, the authors show that a genetic variant near the ROBO2gene is associated with early language acquisition in the general population and highlight a potential genetic link between language-related common genetic variation and a linkage region for dyslexia, speech-sound disorder and reading.

    • Beate St Pourcain
    • , Rolieke A.M. Cents
    •  & George Davey Smith

  • Article
    | Open Access

    Population-based genome sequencing provides an increasingly rich resource for the identification of low-frequency, large effect variants associated with clinically important phenotypes. Timpson et al. use UK10K data to identify a variant of the APOC3gene strongly associated with plasma triglyceride levels.

    • Nicholas J. Timpson
    • , Klaudia Walter
    •  & Hou-Feng Zheng

  • Article
    | Open Access

    Genetic variation in Mycobacterium tuberculosiscomplex (MTBC) bacteria is responsible for differences in factors such as virulence and transmissibility. Here, the authors analyse the genomes of 1,601 MTBC isolates from diverse geographic locations and identify 62 SNPs that may be used to resolve lineages and sublineages of these strains.

    • Francesc Coll
    • , Ruth McNerney
    •  & Taane G. Clark

  • Article
    | Open Access

    RNA sequencing has enabled the global analysis of both gene expression levels and splicing events. Here, the authors develop a multivariate approach that is able to identify SNPs that influence splicing, and investigate the overlap of these with functional domains across the genome, including previously identified GWAS signals.

    • Jean Monlong
    • , Miquel Calvo
    •  & Roderic Guigó

  • Article |

    Senescence is the decline in physiological function associated with age, and the genetic basis of this phenomenon is poorly understood. Here, the authors identify genetic variants in Drosophilathat affect reproduction and lifespan in an age-specific manner, and provide support for the mutation accumulation theory of aging.

    • Mary F. Durham
    • , Michael M. Magwire
    •  & Jeff Leips

  • Article
    | Open Access

    Tracing the source of malarial infections is an important step towards monitoring and controlling the disease. Here, Preston et al. analyse sequence data from 711 isolates and design a genetic barcode based on combined mitochondrial and apicoplast genomes that is able to distinguish between malaria parasites isolated from different geographical regions.

    • Mark D. Preston
    • , Susana Campino
    •  & Taane G. Clark

  • Article |

    The distance that individuals disperse to between birth and first breeding determines the dynamics and genetic composition of natural populations. Here the authors show that in great tits (Parus major), the distance of local dispersal is genetically coupled with exploratory behaviour measured in the lab.

    • Peter Korsten
    • , Thijs van Overveld
    •  & Erik Matthysen

  • Article |

    Uncovering the factors that influence the generation of copy number variation (CNV) across the genome may increase our understanding of the role of CNVs in disease. Here, Makino et al.provide insights into the mechanisms underlying CNV formation and suggest a method for identifying disease-associated CNVs.

    • Takashi Makino
    • , Aoife McLysaght
    •  & Masakado Kawata

  • Article |

    Genetic effects on gene expression by variants at expression quantitative trait loci (eQTLs), can contribute to human genetic diseases. Here, Liet al. present a method to study eQTLs with effects on protein translation on a transcriptome-wide scale.

    • Quan Li
    • , Angeliki Makri
    •  & Hui-Qi Qu

  • Article
    | Open Access

    Quantitative trait loci mapping has traditionally been used to discover desirable alleles in plants. In this study, Lyu et al. use a comparative genome approach to identify an allele that is prevalent in upland rice varieties and alters the function of a protein involved in abscisic acid biosynthesis.

    • Jun Lyu
    • , Shilai Zhang
    •  & Wen Wang

  • Article
    | Open Access

    A variant in the IFITM3gene increases the risk of severe influenza, but homozygosity is rare in Caucasians. The authors show that the variant gene is homozygous in 25% of healthy Chinese people, and 69% of those with severe pandemic influenza, suggesting that this gene influences the epidemiology of influenza in South-East Asia.

    • Yong-Hong Zhang
    • , Yan Zhao
    •  & Tao Dong

  • Article |

    The amount of data supplied by next-generation sequencing technologies presents a challenge for traditional algorithms to detect single-nucleotide polymorphisms. Xu et al.develop an efficient detection program and demonstrate its utility by identifying polymorphisms in cancer genomes and human populations.

    • Feng Xu
    • , Weixin Wang
    •  & Junwen Wang

  • Article
    | Open Access

    miRNAs simultaneously regulate a range of genes, making them potential master players in evolution. Huet al.identify a human-specific miRNA called miR-941, whose copy number remains polymorphic in modern humans, and show that miR-941 is expressed in the brain and could regulate important signalling pathways.

    • Hai Yang Hu
    • , Liu He
    •  & Philipp Khaitovich

  • Article
    | Open Access

    Hunter-gatherer populations in Africa preserve unique information about human history, but genetic sub-structures of these populations remain unclear. Using newly designed microarray and statistical methods, these authors analyse genetic compositions of southern African populations and reveal an ancient link between southern and eastern Africa.

    • Joseph K. Pickrell
    • , Nick Patterson
    •  & Brigitte Pakendorf

  • Article
    | Open Access

    Mutation, selection and random drift determine evolutionary dynamics and can give rise to polymorphisms. Here, an evolutionary game model, in which each new mutation generates a new evolutionary game, is applied to study the emergence of polymorphism, resulting in higher diversity than seen in previous models.

    • Weini Huang
    • , Bernhard Haubold
    •  & Arne Traulsen

  • Article
    | Open Access

    The global prevalence of the Duffy blood group variants is important due to the resistance that the Duffy-negative phenotype generally confers uponPlasmodium vivax infection. Hay et al.generate global frequency maps of the common Duffy alleles to show transmission patterns of the malaria parasite.

    • Rosalind E. Howes
    • , Anand P. Patil
    •  & Simon I. Hay

  • Article |

    Matrilocal and patrilocal populations are predicted to have greater genetic diversity in mitochondrial DNA and the Y-chromosome, respectively. Here, no difference in the diversity of the Y-chromosome was found in two such groups, suggesting that local diversity was caused by male gene flow in expanding populations.

    • Ellen Dröfn Gunnarsdóttir
    • , Madhusudan R. Nandineni
    •  & Mark Stoneking

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