Haplotypes articles within Nature Communications

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  • Article
    | Open Access

    Here the authors show that genetic changes between species often alter gene expression in a cell type-specific manner. Most of this variability is driven by locally functioning cis-acting variation, and this contributes to the speed at which cell types accumulate expression changes.

    • Jasper Panten
    • , Tobias Heinen
    •  & Duncan T. Odom

  • Article
    | Open Access

    For most ancient genomes, low sequencing depth restricts genotyping, limiting their study. Here, the authors test imputation performance of ancient human genomes by estimating error rates and potential bias introduced in downstream analyses.

    • Bárbara Sousa da Mota
    • , Simone Rubinacci
    •  & Olivier Delaneau

  • Article
    | Open Access

    Low-cost targeted approach to construct haplotype-resolved assemblies is needed to facilitate population genetic studies. Here, the authors demonstrate assembling high-quality MHC haplotypes with CRISPR-based enrichment and long-read sequencings.

    • Taotao Li
    • , Duo Du
    •  & Yun Liu

  • Article
    | Open Access

    Whole genome sequencing (WGS) data on non-European and admixed individuals remains scarce. Here, the authors analyse WGS data from 1,171 admixed elderly Brazilians from a census cohort, characterising population-specific genetic variation and exploring the clinical utility of this expanded dataset.

    • Michel S. Naslavsky
    • , Marilia O. Scliar
    •  & Mayana Zatz

  • Article
    | Open Access

    Ethiopia is one of the most ethnically and culturally diverse countries. Here, the authors look at genetic and cultural variation in 1,214 Ethiopians to unravel the relationship between genetic admixture and cultural factors.

    • Saioa López
    • , Ayele Tarekegn
    •  & Garrett Hellenthal

  • Article
    | Open Access

    Accurately measuring genetic relatedness by Identical-By-Descent (IBD) segments is challenging in biobank-level genome data. The authors present IBD method FastSMC, which when applied to the UK Biobank gives a detailed picture of genetic relatedness and evolutionary history in the UK over the past 2000 years.

    • Juba Nait Saada
    • , Georgios Kalantzis
    •  & Pier Francesco Palamara

  • Article
    | Open Access

    Genetic variations present in landraces are critical for crop genetic improvement. Here, the authors map haplotype-trait associations in ~1000 doubled haploid lines derived from three European maize landraces and identify beneficial haplotypes for quantitative traits that are not present in breeding lines.

    • Manfred Mayer
    • , Armin C. Hölker
    •  & Chris-Carolin Schön

  • Article
    | Open Access

    Genetic variation in modern humans can reveal information about a population’s history and migration patterns. Here, the authors describe the ancestry and geospatial genetic structure of the Netherlands, and demonstrate the utility of haplotype-based covariates in genome-wide association studies.

    • Ross P. Byrne
    • , Wouter van Rheenen
    •  & Russell L. McLaughlin

  • Article
    | Open Access

    Multi-nucleotide variants (MNV) are genetic variants in close proximity of each other on the same haplotype whose functional impact is difficult to predict if they reside in the same codon. Here, Wang et al. use the gnomAD dataset to assemble a catalogue of MNVs and estimate their global mutation rate.

    • Qingbo Wang
    • , Emma Pierce-Hoffman
    •  & Daniel G. MacArthur

  • Article
    | Open Access

    GWAS analysis currently relies mostly on linear mixed models, which do not account for linkage disequilibrium (LD) between tested variants. Here, Sesia et al. propose KnockoffZoom, a non-parametric statistical method for the simultaneous discovery and fine-mapping of causal variants, assuming only that LD is described by hidden Markov models (HMMs).

    • Matteo Sesia
    • , Eugene Katsevich
    •  & Chiara Sabatti

  • Article
    | Open Access

    For most human genes nearby regulatory variants explain only a small proportion of their expression variation between individuals. Here the authors show how the impact of a gene’s set of nearby regulatory variant is often linked to the expression levels of distal genes, providing insights into gene networks.

