polygenic risk

Multi-Cancer PRS Constellation Model for Cancer Risk Prediction

This paper develops a multi-cancer PRS constellation model integrating genetic and lifestyle factors to predict cancer risk, finding that lifestyle PRSs have limited utility but genetic PRSs remain important.

Optimizing and benchmarking polygenic risk scores with GWAS summary statistics

This paper introduces a statistical framework to optimize and benchmark polygenic risk scores using GWAS summary statistics, showing improved performance over existing methods.

An integrated polygenic score stratifies risk of peripheral artery disease and adverse limb events in ancestrally diverse cohorts

This paper develops a polygenic score for peripheral artery disease (PAD) that improves risk prediction across diverse populations and identifies high-risk individuals for adverse limb events.

Family-GWAS reveals effects of environment and mating on genetic associations

Family-based GWAS meta-analysis of 34 phenotypes shows standard GWAS effects carry sizeable confounding uncorrelated with direct genetic effects, while assortative mating likely inflates SNP heritability and genetic correlations.

Differential prediction performance between Caribbean- and Mainland-subgroups using state-of-the-art polygenic risk scores for coronary heart disease: Findings from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

This study evaluates polygenic risk scores for coronary heart disease in Hispanic/Latino subgroups, finding better performance in Mainland compared to Caribbean subgroups.

Predicting Lung Cancer in Korean Never-Smokers with Polygenic Risk Scores

This study develops a lung cancer prediction model for Korean never-smokers using polygenic risk scores, finding higher odds ratios and improved AUC with PRSs.

From Biobanking to Personalized Medicine: the journey of the Estonian Biobank

The paper reviews the Estonian Biobank's role in advancing genomics research and personalized medicine through its comprehensive data and translational focus.

The GenoPred Pipeline: A Comprehensive and Scalable Pipeline for Polygenic Scoring.

GenoPred is a pipeline that generates interpretable polygenic scores by integrating GWAS summary statistics and genotype data, supporting diverse populations and improving reproducibility.

Identifying individuals at risk for surgical supravalvar aortic stenosis by polygenic risk score with graded phenotyping

The paper develops polygenic risk scores for surgical supravalvar aortic stenosis using variants from Williams syndrome patients, achieving high AUC and low misclassification rates.

A Genome-wide Association Study Identifies Novel Genetic Variants Associated with Knee Pain in the UK Biobank (N = 441,757)

This paper conducts a GWAS on 441,757 UK Biobank participants to identify genetic variants associated with knee pain, finding 10 significant loci, including eight novel ones, and sex-specific associations.

Evaluating the cost-effectiveness of polygenic risk score-stratified screening for abdominal aortic aneurysm

This study evaluates the cost-effectiveness of polygenic risk score-stratified screening for abdominal aortic aneurysm compared to current strategies.

Polygenic prediction of human longevity on the supposition of pervasive pleiotropy

This study develops a polygenic score to predict exceptional longevity by modeling pleiotropic genetic variants linked to aging-related traits, showing improved lifespan prediction and identifying potential drug targets.

Extensive co-regulation of neighbouring genes complicates the use of eQTLs in target gene prioritisation

The paper benchmarks methods for prioritizing GWAS target genes using eQTLs and finds that assigning pQTLs to closest protein-coding genes outperforms colocalisation methods.

Contribution of rare variants to heritability of a disease is much greater than conventionally estimated: modification of allele distribution model

The paper modifies an allele distribution model to show that rare variants contribute significantly more to disease heritability than previously estimated.

Ensembled best subset selection using summary statistics for polygenic risk prediction

ALL-Sum improves polygenic risk prediction by combining efficient summary statistic-based regression with ensembling, outperforming existing methods in accuracy, speed, and memory usage.

Enhancing Portability of Trans-Ancestral Polygenic Risk Scores through Tissue-Specific Functional Genomic Data Integration

This paper improves trans-ancestral polygenic risk scores by integrating tissue-specific functional genomic data, showing better predictive accuracy across multiple traits.

All of Us diversity and scale improve polygenic prediction contextually with greatest improvements for underrepresented populations

The paper improves polygenic prediction accuracy by using diverse datasets, showing greater benefits for underrepresented populations.

PGSFusion streamlines polygenic score construction and epidemiological applications in biobank-scale cohorts

PGSFusion provides a web tool for constructing polygenic scores using multiple methods and analyzing their epidemiological impact in biobank-scale data.

Colorectal cancer risk stratification using a polygenic risk score in symptomatic patients presenting to primary care -- a UK Biobank retrospective cohort study

This paper develops a polygenic risk score model to predict colorectal cancer risk in symptomatic patients using UK Biobank data, achieving high predictive accuracy.

Addressing Overlapping Sample Challenges in Genome-Wide Association Studies: Meta-Reductive Approach

This paper introduces a meta-reductive approach to adjust GWAS results and improve polygenic risk score accuracy by addressing overlapping sample challenges.

Genetic association and machine learning improves discovery and prediction of type 1 diabetes

This study identifies 165 T1D risk signals and develops a machine learning model, T1GRS, that improves risk prediction for T1D in Europeans and African Americans.

Inferring polygenic negative selection underlying an individual trait as a distribution of fitness effects (DFEs) from GWAS summary statistics

The paper introduces ASSESS, a method to estimate the distribution of fitness effects from GWAS summary statistics, demonstrating its accuracy through simulations and application to human trait data.

Social Determinants of Health and Lifestyle Risk Factors Modulate Genetic Susceptibility for Women's Health Outcomes

The paper examines how genetic and environmental factors, including social determinants of health, influence women's health outcomes by analyzing polygenic risk scores and environmental exposures in the All of Us cohort.

Functional gene embeddings improve rare variant polygenic risk scores

FuncRVP improves rare variant polygenic risk scores by integrating functional gene embeddings, enhancing performance for traits with higher heritability.

Rapid and accurate genotype imputation from low coverage short read, long read, and cell free DNA sequence

QUILT2 enables accurate genotype imputation from low coverage short and long reads and cell-free DNA, improving GWAS and PRS for maternal and fetal genomes.

Polygenic prediction of major depressive disorder and related traits in African ancestries UK Biobank participants.

The paper evaluates the accuracy of polygenic risk scores for MDD in African ancestry UK Biobank participants using European and African GWAS data, finding lower predictive power from European-derived PRS.

Unsupervised representation learning improves genomic discovery and risk prediction for respiratory and circulatory functions and diseases

This paper introduces a deep learning framework, REGLE, that improves genomic discovery and risk prediction for respiratory and circulatory diseases by learning low-dimensional embeddings from high-dimensional clinical data.

Identification of a Novel SLC2A9 Gene Association with LDL-C levels and Evaluation of Polygenic Scores in a Multi-Ancestry Genome Wide Association Study

This study identifies a novel SLC2A9 variant associated with LDL-C levels in Qatar's Middle Eastern population and evaluates polygenic scores across ancestries.

Genome-wide Polygenic Risk Scores Predict Risk of Glioma and Molecular Subtypes

This study develops a novel polygenic risk score (PRS-CS) for glioma that outperforms existing methods, improving risk prediction and subtype classification using genome-wide association study data.

Limitations in next-generation sequencing-based genotyping of breast cancer polygenic risk score loci

This study evaluates the accuracy of next-generation sequencing in capturing allele frequencies for polygenic risk score loci in breast cancer, finding significant deviations affecting risk prediction.