Genetic variation articles within Nature Communications

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  • Article
    | Open Access

    Whole genome sequencing (WGS) holds promise to solve a subset of Mendelian disease cases for which exome sequencing did not provide a genetic diagnosis. Here, Wells et al. report a supervised machine learning model trained on functional, mutational and structural features for rank-scoring and interpreting variants in non-coding regions from WGS.

    • Alex Wells
    • , David Heckerman
    •  & Julia di Iulio

  • Article
    | Open Access

    Exceptional alpine plant diversity exists in the Hengduan Mountains. Here, through genome assembly and population genomics studies, the authors find notable intraspecific divergence among Cushion willow populations isolated by the sky island-like habitats and consider it contributes to speciation and biodiversity.

    • Jia-hui Chen
    • , Yuan Huang
    •  & Hang Sun

  • Article
    | Open Access

    Cucurbits fruits have diverse shapes and sizes, but their genomes evolution and genetic basis of diversity are unclear. Here, the authors show that the wax gourd genome has the most ancestral karyotype among cucurbits and identify candidate genes which contribute to large fruit size by comparative and population genomics analyses.

    • Dasen Xie
    • , Yuanchao Xu
    •  & Zhonghua Zhang

  • Article
    | Open Access

    Various approaches are being used for polygenic prediction including Bayesian multiple regression methods that require access to individual-level genotype data. Here, the authors extend BayesR to utilise GWAS summary statistics (SBayesR) and show that it outperforms other summary statistic-based methods.

    • Luke R. Lloyd-Jones
    • , Jian Zeng
    •  & Peter M. Visscher

  • Article
    | Open Access

    Rare genetic disorders (RGDs) often exhibit significant clinical variability among affected individuals. Here, Oetjens et al. systematically study the contribution of common genetic variation to variable expressivity of RGDs and find it is frequently influenced by polygenic factors identified in genome-wide association studies of relevant traits.

    • M. T. Oetjens
    • , M. A. Kelly
    •  & D. H. Ledbetter

  • Article
    | Open Access

    Date palm is an important fruit crop in the Middle East and North Africa. Here, the authors report an improved genome assembly of this species and perform GWAS mapping of sex determining region and 21 fruit traits using high density SNP data generated from re-sequencing of the mapping population.

    • Khaled M. Hazzouri
    • , Muriel Gros-Balthazard
    •  & Michael D. Purugganan

  • Article
    | Open Access

    Retrotransposition events have been linked to some human disorders. Here, Gardner et al. systematically search for mobile genetic elements (ME) in trio whole exome-sequencing datasets and ascertain 9 de novo MEs and further estimate genome-wide germline ME burden and constraint.

    • Eugene J. Gardner
    • , Elena Prigmore
    •  & Matthew E. Hurles

  • 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

    Low frequency coding single-nucleotide variants (SNVs) are predicted to disproportionately affect protein function. Here, the authors evaluate 2,009 missense SNVs across 2,185 protein-protein interactions using yeast two-hybrid and protein complementation assays and find that disruptive SNVs often occur in disease-associated genes.

    • Robert Fragoza
    • , Jishnu Das
    •  & Haiyuan Yu

  • Article
    | Open Access

    Estimates of mutation rates differ between species. Here, Lindsay et al. perform side-by-side analyses of germline mutation rates using multi-sibling mouse and human pedigrees and find different mutation rates between species, also stratified by sex and temporal stage of mutation acquisition.

    • Sarah J. Lindsay
    • , Raheleh Rahbari
    •  & Matthew E. Hurles

  • Article
    | Open Access

    While many pleiotropic genetic loci have been identified, how they contribute to phenotypes across traits and diseases is unclear. Here, the authors propose decomposition of genetic associations (DeGAs), which uses singular value decomposition, to characterize the underlying latent structure of genetic associations of 2,138 phenotypes.

    • Yosuke Tanigawa
    • , Jiehan Li
    •  & Manuel A. Rivas

  • Article
    | Open Access

    During meiotic recombination, genetic information is transferred or exchanged between parental chromosome copies. Using a large hybrid mouse pedigree, the authors generated high-resolution maps of these transfer/exchange events and discovered new properties governing their processing and resolution.