    • D. Wragg
    • , Q. Liu
    •  & J. G. D. Prendergast

  • Article
    | Open Access

    Haplotype information inferred by phasing is useful in genetic and genomic analysis. Here, the authors develop SHAPEIT4, a phasing method that exhibits sub-linear running time, provides accurate haplotypes and enables integration of external phasing information.

    • Olivier Delaneau
    • , Jean-François Zagury
    •  & Emmanouil T. Dermitzakis

  • Article
    | Open Access

    It is currently unclear how quantitative changes in chromatin loop propensity contribute to differential gene regulation. Here, the authors use phased Hi-C, RNA-seq, and ChIP-seq to show that subtle changes in loop propensity associate with differential gene regulation across cell types and haplotypes.

    • William W. Greenwald
    • , He Li
    •  & Kelly A. Frazer

  • Article
    | Open Access

    High-throughput sequencing and analyzes of antibody repertoire provide important information on immune responses, but current methodologies are limited in sequence assembly precision and haplotype inference validity. Here the authors propose a new Bayesian haplotyping method, and attest its broad application with a large, multi-individual dataset.

    • Moriah Gidoni
    • , Omri Snir
    •  & Gur Yaari

  • Article
    | Open Access

    Proteoforms arise as protein isoforms or as protein haplotypes, which are the result of genetic variation. Here, the authors develop Haplosaurus, a database that computes protein haplotypes genome-wide from existing genotype data and analyse protein haplotype variability in the 1000 Genomes dataset.

    • William Spooner
    • , William McLaren
    •  & Catherine Chaillan Huntington

  • Article
    | Open Access

    Human APOBEC3H has several haplotypes and splice variants with distinct anti-HIV-1 activities, but the genetics underlying the expression of these variants are unclear. Here, the authors identify an intronic deletion in A3H haplotype II resulting in production of the most active splice variant, which is counteracted by HIV-1 protease.

    • Diako Ebrahimi
    • , Christopher M. Richards
    •  & Reuben S. Harris

  • 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

    Genome interpretation and analysis of allelic activity requires appropriate haplotype phasing. Here the authors present phASER, a fast and accurate method for variant phrasing from RNA-seq and genome sequencing data.

    • Stephane E. Castel
    • , Pejman Mohammadi
    •  & Tuuli Lappalainen

  • 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 spatial organization of the genome within the nucleus impacts many processes. Here the authors combine oligo-based DNA FISH with single-molecule super-resolution microscopy to image single-copy genomic regions and, taking advantage of SNPs, distinguish allelic regions of homologous chromosomes.

    • Brian J. Beliveau
    • , Alistair N. Boettiger
    •  & Chao-ting Wu

  • Article |

    Yin–yang haplotypes are stretches of DNA that differ at multiple markers and exhibit two disparate forms. Here, the authors identify a pair of 284-nucleotide-long yin–yang haplotypes that encompass the gephyringene, and show that these human-specific haplotypes evolved rapidly and bear functional implications.

    • Sharlee Climer
    • , Alan R. Templeton
    •  & Weixiong Zhang

  • Article
    | Open Access

    The genetic make-up of people living in the Americas has been shaped heavily by migration. Here the authors use a haplotype-based approach to reconstruct American genomic ancestry using genotype data from 2,500 individuals, revealing a previously unrecognized genetic contribution from European and African populations.

    • Francesco Montinaro
    • , George B.J. Busby
    •  & Cristian Capelli

  • Article
    | Open Access

    Domestication of wild boar populations has led to phenotypically distinct European and Asian pig breeds. Here, the authors show that Asian haplotypes that have introgressed into European pig breeds harbour genes that control economically important traits such as meat quality, development and fertility.

    • Mirte Bosse
    • , Hendrik-Jan Megens
    •  & Martien A. M. Groenen

  • Article |

    Here, Brotherton and colleagues sequence 39 mitochondrial genomes from ancient human remains. They track population changes across Central Europe and find that the foundations of the European mitochondrial DNA pool were formed during the Neolithic rather than the post-glacial period.

    • Paul Brotherton
    • , Wolfgang Haak
    •  & Janet S. Ziegle

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