polygenic risk

Comparative Evaluation of Cross-Ancestry Polygenic Risk Scoring of Type 1 Diabetes in the All of Us Cohort

This study develops and evaluates HLA-ARC, a polygenic risk score for type 1 diabetes, showing improved performance over existing methods in diverse ancestry groups.

A versatile data repository for GWAS summary statistics-based downstream genomic analysis of human complex traits

The paper introduces gact, an R package that integrates GWAS summary statistics with genomic resources to identify causal genes and pathways, demonstrating its application in coronary artery disease and type 2 diabetes.

Polygenic risk scores and Parkinson's disease in South Africa: Moving towards ancestry-informed disease prediction

The paper evaluates polygenic risk scores for Parkinson's disease in a South African cohort, finding modest predictive performance and no ancestry-specific risk variants.

Endophenotype-Informed Polygenic Risk Stratification for Primary Open-Angle Glaucoma in individuals of African Ancestry

This paper develops endophenotype-informed polygenic risk scores for POAG in African ancestry individuals, showing improved clinical interpretability and risk stratification compared to aggregate scores.

Harnessing genome prediction in Brassica napus through a nested association mapping population

This study evaluates genome prediction accuracy in Brassica napus using nested association mapping, finding that rrBLUP and RKHS models and SNaP markers improve prediction accuracy for agronomic traits.

Estimating Disorder Probability Based on Polygenic Prediction Using the BPC Approach

The paper introduces the BPC approach to improve polygenic score calibration for binary disorders, achieving better calibration than existing methods in simulated and empirical data.

PTL-PRS: an R package for transfer learning of polygenic risk scores with pseudovalidation

PTL-PRS improves polygenic risk score prediction in non-European populations using pseudovalidation and software optimizations without requiring individual-level data.

Benchmarking genome-wide association study causal gene prioritization for drug discovery

This study benchmarks GWAS causal gene prioritization methods for drug discovery using 445 diseases, finding the nearest gene method performs as well as more complex approaches.

Policy gradient-guided ensemble learning for enhanced polygenic risk prediction in ultra-high-dimensional genomics

This paper introduces ELAG, an ensemble learning framework for polygenic risk prediction that improves accuracy in high-dimensional genomics data by using policy gradient methods to guide variant selection.

Stratifying Lung Adenocarcinoma Risk with Multi-ancestry Polygenic Risk Scores in East Asian Never-Smokers

The paper develops and validates multi-ancestry polygenic risk scores for LUAD in East Asian never-smokers, showing improved risk prediction compared to East Asian-only models.

The complementary roles of rare variant burden scores and common variant polygenic risk scores in genetic risk prediction of complex disorders

This study combines rare variant burden scores and common variant polygenic risk scores to improve genetic risk prediction for schizophrenia, hypertrophic cardiomyopathy, and major depressive disorder.

Personalized polygenic risk prediction and assessment with a Mixture-of-Experts framework

The paper introduces MoEPRS, a Mixture-of-Experts framework for personalized polygenic risk prediction, showing modest accuracy improvements over single-source models across diverse biobanks.

Optimizing Polygenic Scores for Complex Morphological Traits: A Case Study in Nasal Shape Prediction

This paper improves polygenic prediction of nasal shape by using multivariate GWAS, optimized phenotypes, and benchmarked PGS methods, achieving higher variance explained than traditional approaches.

Genome-wide associations of fitness components reveal antagonistic pleiotropy and sexual conflict in the Florida Scrub-Jay

The paper identifies genetic trade-offs and antagonistic pleiotropy in Florida Scrub-Jays by analyzing fitness components and their genomic associations.

Refining bias correction in genome-wide association analyses of case-control studies

This paper provides guidance for reducing bias in case-control GWAS by addressing genetic relatedness, allelic interactions, and control genotype biases, introducing the AlleliC-GWAS tool.

Exposure accumulation drives age-dependent disease architectures and polygenic risk scores

The paper shows that environmental variance increases with age, reducing heritability and PRS accuracy for multiple traits and diseases, suggesting younger cohorts are better for risk prediction models.

A MULTI-TRAIT APPROACH IMPROVES POLYGENIC RISK SCORES FOR CHRONIC BACK PAIN ACROSS POPULATION-BASED AND CLINICALLY ASCERTAINED SAMPLES

This paper improves polygenic risk scores for chronic back pain by combining multiple traits, showing better performance in clinical samples.

Multivariate genome-wide association analysis of quantitative reading skill and dyslexia improves gene discovery

This study uses a multivariate GWAS approach to identify genetic loci associated with reading ability and dyslexia, finding 35 new genome-wide significant loci and estimating SNP heritability at 24%.

Genome-wide analysis of social behaviour in context: a meta-regression approach across social domains, reporters and developmental stages

This study uses genome-wide meta-regression to analyze social behavior across different contexts, ages, and reporters, identifying six genetic loci and showing modest heritability.

Variational Autoencoder-based Model Improves Polygenic Prediction in Blood Cell Traits

This study introduces VAE-PRS, a deep learning model that improves polygenic prediction for blood cell traits by capturing interaction effects and outperforming traditional methods in 14 out of 16 traits.

Modeling structural variations sequencing information to address missing heritability and enhance risk prediction

The paper develops SVrefiner to refine structural variations, enhancing heritability estimates and risk prediction by integrating refined SVs with SNPs and other variants.

Development and validation of polygenic scores for within-family prediction of disease risks

This paper develops and validates polygenic scores for within-family disease risk prediction, showing strong performance across ancestries and demonstrating their clinical utility in embryo screening.

Distinct Neurodevelopmental Signatures of Sex-Specific Transcriptome-Based Polygenic Risk Scores for Depression

The paper develops sex-specific transcriptome-based polygenic risk scores for depression and evaluates their associations with brain structure and symptoms in adolescents.

Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias

This study improves allele frequency and ancestry proportion estimation by adjusting genotype likelihoods to reduce mapping bias in ancient DNA sequencing.

The genetic architecture of ecotypic differentiation in Chinook salmon of the California Central Valley

The paper identifies two functional domains in a genomic region that influence adult migration timing in Chinook salmon, showing how a simple genetic system interacts with genomic backgrounds to generate ecotypic diversity.

Polygenic prediction of phenotypes with a neural empirical Bayes approach

This paper introduces PRSFNN, a neural empirical Bayesian method for polygenic prediction that outperforms existing methods on 17 of 18 traits in the UK Biobank.

Genetic Architecture and Risk Profile of Alcohol-Related Diseases

This study identifies 93 genetic loci associated with alcohol-related diseases using FinnGen data and shows polygenic risk scores can stratify risk for these diseases and related outcomes.

Imputation and polygenic score performance of low coverage whole-genome sequencing and genotyping arrays in diverse human populations

This study compares imputation accuracy and polygenic score performance between genotyping arrays and low coverage whole-genome sequencing across diverse populations, finding that low coverage sequencing performs competitively and better in underrepresented groups.

Enabling reproducible type 1 diabetes polygenic risk scoring for clinical and translational applications

This paper develops a pipeline for translating type 1 diabetes polygenic risk scores into clinical use, showing they can distinguish type 1 from type 2 diabetes and identify high-risk individuals.

Polygenic prediction of cardiorespiratory fitness: The HUNT Study

This study develops and validates a polygenic score for cardiorespiratory fitness (CRF) and finds it is associated with reduced cardiovascular disease and mortality risks.