A One-Penny Imputed Genome from Next-Generation Reference Panels

2018/08/09 by Brian L. Browning, Ying Zhou, Sharon R. Browning · 73 citations
Biochemistry, Genetics and Molecular Biology · #Genetic Associations and Epidemiology #Genetic and phenotypic traits in livestock #Genetic Mapping and Diversity in Plants and Animals

paper · pdf · doi:10.1016/j.ajhg.2018.07.015

Cited by

• Identifying Areas of Potential Risk Based on Future Genetic Adaptability in Three Arctic Whale Species
• Chimeric reference panels for genomic imputation
• Fast two-stage phasing of large-scale sequence data
• Rapid adaptation and extinction in synchronized outdoor evolution experiments of <i>Arabidopsis</i>
• Genome‐Wide Homozygosity Predicts Inbreeding Depression in the Hihi/Stitchbird ( <i>Notiomystis cincta</i> ) Better Than Realised Load
• Interbreeding between Neanderthals and modern humans was strongly sex biased
• Genetic basis of an adaptive polymorphism controlling butterfly silver iridescence
• Parallel and convergent evolution in genes underlying seasonal migration
• Genetic characterization and curation of diploid A-genome wheat species
• New insights into the genetic loci related to egg weight and age at first egg traits in broiler breeder
• Population specific bottlenecks inflated differentiation measures of Louisiana black bear and negate subspecific status
• Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora
• Genomic approaches to accelerate American chestnut restoration
• Replicate avian hybrid zones reveal the progression of genetic and trait introgression through time
• Benchmarking imputation accuracy in the presence or absence of a reference panel
• Climate and hybridization shape stomatal trait evolution in <i>Populus</i>
• Analysis-ready VCF at Biobank scale using Zarr
• Effects of using deep learning to predict the geographic origin of barley genebank accessions on genome–environment association studies
• Increased genomic predictive ability in mango using GWAS-preselected variants and fixed-effect SNPs
• Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies
• Phenotypically Wild Barley Shows Evidence of Introgression From Domesticated Barley
• Spatial heterogeneity of disease infection attributable to neighbour genotypic identity in barley cultivars
• Revisiting adaptive introgression at the HLA genes in Lithuanian genomes with machine learning
• Genome Scanning Reveals the Genetic Basis of a Color Pattern Morphotype in an Island Population of the European Adder ( <i>Vipera berus</i> )
• Population transcriptome and phenotype analyses reveal that <i>Rht-D1b</i> contributed a larger seedling root to modern bread wheat
• rMVP: A Memory-Efficient, Visualization-Enhanced, and Parallel-Accelerated Tool for Genome-Wide Association Study
• SAI: A Python Package for Statistics for Adaptive Introgression
• Discarded sequencing reads uncover natural variation in pest resistance in Thlaspi arvense
• Distinct adaptation and ancestral retention signals in African and European indigenous cattle genomes
• Genomic Landscape of High‐Altitude Adaptation in East African Mountain Honey Bees ( <scp> <i>Apis mellifera</i> </scp> )
• Identification of a candidate sex determination region and sex-specific molecular markers based on whole-genome re‑sequencing in the sea star <i>Asterias amurensis</i>
• Genomic Prediction of Disease Resistance Provides a Path to Marker Assisted Restoration in a Wetland Foundation Tree Species
• Integrating high-throughput phenotyping and genome-wide association analyses to unravel Mediterranean maize resilience to combined drought and high temperatures
• Genetic regulation of gene expression across multiple tissues in chickens
• The DNA virome varies with human genes and environments
• The first nested association mapping (NAM) population for outbreeding Italian ryegrass reveals candidate genes for seed shattering and related traits
• DeepAnnotation: A novel interpretable deep learning–based genomic selection model that integrates comprehensive functional annotations
• k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance
• Genomic Analysis of Hair Sheep From West/Central Africa Reveals Unique Genetic Diversity and Ancestral Links to Breed Formation in the Caribbean
• A novel genome-wide association study method for detecting quantitative trait loci interacting with complex population structures in plant genetics
• High-quality phenotypic and genotypic dataset of barley genebank core collection to unlock untapped genetic diversity
• Genome‐Wide Diversity in Lowland and Highland Maize Landraces From Southern South America: Population Genetics Insights to Assist Conservation
• Unexpectedly low recombination rates and presence of hotspots in termite genomes
• The relationship between genotype- and phenotype-based estimates of genetic liability to psychiatric disorders, in practice and in theory
• Enoyl‐ <scp>CoA</scp> hydratase genes underlie natural variation of lactones in cultivated and wild strawberries
• Genome-wide association studies
• Genomic regions affecting perinatal and early life survival in dairy calves
• JanusX: an integrated and high-performance platform for scalable genome-wide association studies and genomic selection
• The impact of short tandem repeat variation on gene expression. [europepmc]
• Low coverage whole genome sequencing enables accurate assessment of common variants and calculation of genome-wide polygenic scores. [europepmc]
• Accurate, scalable and integrative haplotype estimation. [europepmc]
• Phenotype Prediction and Genome-Wide Association Study Using Deep Convolutional Neural Network of Soybean. [europepmc]
• A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data. [europepmc]
• Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk. [europepmc]
• Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike ( Esox lucius ) and a Synthesis of Previous Studies. [europepmc]
• Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes. [europepmc]
• Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties. [europepmc]
• Validation of a Genome-Wide Polygenic Score for Coronary Artery Disease in South Asians. [europepmc]
• Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes. [europepmc]
• A Review of Integrative Imputation for Multi-Omics Datasets. [europepmc]
• Genotype imputation using the Positional Burrows Wheeler Transform. [europepmc]
• Demographic history mediates the effect of stratification on polygenic scores. [europepmc]
• Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations. [europepmc]
• The patterns of deleterious mutations during the domestication of soybean. [europepmc]
• Accurate, scalable cohort variant calls using DeepVariant and GLnexus. [europepmc]
• Cotton pan-genome retrieves the lost sequences and genes during domestication and selection. [europepmc]
• Rapid genotype imputation from sequence with reference panels. [europepmc]
• Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes. [europepmc]
• Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk. [europepmc]
• Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project. [europepmc]
• Signatures of copy number alterations in human cancer. [europepmc]
• A multi-tissue atlas of regulatory variants in cattle. [europepmc]
• Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes. [europepmc]