Topic 145

genetics genotype population haplotype genetic method allele accuracy individuals data haplotypes methods populations imputation statistical genomic genotypes simulated genotyping association genome linkage variants ancestry accurate existing simulation power sample error real loci when snp frequencies snps bioinformatics sizes large using estimates disequilibrium genotyped approach reference sequencing available genomics analyses frequency size trait based inference datasets studies can estimating phenotype present phasing estimate panels coverage than information efficient pedigree scenarios implemented software relatedness rare false descent detect project used package paper compared applied segments wide cost more variant errors algorithm use test application detecting fast then simulations 1000 sets pedigrees missing

124 items. Top items listed below.

Using high-throughput phenotypes to enable genomic selection by inferring genotypes 145 53 19 4

Controlling for Human Population Stratification in Rare Variant Association Studies 145 123 19 4

Unbalanced Sample Size Introduces Spurious Correlations to Genome-wide Heterozygosity Analyses 145 19 4

Efficient phasing and imputation of low-coverage sequencing data using large reference panels 145 97 4

Power analysis of transcriptome-wide association study: implications for practical protocol choice 145 123 19 4

Accurate, ultra-low coverage genome reconstruction and association studies in Hybrid Swarm mapping populations 145 19 4

Efficient approaches for large scale GWAS studies with genotype uncertainty 145 83 4

Genotype-free individual genome reconstruction of Multiparental Population Models by RNA sequencing data 145 13 4

Genotype imputation using the Positional Burrows Wheeler Transform 145 4

Phasing and imputation of single nucleotide polymorphism data of missing parents of bi-parental plant populations 145 4

Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics 19 4

Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays 145 19 4

Why are rare variants hard to impute? Coalescent models reveal theoretical limits in existing algorithms. 145 83 19 4

Ancestral Haplotype Reconstruction in Endogamous Populations using Identity-By-Descent 145 83 4

Evaluation of consensus strategies for haplotype phasing 145 13 4

A genome-wide case-only test for the detection of digenic inheritance in human exomes 145 19 4

A deep learning framework for characterization of genotype data 26 4

Multiple Haplotype Reconstruction from Allele Frequency Data 145 83 4

Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform 145 13 4

Controlling for off-target genetic effects using polygenic scores improves the power of genome-wide association studies 19 4

Theoretical and empirical quantification of the accuracy of polygenic scores in ancestry divergent populations 19 5 4

Distinct error rates for reference and non-reference genotypes estimated by pedigree analysis 145 83 19 4

A new approach of dissecting genetic effects for complex traits 19 4

Adapting genotyping-by-sequencing and variant calling for heterogeneous stock rats 145 97 4

Integrating Genomic Correlation Structure Improves Copy Number Variations Detection 145 4

Rare variant enriched identity-by-descent enables the detection of distant relatedness and older divergence between populations 145 83 4

Boundary-Forest Clustering: Large-Scale Consensus Clustering of Biological Sequences 145 4

Efficient variance components analysis across millions of genomes 19 4

Pathway Analysis within Multiple Human Ancestries Reveals Novel Signals for Epistasis in Complex Traits 19 4

GxEsum: genotype-by-environment interaction model based on summary statistics 19 4

Probabilistic Approach to Understand Errors in Sequencing and its based Applications 145 4

Detecting sex-linked genes using genotyped individuals sampled in natural populations 145 83 4

Genomic prediction in the wild: A case study in Soay sheep 145 19 5 4

Fast and accurate approximation of the joint site frequency spectrum of multiple populations 145 83 4

Insights into dispersed duplications and complex structural mutations from whole genome sequencing 706 families 97 19 4

Detection of complex genetic architecture using two-locus population differentiation: modeling epistasis 19 9 4

Inferring the Allelic Series at QTL in Multiparental Populations 145 83 19 4

MRLocus: identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity 19 13 4

LEA 3: Factor models in population genetics and ecological genomics with R 145 83 4

Single Individual Haplotype Reconstruction Using Fuzzy C-Means Clustering With Minimum Error Correction 145 4

Kmer2SNP: reference-free SNP calling from raw reads based on matching 13 4

Improving the coverage of credible sets in Bayesian genetic fine-mapping 19 4

Model-based genotype and ancestry estimation for potential hybrids with mixed-ploidy 145 83 21 19 5 4

Estimation of Non-null SNP Effect Size Distributions Enables the Detection of Enriched Genes Underlying Complex Traits 19 4

The influence of QTL allelic diversity on QTL detection in multi-parent populations: a simulation study in sugar beet 145 19 5 4

BaseQTL: a Bayesian method to detect eQTLs from RNA-seq data with or without genotypes 145 19 9 4

