PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

2007/08/08 by Shaun Purcell, Benjamin Neale, Benjamin M. Neale +14 · 497 citations
Biochemistry, Genetics and Molecular Biology · #Genetic Associations and Epidemiology #Genetic Mapping and Diversity in Plants and Animals #Bioinformatics and Genomic Networks

paper · pdf · doi:10.1086/519795

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• Genetic isolation of an amphidromous goby species, Luciogobius ryukyuensis, highlights limited gene flow in small island populations
• Multi-ancestry genome-wide meta-analysis of 56,241 individuals identifies known and novel cross-population and ancestry-specific associations as novel risk loci for Alzheimer’s disease
• Genetic Formation of Neolithic Hongshan People and Demic Expansion of Hongshan Culture Inferred From Ancient Human Genomes
• Effects of parental socioeconomic status on offspring’s fetal neurodevelopment
• Revisiting the species problem in Northeast Pacific ribbon kelp lineages (genus <i>Alaria</i>): Lessons learned using whole genome data
• Epistasis regulates genetic control of cardiac hypertrophy
• Genetic regulation of gene expression across multiple tissues in chickens
• Genomic vulnerability and local adaptation of an arid tolerant tree species on the Qinghai–Tibet Plateau
• Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species
• A biGWAS strategy reveals the genetic architecture of the interaction between wheat and <i>Blumeria graminis</i> f. sp. <i>tritici</i>
• Runs of homozygosity under different demographic histories and selection scenarios in red deer
• Accurate genomic prediction for grain yield and grain moisture content of maize hybrids using multi‐environment data
• Metapipeline-DNA: A Comprehensive Germline &amp; Somatic Genomics Nextflow Pipeline
• Methylation-based enrichment facilitates low-cost, noninvasive genomic scale sequencing of populations from feces
• Sequence‐Based Multi Ancestry Association Study Reveals the Polygenic Architecture of <i>Varroa destructor</i> Resistance in the Honeybee <i>Apis mellifera</i>
• Disentangling the consequences of type 2 diabetes on targeted metabolite profiles using causal inference and interaction QTL analyses
• Lipids mediate supramolecular outer membrane protein assembly in bacteria
• Genetic basis of early onset and progression of type 2 diabetes in South Asians
• Releasing a sugar brake generates sweeter tomato without yield penalty
• Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds
• Genomic differentiation and gene flow among <i>Rattus</i> species distributed in China and adjacent regions
• Evidence for dynastic succession among early Celtic elites in Central Europe
• Patterns of Genetic And Epigenetic Diversity Across A Range Expansion in The White-Footed Mouse (<i>Peromyscus Leucopus</i>)
• Standing genetic variation and <i>de novo</i> mutations underlie parallel evolution of island bird phenotypes
• The contribution of recent and historical demographic histories to genomic diversity and conservation status in plant species
• Effective Purging and Conservation of Heterozygous Regions During Independent Evolution to High‐Level Inbreeding in Wild Paradise Fishes
• Runs of homozygosity: current knowledge and applications in livestock
• Genetic basis of resistance to avian influenza in different commercial varieties of layer chickens
• Musical rhythm abilities and risk for developmental speech-language problems and disorders: epidemiological and polygenic associations
• Life on the edge: A new toolbox for population‐level climate change vulnerability assessments
• Comparative Genomics Provide Insight Into the Evolution of European <i>Aphanomyces euteiches</i> Strains
• Impact of population structure in the estimation of recent historical effective population size by the software GONE
• TGF-β Pathway–Based Polygenic Risk Score Modifies the Association between Red Meat Intake and Colorectal Cancer Risk: Application of a Novel Pathway-Based PRS Method
• Identification and Genome-Wide Association Analysis of Wheat FHB Resistance Genes
• A Population Genomics Approach to Understand the Diversity, Migration, and Reproduction of the Rice Pathogen <i>Cercospora janseana</i>
• Genomic insights into the admixture history and adaptive evolution of the Zhuang people
• Genomic Evidence for Elevational Segregation and Adaptive Introgression in Prunellidae Radiation
• Selection shapes the evolution of genome size in a globally invasive plant
• Genomic and neurobiological bases of variation in fighting strategies in gamecocks
• Cost-efficient assignment panel for ducks. Setup of a cost-efficient assignment panel for duck populations.