    • Ran Li
    • , Emmanuelle Bitoun
    •  & Simon R. Myers

  • Article
    | Open Access

    Remains of several hundred humans are scattered around Roopkund Lake, situated over 5,000 meters above sea level in the Himalayan Mountains. Here the authors analyze genome-wide data from 38 skeletons and find 3 clusters with different ancestries and dates, showing the people were desposited in multiple catastrophic events.

    • Éadaoin Harney
    • , Ayushi Nayak
    •  & Niraj Rai

  • Article
    | Open Access

    Theory suggests that neutral genetic diversity is determined by census population size, but this is not observed empirically. Here, the authors show that in butterflies, neutral genetic diversity correlates with both body size and chromosome number, suggesting that linked selection is also an important factor.

    • Alexander Mackintosh
    • , Dominik R. Laetsch
    •  & Konrad Lohse

  • Article
    | Open Access

    The contribution of transposable elements (TEs) to the creation of heritable mutations is unknown. Here the authors show in Arabidopsis that TEs accumulate exponentially once mobilized and that COPIA retrotransposons preferentially integrate in environmental response genes in a H2A.Z-dependent manner.

    • Leandro Quadrana
    • , Mathilde Etcheverry
    •  & Vincent Colot

  • Article
    | Open Access

    Genetic adaptation and physiological acclimation can potentially buffer species against climate change. Here, the authors perform a long-term warming experiment of Antarctic encrusting communities and show that focal animal species failed to acclimate and lacked genetic variation in tolerance to warming.

    • Melody S. Clark
    • , Leyre Villota Nieva
    •  & Lloyd S. Peck

  • Article
    | Open Access

    While the role of effective population size (Ne) in explaining variation in genetic diversity has received much attention, the role of spontaneous mutation rate is largely ignored. Here, Xu et al. show that giant duckweed has a high Ne yet low genetic diversity, likely due to its low mutation rate.

    • Shuqing Xu
    • , Jessica Stapley
    •  & Meret Huber

  • Article
    | Open Access

    Despite the importance of grapevine cultivation in human history and the economic values of cultivar improvement, large-scale genomic variation data are lacking. Here the authors resequence 472 Vitis accessions and use the identified genetic variations for domestication history, demography, and GWAS analyses.

    • Zhenchang Liang
    • , Shengchang Duan
    •  & Yang Dong

  • Article
    | Open Access

    The burden of asthma varies between ancestries, but GWAS have so far focused on mainly European ancestry populations. Here, Daya et al. perform GWAS for asthma in 14,654 individuals of African ancestry and, besides confirming previously known loci, identify two potentially African ancestry-specific loci.

    • Michelle Daya
    • , Nicholas Rafaels
    •  & Maria Yazdanbakhsh

  • Article
    | Open Access

    Researchers can make use of a variety of computational tools to prioritize genetic variants and predict their pathogenicity. Here, the authors evaluate the performance of six of these tools in three typical biological tasks and find generally low concordance of predictions and experimental confirmation.

    • Li Liu
    • , Maxwell D. Sanderford
    •  & Sudhir Kumar

  • Article
    | Open Access

    Introgression of Neanderthals and Denisovans left genomic signals in anatomically modern human after Out-of-Africa event. Here, the authors identify a third archaic introgression common to all Asian and Oceanian human populations by applying an approximate Bayesian computation with a Deep Learning framework.

    • Mayukh Mondal
    • , Jaume Bertranpetit
    •  & Oscar Lao

  • Article
    | Open Access

    The origin of Tibetan barley (qingke) has been a controversial issue for many years. Here, the authors conduct population genomics study to support that qingke is derived from eastern domesticated barley instead of Tibetan wild barley and suggest southern Tibetan Plateau as its introduction route.

    • Xingquan Zeng
    • , Yu Guo
    •  & Nyima Tashi

  • Article
    | Open Access

    Male pattern baldness (MPB) is a polygenic trait that affects the majority of European men. Here, Yap et al. estimate heritability, partitioned by autosomes and the X-chromosome, of MPB in the UK Biobank cohort, perform GWAS for MPB and find genetic correlation with other sex-specific traits.

    • Chloe X. Yap
    • , Julia Sidorenko
    •  & Peter M. Visscher

  • Article
    | Open Access

    Latin Americans trace their ancestry to the admixture of Native Americans, Europeans and Sub-Saharan Africans. Here, the authors develop a novel haplotype-based approach and analyse over 6,500 Latin Americans to infer the geographically-detailed genetic structure of this population.

