Genetic variation articles within Nature

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  • Article
    | Open Access

    Reference assemblies of great ape sex chromosomes show that Y chromosomes are more variable in size and sequence than X chromosomes and provide a resource for studies on human evolution and conservation genetics of non-human apes.

    • Kateryna D. Makova
    • , Brandon D. Pickett
    •  & Adam M. Phillippy

  • Article
    | Open Access

    A study describes the release of clinical-grade whole-genome sequence data for 245,388 diverse participants by the All of Us Research Program and characterizes the properties of the dataset.

    • Alexander G. Bick
    • , Ginger A. Metcalf
    •  & Joshua C. Denny

  • Article |

    Analysis of data from the Born in Guangzhou Cohort Study comprising mainly of trios and mother–infant pairs reveals novel East Asian-specific genetic associations with maternal bile acid, gestational weight gain and infant cord blood traits.

    • Shujia Huang
    • , Siyang Liu
    •  & Xiu Qiu

  • Article
    | Open Access

    Population-scale whole-genome sequencing across four remote Indigenous Australian communities reveals a large fraction of structural variants that are unique to these populations, emphasizing the genetic distinctiveness of and diversity among Indigenous Australians.

    • Andre L. M. Reis
    • , Melissa Rapadas
    •  & Ira W. Deveson

  • Article
    | Open Access

    Analysis of the genomes of 159 individuals from four Indigenous communities in Australia shows a high level of genetic variation and demonstrates the need for greater representation of Indigenous Australians in reference panels and clinical databases.

    • Matthew Silcocks
    • , Ashley Farlow
    •  & Stephen Leslie

  • Article |

    A genomic constraint map for the human genome constructed using data from 76,156 human genomes from the Genome Aggregation Database shows that non-coding constrained regions are enriched for regulatory elements and variants associated with complex diseases and traits.

    • Siwei Chen
    • , Laurent C. Francioli
    •  & Konrad J. Karczewski

  • Article
    | Open Access

    Whole-genome alignment of 239 primate species reveals noncoding regulatory elements that are under selective constraint in primates but not in other placental mammals, that are enriched for variants that affect human gene expression and complex traits in diseases.

    • Lukas F. K. Kuderna
    • , Jacob C. Ulirsch
    •  & Kyle Kai-How Farh

  • Article
    | Open Access

    We gathered genetic data for 1,763 individuals from 147 populations across 14 African countries, and 12 Late Iron Age individuals, to trace the expansion of Bantu-speaking peoples over the past 6,000 years.

    • Cesar A. Fortes-Lima
    • , Concetta Burgarella
    •  & Carina M. Schlebusch

  • Article
    | Open Access

    Genotype and exome sequencing of 150,000 participants and whole-genome sequencing of 9,950 selected individuals recruited into the Mexico City Prospective Study constitute a valuable, publicly available resource of non-European sequencing data.

    • Andrey Ziyatdinov
    • , Jason Torres
    •  & Roberto Tapia-Conyer

  • Review Article |

    This Review provides a perspective on the development of non-cancer therapies based on human genetics studies and suggests measures that can be taken to streamline the pipeline from initial genetic discovery to approved therapy.

    • Katerina Trajanoska
    • , Claude Bhérer
    •  & Vincent Mooser

  • Article |

    We present the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference.

    • Arang Rhie
    • , Sergey Nurk
    •  & Adam M. Phillippy

  • Article
    | Open Access

    A study reports data from the first phase of the Chinese Pangenome Consortium including 116 de novo assemblies from 58 core samples representing 36 minority Chinese ethnic groups.

    • Yang Gao
    • , Xiaofei Yang
    •  & Shuhua Xu

  • Article
    | Open Access

    An analysis of 780 breast cancer genomes shows that focal amplifications are frequently preceded by dicentric chromosome formation from inter-chromosomal translocations associated with oestrogen receptor binding, which leads to chromosome bridge formation and breakage, initiating the amplification process.

    • Jake June-Koo Lee
    • , Youngsook Lucy Jung
    •  & Peter J. Park

  • Article
    | Open Access

    A study comparing the pattern of single-nucleotide variation between unique and duplicated regions of the human genome shows that mutation rate and interlocus gene conversion are elevated in duplicated regions.

    • Mitchell R. Vollger
    • , Philip C. Dishuck
    •  & Evan E. Eichler

  • Article
    | Open Access

    This study illustrates long interspersed nuclear element-1 retrotransposition-induced somatic mosaicism in normal cells and provides insights into the genomic and epigenomic regulation of transposable elements over the human lifetime.

    • Chang Hyun Nam
    • , Jeonghwan Youk
    •  & Young Seok Ju

  • Article
    | Open Access

    Comparisons within the human pangenome establish that homologous regions on short arms of heterologous human acrocentric chromosomes actively recombine, leading to the high rate of Robertsonian translocation breakpoints in these regions.

    • Andrea Guarracino
    • , Silvia Buonaiuto
    •  & Erik Garrison

  • Article
    | Open Access

    Analysis of ancient human DNA from the Swahili coast reveals that predominantly African female ancestors and Asian male ancestors formed families after around ad 1000 and lived in elite communities in coastal stone towns.

    • Esther S. Brielle
    • , Jeffrey Fleisher
    •  & Chapurukha M. Kusimba

  • Article |

     An analysis of rare coding variants across 22 common traits and diseases indicates that these variants will contribute substantially to biological insights but modestly to population risk stratification.

