polygenic risk

XPRS: A Tool for Interpretable and Explainable Polygenic Risk Score

XPRS decomposes polygenic risk scores into gene and SNP contributions using SHAP values and provides visualization tools to enhance interpretability and clinical communication.

Efficient blockLASSO for Polygenic Scores with Applications to All of Us and UK Biobank

The paper introduces blockLASSO, a method for training polygenic scores that is computationally efficient and effective across multiple phenotypes and ancestry groups.

Integrating Glaucoma Endophenotypes Improves Polygenic Risk Prediction for Primary Open-Angle Glaucoma Across Ancestries

This paper develops a multi-trait polygenic risk score framework to improve POAG prediction across ancestries by integrating glaucoma endophenotypes.

Causal variant capture in genotype discovery approaches drives polygenic prediction performance across traits and populations

This study compares polygenic scores from genotyping arrays and whole-genome sequencing across traits and populations, finding that WGS generally improves prediction accuracy but with context-dependent advantages.

Bayesian inference of genetic pleiotropy identifies drug targets and repurposable medicines for human complex diseases

The paper uses a Bayesian model to identify shared genetic components across complex diseases, finding potential drug targets with lower side effects and repurposing opportunities.

Exploring the application of deep learning methods for polygenic risk score estimation

This paper demonstrates that deep learning can generate polygenic risk scores with high accuracy, even with missing data, and shows that a single model can predict multiple scores.

An improved polygenic score for Parkinson's disease partly explains variable penetrance of genetic Parkinson's disease

The paper develops an improved polygenic score for idiopathic Parkinson's disease, showing higher discriminative performance and explaining variable penetrance in genetic forms of the disease.

Using twin-pairs to assess potential bias in polygenic prediction of externalising behaviours across development

The paper assesses bias in polygenic prediction of externalising behaviours using twin-pairs, finding minimal rGE bias but less variance prediction for callous-unemotional traits.

Evaluation of polygenic score for hypertrophic cardiomyopathy in the general population and across clinical settings

This study evaluates polygenic scores for hypertrophic cardiomyopathy (HCM) in the general population and clinical settings, showing increased risk with higher scores and potential for clinical application.

Type 2 diabetes polygenic risk score demonstrates context-dependent effects and associations with type 2 diabetes-related risk factors and complications across diverse populations

Long-read sequencing of 945 Han individuals identifies novel structural variants associated with phenotypic diversity and disease susceptibility

The paper identifies novel structural variants in Han Chinese genomes using long-read sequencing and links them to phenotypic diversity and disease susceptibility.

IQI: Individualized Quantitative trait loci (QTL) Index

The paper introduces IQI, an individualized QTL index, to detect and characterize differences in QTL effects across individuals and populations, enabling more precise genetic analysis.

A Litmus Test for Confounding in Polygenic Scores

This paper introduces PGSUS, a method to assess the influence of stratification and assortative mating effects on polygenic scores, revealing that direct genetic effects often contribute little to PGS variation.

Modeling diagnostic code dropout of schizophrenia in electronic health records improves phenotypic data quality and cross-ancestry transferability of polygenic scores

This paper models diagnostic code dropout in EHR data to improve phenotyping for schizophrenia, enhancing polygenic score transferability across ancestries.

Improving polygenic prediction from summary data by learning patterns of effect sharing across multiple phenotypes.

This paper introduces mr.mash-rss, a method for polygenic prediction using GWAS summary statistics, showing improved accuracy over existing methods in various scenarios.

Leveraging haplotype information in heritability estimation and polygenic prediction

This paper introduces a haplotype-based framework for heritability estimation and reference-free polygenic prediction, showing improved performance over genotype-based methods in depression and schizophrenia.

Uncovering the genetic underpinnings for different psychiatric disorder combinations

This study uses CombGWAS to analyze genetic correlations between psychiatric disorder combinations and cardiovascular disease, identifying shared and unique genetic factors.

Genal: A Python Toolkit for Genetic Risk Scoring and Mendelian Randomization

Genal provides a Python toolkit for genetic risk scoring and Mendelian Randomization, streamlining population genetic analyses with user-friendly functions.

Within-Family GWAS does not Ameliorate the Decline in Prediction Accuracy across Populations

This study shows that within-family GWAS does not improve prediction accuracy in admixed populations, suggesting genetic architecture differences, not confounding factors, drive the decline in polygenic index performance.

Association of Genetically Predicted Levels of Circulating Blood Lipids with Coronary Artery Disease Incidence

This paper evaluates polygenic risk scores (PRS) for CAD and blood lipids to predict CAD incidence in UK Biobank participants.

One score to rule them all: regularized ensemble polygenic risk prediction with GWAS summary statistics

This paper introduces a statistical framework for regularized ensemble polygenic risk prediction using GWAS summary statistics, showing improved performance across traits and populations.

The Genomic portrait of the Picene culture: new insights into the Italic Iron Age and the legacy of the Roman expansion in Central Italy.

The paper analyzes genomic data from the Picene culture to explore genetic continuity and change during the Iron Age and Roman expansion in Central Italy.

Highly Accurate Non-Invasive Preimplantation Genetic Testing for Monogenic and Polygenic Diseases from Spent Medium

This paper presents a non-invasive preimplantation genetic testing method using spent embryo culture medium, achieving high accuracy for monogenic and polygenic disease detection without modifying IVF workflows.

From a genomic risk model to clinical trial implementation in a learning health system: the ProGRESS Study

The paper develops a polygenic risk model for prostate cancer using VA data and validates it in external cohorts, showing its clinical utility in risk stratification.

Heterogeneous effects of antidepressants on suicidal ideation: role of polygenic scores

The paper investigates how antidepressants affect suicidal ideation in patients with major depressive disorder, finding that genetic predisposition to psychiatric disorders influences this risk differently across antidepressant types.

MegaLMM improves genomic predictions in new environments using environmental covariates

MegaLMM improves genomic predictions in new environments by incorporating environmental covariates into a statistical model, showing higher accuracy than traditional methods in maize breeding.

Improving GWAS performance in underrepresented groups by appropriate modeling of genetics, environment, and sociocultural factors

This paper improves GWAS performance in underrepresented groups by reassigning ambiguous ethnicity codes, using ancestry-matched imputation panels, and incorporating environmental covariates.

Deep learning for polygenic prediction: The role of heritability, interaction type and sample size

This study evaluates deep learning methods for polygenic prediction, showing that MLP benefits most from larger sample sizes and one-hot encoding improves performance across methods.

A genotype-phenotype transformer to assess and explain polygenic risk

This paper introduces a Transformer model called G2PT to predict metabolic traits from genetic variants and shows it outperforms existing methods across populations.

The NHGRI-EBI GWAS Catalog: standards for reusability, sustainability and diversity

The GWAS Catalog now holds 625,113 curated SNP-trait associations from 6,921 publications plus >85K summary statistics datasets, with a new GWAS-SSF submission standard and GRCh38 harmonisation.