polygenic risk

STELLAR: A flexible ensemble learning framework integrating rare variants to enhance polygenic risk prediction

STELLAR improves polygenic risk prediction by integrating rare and common variants using ensemble learning, enhancing accuracy and refining risk stratification.

Contextualizing the Utility of Polygenic Risk Scores using Absolute Risk Models in Diverse Ancestry Populations

This paper evaluates polygenic risk scores (PRSs) in diverse populations using absolute risk models, finding that PRSs can provide greater utility in risk stratification for certain diseases in non-European populations.

A Favorable Modifiable Risk Factor Profile Mitigates Polygenic Risk for Alzheimers Disease and Related Dementia

This study shows that a favorable lifestyle reduces ADRD risk even in individuals with high polygenic risk, but APOE ε4 genotype remains a strong risk factor.

Genomic Population Structure of the Sunda Pangolin (Manis javanica) in Thailand: Implications for Conservation and Wildlife Forensics

This study analyzes whole genome sequences of Sunda pangolins in Thailand to identify genetic populations and diversity, informing conservation and forensic tools.

Estimation of Direct and Indirect Polygenic Effects and Gene-Environment Interactions using Polygenic Scores in Case-Parent Trio Studies

This paper introduces PGS-TRI, a framework to estimate direct and indirect polygenic effects and gene-environment interactions in case-parent trio studies, applied to autism and orofacial clefts.

Locally adaptive conformal prediction intervals for polygenic score-based phenotype prediction via residual normalization and data-driven stratification

This paper introduces C-SCNR, a framework for constructing calibrated prediction intervals for polygenic score-based phenotype prediction, outperforming existing methods in diverse error distributions and subgroups.

Genome-wide analysis and polygenic prediction of clinical obesity and comparison with body mass index

The paper conducts a genome-wide analysis of clinical obesity, identifies distinct genetic loci, and shows that a clinical obesity polygenic score improves cardiovascular risk prediction compared to BMI-based scores.

Characterising the Stability of Polygenic Risk Scores: implications for risk stratification

This study examines how individual polygenic risk scores (PRS) rankings change across GWAS releases and their implications for risk stratification.

Calibrated Prediction Intervals for Polygenic Scores: Updated Comparisons, Contextual Calibration, and Data Normalization

This paper compares two methods for creating calibrated prediction intervals for polygenic scores, showing their performance and the importance of normalization and preprocessing.

An Efficient Lasso Framework for Admixture-Aware Polygenic Scores

HAUDI improves polygenic score construction for admixed populations by efficiently extending the GAUDI method to multi-way admixture with faster computation and better performance.

Characterizing the Uncertainty, Misclassification and Inconsistency of Polygenic Prediction

This study develops a framework to calibrate polygenic risk scores and analyze misclassification and inconsistency in risk stratification.

Diverse mediators of cancer predisposition uncovered by germline whole genome sequencing of unexplained familial cancers

The paper identifies polygenic risk factors and rare variants in unexplained familial cancers using whole genome sequencing and family history data.

Heterogeneous endocrine cell composition defines human islet functional phenotypes

In 299 islet preparations from donors without diabetes, endocrine cell composition, not donor demographics, tracked insulin secretion, and δ cell percentage rose with type 2 diabetes genetic risk.

Optimizing phenotype scale improves genetic analyses in large-scale biobanks

SIQReg optimizes phenotype scales in genetic analyses, improving both additive and non-additive signal detection in large biobanks.

Low genetic diversity in Colobus vellerosus populations in Kikele Sacred and Okuta Kobunan Forests, Benin

The study analyzes genetic diversity in two small populations of Colobus vellerosus in Benin using mitochondrial markers, finding very low diversity due to a potential genetic bottleneck.

Information Bottleneck Dominates Adversarial Training for Ancestry-Invariant Polygenic Risk Prediction: Dimensionality, Not Gradient Reversal, Controls the Fairness-Accuracy Tradeoff

This paper shows that latent dimensionality, not adversarial training, is the main factor controlling ancestry invariance in polygenic risk prediction, with dimensionality changes having a much larger impact on leakage than gradient reversal coefficients.

Evaluation of the genome-informed risk assessment (GIRA) approach from eMERGE in an independent health system

This study evaluates the GIRA approach in a health system, finding 30.4% of patients labeled high-risk based on genomic data, with ancestry differences and social deprivation influences.

Evaluating a Genome-Wide Polygenic Score for Handgrip Strength and Its Interplay with Leisure-Time Physical Activity Across the IGEMS Twin Cohorts

The paper evaluates a polygenic score for handgrip strength and its interaction with physical activity across twin cohorts, finding a significant genetic association and effect modification by physical activity.

Multi-ancestry polygenic risk scores for the prediction of type 2 diabetes and complications in diverse ancestries.

This paper develops and validates multi-ancestry polygenic risk scores for type 2 diabetes prediction and complications across diverse populations.

Environment-aware genomic prediction enhances the transferability of polygenic resistance to ash dieback in Fraxinus excelsior

This study improves genomic prediction of ash dieback resistance by incorporating environmental factors, showing enhanced transferability across environments.

Ancient regulatory evolution shapes individual language abilities in present-day humans

Polygenic score variants in HAQERs (Human Ancestor Quickly Evolved Regions, <0.1% of the genome) predict spoken language but not nonverbal IQ; language associations replicate in SPARK, ABCD and UK Biobank.

CalPred yields calibrated intervals for polygenic risk prediction

CalPred provides well-calibrated prediction intervals for polygenic risk scores, maintaining calibration across different contextual factors unlike other methods.

Sex stratified analyses enable new genetic insights into brain imaging phenotypes

The paper performs sex-stratified genetic analyses of neuroimaging phenotypes, finding new associations and improving heritability estimates when analyzing males and females separately.

Biobank-scale survey of gene-diet interactions informs precision nutrition polygenic scores

The paper assesses gene-diet interactions in UK Biobank data to derive polygenic scores that associate with cardiometabolic outcomes and clinical conditions like gout.

Evaluating Individual Level Performance of Polygenic Risk Scores Using Early Onset High Genetic Risk Coronary Artery Disease as a Benchmark

The paper evaluates individual-level performance of polygenic risk scores (PRSs) using a benchmark cohort of early-onset coronary artery disease patients, showing variability in PRS accuracy and highlighting the need for individual-level validation.

Phenome-derived polygenic scores and social determinants jointly shape context-dependent disease risk

This paper constructs phenome-derived polygenic scores and evaluates how they, along with social determinants of health, influence disease risk across different populations and diseases.

EGP1K: Whole-Genome Sequencing of 1,024 Egyptians Characterizes Population Structure and Genetic Diversity

EGP1K sequenced 1,024 Egyptians to characterize genetic diversity and population structure, revealing distinct ancestry components and highlighting issues with European-derived polygenic risk score thresholds.

Functionality-Informed Fine-Mapping Dissects Common Variant Contributions to Coronary Artery Disease and Identifies Causal Variants and Pathways

This study uses functionality-informed fine mapping to identify causal variants and pathways contributing to coronary artery disease risk using GWAS summary statistics from over a million individuals.

SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation

SPrUCE estimates genetic diversity from UCE data by correcting underestimation bias using a Gompertz function model, providing accurate results comparable to whole-genome methods.

Population-specific polygenic risk for Alzheimer's disease is associated with Mini-Mental State Examination-based cognitive decline in a Japanese cohort

The paper examines the association between Alzheimer's disease polygenic risk scores and cognitive decline measured by MMSE in a Japanese cohort, finding stronger associations with scores derived from Japanese GWAS.