polygenic risk

Leveraging fine-mapping and non-European training data to improve cross-population polygenic risk scores

This paper introduces PolyPred and PolyPred+ to improve cross-population polygenic risk score accuracy by addressing LD, MAF, and causal effect size differences using fine-mapping and non-European training data.

Significant Sparse Polygenic Risk Scores across 813 traits in UK Biobank

The paper develops sparse polygenic risk scores for 813 traits using UK Biobank data, showing significant predictive performance and a correlation between variant count and performance.

Using Local Genetic Correlation Improves Polygenic Score Prediction Across Traits

This study improves polygenic score prediction across traits by incorporating local genetic correlation and heritability estimates from genetically correlated phenotypes.

Penetrance of HFE haemochromatosis variants to clinical disease: polygenic risk score associations in UK Biobank

This study shows that polygenic risk scores for iron levels and related diseases increase the risk of clinical outcomes in HFE p.C282Y homozygotes, but not in females or compound heterozygotes.

Polygenic risk vectors (PRV) improve genetic risk stratification for cardio-metabolic diseases

This paper introduces polygenic risk vectors (PRV) to improve genetic risk stratification for cardio-metabolic diseases by combining additive and dominant genetic effects, outperforming traditional polygenic risk scores.

Multivariate genetic analysis of personality and cognitive traits reveals abundant pleiotropy and improves prediction

This study uses a multivariate genetic approach to analyze personality and cognitive traits, identifying pleiotropy and improving polygenic prediction.

BayesRB: a Markov chain Monte Carlo-based polygenic genetic risk score algorithm for dichotomous traits

This paper introduces BayesRB, an extension of BayesR for dichotomous traits, showing improved SNP effect estimation and disease risk prediction compared to traditional methods.

Genomic characterization of world's longest selection experiment in mouse reveals the complexity of polygenic traits.

This study characterizes the genomes of mouse lines selected for specific traits over 140 generations, revealing genetic variation and candidate genes associated with fertility, obesity, and endurance.

Leveraging genetics to improve Body Mass Index increase prediction in the first-episode of psychosis

This study uses polygenic risk scores to predict BMI increase in first-episode psychosis patients, finding shared genetic variants between schizophrenia and BMI contribute significantly to the prediction.

Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast

The paper introduces BB-QTL mapping to study complex traits in yeast, revealing polygenic, pleiotropic, and epistatic genetic architectures with increased sample size.

Partitioning gene-mediated disease heritability without eQTLs

The paper estimates the fraction of disease heritability mediated by genes linked to SNPs without using eQTLs, finding that the closest gene mediates 27% of heritability and some genes outside the top ten also contribute significantly.

Strong genotype by environment interactions in the rice Global MAGIC population across seedling stage drought

The paper studies genotype by environment interactions in rice under drought conditions using the Global MAGIC population, finding that most alleles have conditionally neutral effects and that shoot growth during drought is linked to crown root number.

Assortative Mating Biases Marker-based Heritability Estimators

The paper shows that marker-based heritability estimators are biased under assortative mating and proposes corrected estimators for traits under equilibrium assortative mating.

Stability of Polygenic Scores Across Discovery Genome-Wide Association Studies

This study evaluates the stability of polygenic scores across different genome-wide association studies, finding low individual-level consistency and highlighting challenges for precision medicine.

Overestimated Polygenic Prediction due to Overlapping Subjects in Genetic Datasets

This paper shows that polygenic risk scores (PRS) overestimate predictive accuracy when datasets have overlapping subjects, using Alzheimer's disease and other traits as examples.

Genome-wide pleiotropy analysis identifies novel blood pressure variants and improves its polygenic risk scores

This study identifies novel blood pressure variants through pleiotropy analysis and improves polygenic risk scores for hypertension and cardiovascular disease.

High-resolution portability of 245 polygenic scores when derived and applied in the same cohort

This study evaluates the portability of polygenic scores within the same cohort across nine ancestry groups, showing reduced accuracy with increasing genetic distance.

PAGEANT: Personal Access to Genome and Analysis of Natural Traits

PAGEANT provides a framework for genetic reporting tools by analyzing genomic data to assess health risks and genetic traits, using publicly available genome datasets.

Accurate assignment of disease liability to genetic variants using only population data

This paper introduces BayPR, a Bayesian method that assigns pathogenicity probabilities to genetic variants using population data, achieving high accuracy for Mendelian disorders.

Breast and prostate cancer risk: the interplay of polygenic risk, high-impact monogenic variants, and family history

This study assesses how polygenic risk scores, high-impact monogenic variants, and family history influence breast and prostate cancer risk using UK Biobank data.

A Deep Learning-based Genome-wide Polygenic Risk Score for Common Diseases Identifies Individuals with Risk

This paper introduces DeepPRS, a deep learning-based polygenic risk score model that outperforms existing methods in predicting risk for common diseases using genome-wide genotype data.

Prioritising Autoimmunity Risk Variants for Functional Analyses by Fine-Mapping Mutations Under Natural Selection

The paper identifies candidate SNPs under natural selection in autoimmune disorder risk loci and shows they colocalize with selected variants, suggesting functional relevance and implications for autoimmunity.

Genetic risk prediction of COVID-19 susceptibility and severity in the Indian population

The paper computes polygenic risk scores for COVID-19 severity in Indian sub-populations using GWAS summary statistics and finds a positive correlation between genetic risk scores and mortality.

Genome-wide association, prediction and heritability in bacteria

This paper applies genome-wide association, prediction, and heritability analyses to bacterial data, identifying genetic factors influencing antibiotic resistance and within-host survival in Streptococcus pneumoniae.

Pathfinder: A gamified measure to integrate general cognitive ability into the biological, medical, and behavioural sciences

The paper introduces a gamified cognitive ability measure, Pathfinder, which shows heritability and genetic prediction of general cognitive ability.

Polygenic Scores Predict the Development of Alcohol and Nicotine Use Problems from Adolescence through Young Adulthood

This study shows that polygenic scores for drinking and smoking predict alcohol and nicotine use problems from adolescence to young adulthood, with smoking PGS also capturing broader genetic liability for substance use.

Polygenic signals of sex differences in selection in contemporary humans

This study identifies polygenic signals of sex-differential selection in humans using UK Biobank data, showing sex-specific effects on survival, reproduction, and fitness.

Genomic Heritability: A Ragged Diagonal Between Bias and Variance

The paper introduces a new genomic relationship matrix that improves genomic heritability estimation and breeding value prediction across populations.

The genetic basis of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping

This study investigates the genetic basis of Drosophila melanogaster's defense against Beauveria bassiana using QTL mapping and evolve and resequence approaches, revealing genetic variation and trade-offs in immune defense.

On Cross-ancestry Cancer Polygenic Risk Scores

This study evaluates the utility of breast and prostate cancer polygenic risk scores across different ancestry groups using UK Biobank data, showing significant enrichments in cancer cases within top PRS percentiles.