    • Daniel J. Weiner
    • , Ajay Nadig
    •  & Luke J. O’Connor

  • Article
    | Open Access

    Genome-wide association studies of individuals from an isolated population (data from the Finnish biobank study FinnGen) and consequent meta-analyses facilitate the identification of previously unknown coding variant associations for both rare and common diseases.

    • Mitja I. Kurki
    • , Juha Karjalainen
    •  & Aarno Palotie

  • Article
    | Open Access

    Single-cell whole-genome sequencing shows that 'foreground' cell-to-cell structural variation and alterations in copy number are associated with genomic diversity and evolution in triple-negative breast and high-grade serous ovarian cancers.

    • Tyler Funnell
    • , Ciara H. O’Flanagan
    •  & Samuel Aparicio

  • Article
    | Open Access

    Genetic data for 13 Neanderthals from 2 Middle Palaeolithic sites in the Altai Mountains of southern Siberia presented provide insights into the social organization of an isolated Neanderthal community at the easternmost extent of their known range.

    • Laurits Skov
    • , Stéphane Peyrégne
    •  & Benjamin M. Peter

  • Article
    | Open Access

    To measure selection on variants, whole-genome sequencing of approximately 150,000 individuals from the UK Biobank is used to rank sequence variants by their level of depletion.

    • Bjarni V. Halldorsson
    • , Hannes P. Eggertsson
    •  & Kari Stefansson

  • Article
    | Open Access

    A precise catalogue of more than 19 million variants from 838 tomato genomes, including 32 new reference-level genome assemblies, advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.

    • Yao Zhou
    • , Zhiyang Zhang
    •  & Sanwen Huang

  • Article
    | Open Access

    A meta-analysis combining whole-exome sequencing data from UK Biobank participants and imputed genotypes from FinnGen participants enables identification of genetic associations with human disease in the rare and low-frequency allelic spectrum

    • Benjamin B. Sun
    • , Mitja I. Kurki
    •  & Heiko Runz

  • Article
    | Open Access

    Data on de novo mutations in Arabidopsis thaliana reveal that mutations do not occur randomly; instead, epigenome-associated mutation bias reduces the occurrence of deleterious mutations.

    • J. Grey Monroe
    • , Thanvi Srikant
    •  & Detlef Weigel

  • Article |

    Genome-wide ancient DNA data from individuals from the Middle Bronze Age to Iron Age documents large-scale movement of people from the European continent between 1300 and 800 bc that was probably responsible for spreading early Celtic languages to Britain.

    • Nick Patterson
    • , Michael Isakov
    •  & David Reich

  • Article
    | Open Access

    Whole-genome sequencing of 3,171 cultivated and 195 wild chickpea accessions is used to construct a chickpea pan-genome, providing insight into chickpea evolution and enabling breeding strategies that could improve crop productivity.

    • Rajeev K. Varshney
    • , Manish Roorkiwal
    •  & Xin Liu

  • Article
    | Open Access

    Whole-exome sequencing analysis of 454,787 individuals in the UK Biobank is used to examine the association of protein-coding variants with nearly 4,000 health-related traits, identifying 564 distinct genes with significant trait associations.

    • Joshua D. Backman
    • , Alexander H. Li
    •  & Manuel A. R. Ferreira

  • Article |

    Laser-capture microdissection and mini-bulk exome sequencing are combined to analyse somatic mutations in morphologically normal tissues from nine organs from five donors, revealing variation in mutation burdens, mutational signatures and clonal expansions.

    • Ruoyan Li
    • , Lin Di
    •  & Chen Wu

  • Article |

    The authors report the mutational landscape of 29 cell types from microdissected biopsies from 19 organs and explore the mechanisms underlying mutation rates in normal tissues.

    • Luiza Moore
    • , Alex Cagan
    •  & Raheleh Rahbari

  • Article |

    Genomic analyses of human populations in the Pacific provide insights into the peopling history of the region and reveal episodes of biological adaptation relating to the immune system and lipid metabolism through introgression from archaic hominins and polygenic adaptation.

    • Jeremy Choin
    • , Javier Mendoza-Revilla
    •  & Lluis Quintana-Murci

  • Article |

    Genome-wide data from 166 East Asian individuals dating to between 6000 bc and ad 1000 and from 46 present-day groups provide insights into the histories of mixture and migration of human populations in East Asia.

    • Chuan-Chao Wang
    • , Hui-Yuan Yeh
    •  & David Reich

  • Article |

    Siberian mammoth genomes from the Early and Middle Pleistocene subepochs reveal adaptive changes and a key hybridization event, highlighting the value of deep-time palaeogenomics for studies of speciation and long-term evolutionary trends.

    • Tom van der Valk
    • , Patrícia Pečnerová
    •  & Love Dalén

  • Article
    | Open Access

    The goals, resources and design of the NHLBI Trans-Omics for Precision Medicine (TOPMed) programme are described, and analyses of rare variants detected in the first 53,831 samples provide insights into mutational processes and recent human evolutionary history.

    • Daniel Taliun
    • , Daniel N. Harris
    •  & Gonçalo R. Abecasis

  • Article
    | Open Access

    The genome of the biofuel crop switchgrass (Panicum virgatum) reveals climate–gene–biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.

    • John T. Lovell
    • , Alice H. MacQueen
    •  & Jeremy Schmutz

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