• Single-nucleus multi-omics identifies shared and distinct pathways in Pick’s and Alzheimer’s disease
• Boost or Bust? The Impact of Supplementation on Functional Genetic Diversity and Selective Processes in Tasmanian Devils
• Estimation of genome-wide coupling in rattlesnake hybrids provides insight into the process of speciation and its progress
• DNA methylation-estimated phenotypes, telomere length and risk of ischemic stroke: epigenetic age acceleration of screening and a Mendelian randomization study
• Origin and de novo domestication of sweet orange
• Molecular Phylogeographic Variation in the Siberian Weasel (Mustela sibirica) in Asia, Including Japan, Examined by ddRAD-Seq Analysis
• Unravelling the genetic landscape of <scp> <i>Channa argus</i> </scp> in Shandong Province: Insights into population differentiation, adaptation and conservation from whole‐genome resequencing
• Genomic Data Reveals Cryptic Diversity in the Soda Lake Cichlid <scp><i>Oreochromis amphimelas</i></scp>
• Florida scrub-jay genomes across space and time reveal impacts of population decline and reduced gene flow
• Predicting complex phenotypes using multi-omics data in maize
• FreezeNet: A Lightweight Model for Enhancing Freeze Tolerance Assessment and Genetic Analysis in Wheat
• SNP Data Quality Control in the Uruguayan Sheep Breeding Program Database
• Influence of Ploidy and Genetic Background on Stress Tolerance of Intraspecific Yeast Hybrids
• Construction of High‐Precision Genomic Assembled Sequences and Assessment of the Effect of Its Quality to Population Genetic Analysis of Endangered Okinawa Rail and Japanese Golden Eagle
• PanVariants: Best Practice for Pangenome-based Variant Calling Pipeline and Framework
• Genetic and Environmental Similarities Drive Repeated Genomic Evolution in Island Lizards
• Genetic and transcriptome analyses of the effect of genotype-by-environment interactions on <i>Brassica napus</i> seed oil content
• Genomic Assessment of Giraffes in North American Collections Highlights Conservation Challenges
• The Genomic Legacy of the Norman Conquest in Rural England
• Description of a species of the genus Paramesotriton (Caudata, Salamandridae) from Guizhou, China, based on morphological and genomic evidence
• Harmonizing genotype array data to understand genetic risk for brain amyloid burden in the AMYPAD PNHS Consortium
• Bovine SNP array-based genetic assessment of American plains bison at American Prairie
• Correcting for Genomic Inflation Leads to Loss of Power in Large‐Scale Genome‐Wide Association Study Meta‐Analysis
• Haplotype-resolved genome assembly and genome-wide association study identifies the candidate gene closely related to sugar content and tuber yield in <i>Solanum tuberosum</i>
• Dissecting genotype-environment relationships with functional implications for parental selection in <i>Cannabis</i> breeding
• Genetic history of Scythia
• A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach
• Variation in phenotype, genotype, and somatic diversity among asexual Schmidtea mediterranea planarians
• Runs of homozygosity assessment using reduced representation sequencing highlight the evidence of random mating in emu (<i>Dromaius novaehollandiae</i>)
• Identifying candidate genetic variants for egg number by analyzing over 1,000 fully sequenced layers
• PlantVarFilter: A Comprehensive Pipeline for Variant Filtering and Genome-Wide Association Analysis in Plant Genomics
• High-resolution genome assembly and population genetic study of the endangered maple <i>Acer pentaphyllum</i> (Sapindaceae): implications for conservation strategies
• Association between methylation quantitative trait loci and colorectal cancer risk, survival and cancer recurrence
• Genome Structural Variants Shape Adaptive Success of an Invasive Urban Malaria Vector <i>Anopheles stephensi</i>
• The genetic structure and diversity of smallholder dairy cattle in Rwanda
• Population Genomics Provides Insights Into Genomic Features of Inbreeding Depression in <i>Arma Chinensis</i>
• Moderation of treatment outcomes by polygenic risk for alcohol‐related traits in placebo‐controlled trials of topiramate
• Evolution and genetic adaptation of fishes to the deep sea
• Integration of ss<scp>GWAS</scp> and <scp>ROH</scp> analyses for uncovering genetic variants associated with reproduction traits in Large White pigs
• A chromosome-level genome assembly of the Chinese herring ( <i>Ilisha elongata</i> ) uncovered its population dynamics and genes related to lipid metabolism
• Genomics Reveals the Origins of Historical Specimens
• The genome-wide structure of the Jewish people
• DNA-guided transcription factor cooperativity shapes face and limb mesenchyme
• Genomic Introgression and Adaptation of Southern Seabird Species Facilitate Recent Polar Colonization
• Multiple Origins or Widespread Gene Flow in Agricultural Fields? Regional Population Genomics of Herbicide Resistance in <scp><i>Bromus tectorum</i></scp>
• eDNA metabarcoding and whole genome sequencing detect European-American Eel hybrids in northeastern Canada
• Population genomics of Vitis pseudoreticulata reveals the genetic basis of fungal resistance in grapevine
• DeepKin: Predicting relatedness from low-coverage genomes and paleogenomes with convolutional neural networks
• Heritability and genomic basis of age-at-maturity in Chinook Salmon
• A novel genome-wide association study method for detecting quantitative trait loci interacting with complex population structures in plant genetics
• The role of mating systems in postzygotic reproductive isolation between two recently divergent <i>Aquilegia</i> Species
• Moroccan genome project: genomic insight into a North African population
• Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data
• Genome-Wide Association Study Identifies Variants Associated With Progression of Liver Fibrosis From HCV Infection
• Insights into the genomic and phenotypic diversity of <i>Monosporozyma unispora</i> strains isolated from anthropic environments
• Integrative genomics sheds light on the immunogenetics of tuberculosis in cattle
• Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
• Widespread, long‐term admixture between grey wolves and domestic dogs across Eurasia and its implications for the conservation status of hybrids
• Leaf Spectroscopy Reveals Drought Response Variation in <i>Fagus sylvatica</i> Saplings From Across the Species' Range
