polygenic risk

R2ROC: An efficient method of comparing two or more correlated AUC from out-of-sample prediction using polygenic scores

The paper introduces R2ROC, a method to compare AUC values from polygenic scores efficiently, offering faster computation and direct mapping to R2 for better interpretation.

Calibrated prediction intervals for polygenic scores across diverse contexts

The paper introduces context-aware prediction intervals for polygenic scores to improve calibration across diverse populations and traits.

Using lifestyle information in polygenic modeling of blood pressure traits: a simple method to reduce bias

This paper improves polygenic prediction of blood pressure traits by incorporating lifestyle variables and their interactions with genetic data, reducing bias and increasing accuracy.

Multi-ancestry polygenic risk scores for venous thromboembolism

This study develops multi-ancestry polygenic risk scores for venous thromboembolism using diverse GWAS data and shows improved predictive performance across European- and African-ancestry populations.

Multi-Polygenic prediction of Frailty and its Trajectories highlights Chronic Pain, Rheumatoid Arthritis, and Educational Attainment pathways

This paper uses multi-polygenic scores to predict frailty and its trajectories, identifying chronic pain, rheumatoid arthritis, and educational attainment as key pathways.

How group structure impacts the numbers at risk for coronary artery disease: polygenic risk scores and non-genetic risk factors in the UK Biobank cohort

The paper uses the Mundlak model to address group-level prediction challenges in UK Biobank data, showing how population structure affects coronary artery disease risk.

LDER-GE estimates phenotypic variance component of gene-environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information

What's UPDOG? A novel tool for trans-ancestral polygenic score prediction

UPDOG improves trans-ancestral polygenic score prediction by considering genetic architecture of both discovery and test cohorts, showing improvements in two-thirds of cases across four ancestries and six phenotypes.

Development of a comprehensive genome-wide cardiovascular disease genetic risk assessment test

This paper develops a genome-wide cardiovascular disease genetic risk assessment test that includes monogenic conditions, risk alleles, pharmacogenomic variants, and polygenic risk scores, showing high performance and scalability.

ShaPRS: Leveraging shared genetic effects across traits or ancestries improves accuracy of polygenic scores

ShaPRS improves polygenic score accuracy by leveraging shared genetic effects across traits or ancestries, enhancing performance for complex diseases and across populations.

Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries

This paper introduces SBayesRC, a method that improves polygenic prediction of complex traits by integrating GWAS summary statistics with functional genomic annotations, showing significant accuracy gains across ancestries.

Genome-wide study of half a million individuals with major depression identifies 697 independent associations, infers causal neuronal subtypes and biological targets for novel pharmacotherapies.

This study identifies 697 genetic associations for major depression using GWAS, infers causal neuronal subtypes, and suggests potential drug targets and repurposing opportunities.

A cross ancestry genetic study of psychiatric disorders from India

This study evaluates the predictive accuracy of polygenic scores for psychiatric disorders in an Indian population using European GWAS data, finding moderate-to-high accuracy for bipolar disorder but lower for OCD and externalizing traits.

The genetic architecture of cerebellar lobules: Insights from the UK Biobank

This study investigates the genetic architecture of cerebellar lobules using UK Biobank data, revealing regional heritability and associations with psychiatric disorders and cognitive traits.

Discovering non-additive heritability using additive GWAS summary statistics

This paper introduces i-LDSC, an extension of LDSC that accounts for genetic interactions, showing it recovers additional genetic variance in 25 traits from UK Biobank and BioBank Japan.

Haplotype Function Score improves biological interpretation and cross-ancestry polygenic prediction of human complex traits

The paper introduces Haplotype Function Score (HFS) to improve genetic association analysis and polygenic prediction by replacing genotypes with functional scores, showing increased causal findings and better cross-ancestry prediction.

Delphi: Deep Learning for Polygenic Risk Prediction

Delphi is a deep learning method for polygenic risk prediction that outperforms traditional models and improves performance for under-represented ancestries.

Genetic modifiers of rare variants in monogenic developmental disorder loci

The paper investigates how rare variants in monogenic developmental disorder genes interact with common variants to affect cognitive and socio-economic traits, finding that higher educational attainment polygenic scores can partially counterbalance adverse effects.

An Ensemble Penalized Regression Method for Multi-ancestry Polygenic Risk Prediction

This paper introduces PROSPER, an ensemble penalized regression method for multi-ancestry polygenic risk prediction, showing improved performance across diverse populations.

Epigenetic age is accelerated in schizophrenia with age- and sex-specific effects and associated with polygenic disease risk

The paper investigates epigenetic age acceleration in schizophrenia, finding age- and sex-specific effects and associations with polygenic risk scores.

MUSSEL: Enhanced Bayesian Polygenic Risk Prediction Leveraging Information across Multiple Ancestry Groups

MUSSEL improves polygenic risk prediction across populations by integrating GWAS summary statistics and using Bayesian hierarchical modeling with ensemble learning.

Population Structure and Migration in the Eastern Highlands of Papua New Guinea; a Region Impacted by the kuru Epidemic

The paper analyzes population genetics in the Eastern Highlands of Papua New Guinea using genome-wide data, revealing genetic structure, admixture events, and evidence of female-biased migration linked to the kuru epidemic.

Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases

Cross-trait Elastic Net mixing of PGS Catalog scores (PRSmix+) lifted mean PRS accuracy 1.72-fold in Europeans and 1.42-fold in South Asians over the best single score.

Sequence composition and conservation predict the phenotypic relevance of transposable elements

The paper shows that TE sequence and conservation features predict their phenotypic relevance, with ERV1 TEs being an exception due to their unique role in environmental interactions.

Dissecting the contribution of common variants to risk of rare neurodevelopmental conditions

This study investigates how common genetic variants contribute to risk for rare neurodevelopmental conditions and examines indirect genetic effects through parental non-transmitted alleles.

Expression based polygenic scores - A gene network perspective to capture individual differences in biological processes.

The paper introduces expression-based polygenic scores (ePGS) that integrate gene co-expression networks to better capture individual differences in biological processes compared to traditional polygenic risk scores.

Polygenic effects on the risk of Alzheimer's disease in the Japanese population

This paper evaluates the polygenic risk score for Alzheimer's disease in Japanese individuals, showing its utility despite genetic differences from European populations.

Evaluating and Improving Health Equity and Fairness of Polygenic Scores

This paper improves the portability and fairness of polygenic scores by introducing Joint-Lassosum, which outperforms existing methods in diverse ancestries.

Sourcing Bivariate Genetic Overlap for Polygenic Prediction using MiXeR-Pred

MiXeR-Pred improves polygenic prediction by leveraging genetic overlap between complex phenotypes, outperforming primary GWAS and MTAG approaches.

Ancestry Specific Polygenic Risk Score, Dietary Patterns, Physical Activity, and Cardiovascular Disease

The paper examines how ancestry-specific polygenic risk scores interact with diet and physical activity to influence ASCVD risk in European Americans and African Americans.