Multi-tissue transcriptome-wide association studies 19 4

Non-parametric polygenic risk prediction using partitioned GWAS summary statistics 19 4

Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs 145 19 4

Relative matching using low coverage sequencing 145 97 4

Demographic history impacts stratification in polygenic scores 19 5 4

Novel Methods for Epistasis Detection in Genome-Wide Association Studies 145 19 4

SVCollector: Optimized sample selection for cost-efficient long-read population sequencing 145 97 4

Genetic signatures of human brain structure: A comparison between GWAS and relatedness-based regression 19 4

Ancestry Inference Using Reference Labeled Clusters of Haplotypes 145 83 4

SPEARS: Standard Performance Evaluation of Ancestral Reconstruction through Simulation 145 13 4

Evaluation of the minimum sampling design for population genomic and microsatellite studies. An analysis based on wild maize. 145 83 21 5 4

Polygenic scores for height in admixed populations 19 4

Estimating and accounting for genotyping errors in RAD-seq experiments 145 83 4

Identifying non-identical-by-descent rare variants in population-scale whole genome sequencing data 145 83 21 4

Partitioning gene-based variance of complex traits by gene score regression 19 13 4

Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores 19 4

Inference of Population Admixture Network from Local Gene Genealogies: a Coalescent-based Maximum Likelihood Approach 83 4

An evaluation of the interpretability and predictive performance of the BayesR model for genomic prediction 145 19 4

Leveraging functional annotation to identify genes associated with complex diseases 19 9 4

Optimizing Sequencing Resources in Genotyped Livestock Populations Using Linear Programming 145 97 4

MegaLMM: Mega-scale linear mixed models for genomic predictions with thousands of traits 145 19 4

Efficient and Flexible Integration of Variant Characteristics in Rare Variant Association Studies Using Integrated Nested Laplace Approximation 145 13 4

Mendelian imputation of parental genotypes for genome-wide estimation of direct and indirect genetic effects 19 7 4

Assessing the Performance of qpAdm: A Statistical Tool for Studying Population Admixture 145 83 4

Hierarchical modeling of haplotype effects based on a phylogeny 83 4

Robust, flexible, and scalable tests for Hardy-Weinberg Equilibrium across diverse ancestries 145 13 4

The usefulness of multi-parent multi-environment QTL analysis: an illustration in different NAM populations 145 83 19 4

Empirical variance component regression for sequence-function relationships 145 4

Estimating heritability and its enrichment in tissue-specific gene sets in admixed populations 19 4

Using a supervised principal components analysis for variable selection in high-dimensional datasets reduces false discovery rates 123 83 4

Opportunities and limits of combining microbiome and genome data for complex trait prediction 19 4

Privacy-preserving genotype imputation with fully homomorphic encryption 145 4

Inferring the ancestry of parents and grandparents from genetic data 83 4

Leveraging expression from multiple tissues using sparse canonical correlation analysis (sCCA) and aggregate tests improves the power of transcriptome-wide association studies (TWAS) 19 4

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs 25 19 9 4

Computationally efficient whole genome regression for quantitative and binary traits 145 19 4

A fully joint Bayesian quantitative trait locus mapping of human protein abundance in plasma 19 4

A powerful subset-based gene-set analysis method identifies novel associations and improves interpretation in UK Biobank 19 4

The impact of non-additive genetic associations on age-related complex diseases. 19 9 4

Modeling Epistasis in Mice and Yeast Using the Proportion of Two or More Distinct Genetic Backgrounds: Evidence for "Polygenic Epistasis" 19 5 4

Spatial modelling improves genetic evaluation in smallholder breeding programs 145 83 5 4

Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome 21 5 4

Estimating Genetic Similarity Matrices using Phylogenies 145 83 4

Population Stratification at the Phenotypic Variance level and Implication for the Analysis of Whole Genome Sequencing Data from Multiple Studies 145 123 19 4

High-resolution population-specific recombination rates and their effect on phasing and genotype imputation 145 97 25 19 5 4

Recessive deleterious variation has a limited impact on signals of adaptive introgression in human populations 21 5 4

Sequencing depth and genotype quality: Accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops 53 19 4

Improved analyses of GWAS summary statistics by reducing data heterogeneity and errors 19 4

Detecting selection with a genetic cross 21 19 5 4

Polygenic risk score based on weight gain trajectories is a strong predictor of childhood obesity 19 4

Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics. 19 4

Design and power analysis for multi-sample single cell genomics experiments 43 4

Detecting and quantifying natural selection at two linked loci from time series data of allele frequencies with forward-in-time simulations 83 4

Neighbor GWAS: incorporating neighbor genotypic identity into genome-wide association studies of field herbivory 19 4