• Comparative population genomics of manta rays has global implications for management
• High-quality phenotypic and genotypic dataset of barley genebank core collection to unlock untapped genetic diversity
• Enhancing inbreeding estimation and global conservation insights through chromosome-level assemblies of the Chinese and Malayan pangolin
• Comparison of kinship‐identification methods for robust stock assessment using close‐kin mark–recapture data for Pacific bluefin tuna
• Evaluating genome-wide and targeted forensic sequencing approaches to kinship determination
• Grapevine pangenome facilitates trait genetics and genomic breeding
• Rare, long‐distance dispersal underpins genetic connectivity in the pink sea fan, <i>Eunicella verrucosa</i>
• The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses
• Unidirectional <scp>trans‐Atlantic</scp> gene flow and a mixed spawning area shape the genetic connectivity of Atlantic bluefin tuna
• Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease
• Mapping associations of polygenic scores with autistic and ADHD traits in a single city region
• The blood metabolome of brain health in midlife and influences of genes, microbiome and exposome
• Genomic survey of the ex situ Palm Cockatoo (Probosciger aterrimus) population identifies an undiscovered species-level lineage endemic to Yapen Island
• Association of Multiple-trait Polygenic Risk Score with Obesity and Cardiometabolic Diseases in Korean Population
• Intraspecific neighbourhood effects on male and female fitness in <i>Moricandia moricandioides</i>
• Diversity and Structure of <i>Diaporthe humulicola</i> Populations from Eastern North America
• Fine-scale structure of a whole regional population through genetics and genealogies
• Uncovering genetic relationships and designing markers for genotyping European pear varieties
• Combining nuclear genome, chloroplast fragments and morphology to solve the species delimitation of Aquilegia incurvata (Ranunculaceae)
• Genome-Wide Association Studies of Stripe Rust Resistance in Spring Wheat Landraces from Northwest China
• Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in China
• The Late Quaternary climate impact on the genome of the woodland strawberry (Fragaria vesca), a perennial herb
• Exploring the genetic diversity of Mediterranean fig trees highlights genes associated with fruit traits
• Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield
• BTS: a scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across &amp;gt;1,000s of omics datasets
• Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands
• Genome-wide association study identifies susceptibility loci for IgA nephropathy
• Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits
• Mendelian Randomization Methods for Causal Inference: Estimands, Identification and Inference
• Integrative Genotyping and Analysis of Canine Structural Variation Using Long-read and Short-read Data
• Современные отечественные программные комплексы интерпретации гравимагнитных данных
• Genome-wide association studies
• Methodologies underpinning polygenic risk scores estimation: a comprehensive overview
• Statistical inference in two-sample summary-data Mendelian randomization using robust adjusted profile score
• Genetic susceptibility to feline infectious peritonitis in Birman cats
• Association between Common Variation in Genes Encoding Sweet Taste Signaling Components and Human Sucrose Perception
• The deep population history of northern East Asia from the Late Pleistocene to the Holocene
• Comprehensive whole-genome analyses of the UK Biobank reveal significant sex differences in both genotype missingness and allele frequency on the X chromosome
• Association of common genetic variants with human skin color variation in Indian populations
• Genomic regions affecting perinatal and early life survival in dairy calves
• Genomic analyses reveal the stepwise domestication and genetic mechanism of curd biogenesis in cauliflower
• Phenome-wide analysis of copy number variants in 470,727 UK Biobank genomes
• Phenotypic diversity and population structure of Pecan (Carya illinoinensis) collections reveals geographic patterns
• Beyond Single Variants: A Pathway-Based Approach to Explore the Genetic Basis of Memory
• Cancer classification and pathway discovery using non-negative matrix factorization
• A second generation human haplotype map of over 3.1 million SNPs. [europepmc]
• Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. [europepmc]
• Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. [europepmc]
• Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. [europepmc]
• Genome-wide association study reveals genetic risk underlying Parkinson's disease. [europepmc]
• Functional impact of global rare copy number variation in autism spectrum disorders. [europepmc]
• Common SNPs explain a large proportion of the heritability for human height. [europepmc]
• Hundreds of variants clustered in genomic loci and biological pathways affect human height. [europepmc]
• Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. [europepmc]
• MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. [europepmc]
• Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. [europepmc]
• A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. [europepmc]
• Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. [europepmc]
• Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. [europepmc]
• Second-generation PLINK: rising to the challenge of larger and richer datasets. [europepmc]
• Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. [europepmc]
• Functional mapping and annotation of genetic associations with FUMA. [europepmc]
• The Human Transcription Factors. [europepmc]
• The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. [europepmc]
• Discovery of the first genome-wide significant risk loci for attention deficit/hyperactivity disorder. [europepmc]
• Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. [europepmc]
• Tutorial: a guide to performing polygenic risk score analyses. [europepmc]
• Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression. [europepmc]
• A cross-population atlas of genetic associations for 220 human phenotypes. [europepmc]
• Mapping genomic loci implicates genes and synaptic biology in schizophrenia. [europepmc]