    • Juan-Camilo Chacón-Duque
    • , Kaustubh Adhikari
    •  & Andrés Ruiz-Linares

  • Article
    | Open Access

    Rare genetic variants can contribute to complex traits but this contribution is not well understood. Here, the authors analyse deep whole genome sequencing data across 1457 individuals from an isolated Greek population and find association of rare variant burdens with cardiometabolic traits.

    • Arthur Gilly
    • , Daniel Suveges
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Mutations in genes encoding NAPDH oxidase subunits are known to be causative for the primary immunodeficiency chronic granulomatous disease (CGD). Here, the authors identify CYBC1 mutations in patients with CGD and show that CYBC1 is important for formation of the NADPH complex and respiratory burst.

    • Gudny A. Arnadottir
    • , Gudmundur L. Norddahl
    •  & Kari Stefansson

  • Article
    | Open Access

    Short-tandem repeats (STR), similar to single nucleotide polymorphisms (SNP), contribute to complex traits, but their ascertainment by next-generation sequencing is costly. Here, Saini et al. provide a SNP+STR haplotype reference panel that allows imputation of STRs from SNP array data.

    • Shubham Saini
    • , Ileena Mitra
    •  & Melissa Gymrek

  • Article
    | Open Access

    The harlequin ladybird beetle, Harmonia axyridis, has remarkable phenotypic diversity, with over 200 colour patterns. Here, Ando et al. show that this patterning is regulated by the transcription factor gene pannier and has diversified by repeated inversions and cis-regulatory modifications of pannier.

    • Toshiya Ando
    • , Takeshi Matsuda
    •  & Teruyuki Niimi

  • Article
    | Open Access

    Common genetic variants associated with plasma lipids have been extensively studied for a better understanding of common diseases. Here, the authors use whole-genome sequencing of 16,324 individuals to analyze rare variant associations and to determine their monogenic and polygenic contribution to lipid traits.

    • Pradeep Natarajan
    • , Gina M. Peloso
    •  & Sebastian Zoellner

  • Article
    | Open Access

    Japonica rice can grow further north than wild or indica rice and is more tolerant of cold climates. Here, the authors show that bZIP73 likely underwent selection in the early phase of rice domestication to facilitate cold tolerance in japonica by modulating ABA and ROS homeostasis.

    • Citao Liu
    • , Shujun Ou
    •  & Chengcai Chu

  • Article
    | Open Access

    Clustering methods such as STRUCTURE and ADMIXTURE are widely used in population genetic studies to investigate ancestry. Here, the authors provide a tutorial on how to interpret results of these analyses and a tool to test the goodness of fit of the model.

    • Daniel J. Lawson
    • , Lucy van Dorp
    •  & Daniel Falush

  • Article
    | Open Access

    The majority of the human reference genome assembly is represented as a single consensus haplotype. Here, Wong et al. analyze de novo assemblies of 17 diverse, haplotype-resolved genomes to gain insights into the structure of genetic diversity and compile a list of alternative haplotypes across populations.

    • Karen H. Y. Wong
    • , Michal Levy-Sakin
    •  & Pui-Yan Kwok

  • Article
    | Open Access

    Dominance is difficult to measure in natural populations as it is confounded with fitness. Here, Huber et al. developed a new approach to co-estimate dominance and selection coefficients, and found that the observed relationship is best fit by a new model of dominance based on gene expression level.

    • Christian D. Huber
    • , Arun Durvasula
    •  & Kirk E. Lohmueller

  • Article
    | Open Access

    Since the 1980s, hypervirulent clonal-group CG23 serotype K1 Klebsiella pneumoniae has been recognised as a prominent cause of community-acquired liver abscess and other severe infections. Here, the authors investigate the genomic evolutionary history of CG23 and suggest a new reference strain for CG23.

    • Margaret M. C. Lam
    • , Kelly L. Wyres
    •  & Kathryn E. Holt

  • Article
    | Open Access

    Human embryonic stem cell-derived cardiomyocytes (hESC-CM) are a widely used model to study cardiac genomics. Here, Choy et al. perform promoter capture Hi-C to map long-range chromosomal interactions of hESC-CMs and to study overlap of such regions with genetic loci associated with cardiac phenotypes.

    • Mun-Kit Choy
    • , Biola M. Javierre
    •  & Bernard D. Keavney

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