polygenic risk

Population genomics of the Viking world

This study analyzes ancient genomes from the Viking Age to understand genetic structure and migration patterns, finding significant foreign gene flow and population differentiation.

Polygenic Risk Scores for Kidney Function to the Circulating Proteome, and Incident Kidney Diseases: the Atherosclerosis Risk in Communities Study

This study develops a polygenic risk score for eGFR and shows its association with kidney disease outcomes and plasma proteins in the ARIC study.

Bioarchaeological analysis of one of the earliest Islamic burials in the Levant

This study presents the first genomic analysis of early Islamic burials in the Levant, finding genomic similarity to modern Bedouins and Saudis rather than neighboring Levantine groups.

Assessing performance of pathogenicity predictors using clinically-relevant variant datasets

The paper evaluates pathogenicity predictors using two clinically-relevant variant datasets, finding that newer meta-predictors outperform older tools but still have limited accuracy in clinical data.

Recommendations for Primary Prevention of Skin Melanoma

The paper develops a polygenic risk score-based pipeline to provide personalized recommendations for melanoma prevention by integrating genetic risk with health behavior.

Haplotype genetic score analysis in 10,734 mother/infant pairs reveals complex maternal and fetal genetic effects underlying the associations between maternal phenotypes, birth outcomes and adult phenotypes

The paper uses haplotype genetic scores in mother/infant pairs to show maternal and fetal genetic effects influence gestational duration, birth outcomes, and adult phenotypes.

Precision Prostate Cancer Screening with a Polygenic Risk Score

This paper constructs a polygenic risk score (PRS) model for prostate cancer risk prediction and develops personalized screening recommendations using population-specific data.

CORE GREML: Estimating covariance between random effects in linear mixed models for genomic analyses of complex traits

The paper introduces CORE GREML, a method to estimate covariance between random effects in LMMs for genomic analyses, showing improved performance in variance partitioning.

Polygenic background modifies penetrance of monogenic variants conferring risk for coronary artery disease, breast cancer, or colorectal cancer

The paper examines how polygenic risk modifies the penetrance of monogenic variants in coronary artery disease, breast cancer, and colorectal cancer across multiple cohorts.

Precision Colorectal Cancer Screening with Polygenic Risk Score

This paper develops a sex-specific polygenic risk score model for colorectal cancer screening, showing it can stratify risk and inform individualized screening recommendations.

Precision Breast Cancer Screening with a Polygenic Risk Score

The paper revalidates a polygenic risk score (PRS) model for breast cancer risk prediction and develops a pipeline for individualized screening recommendations using population-specific data.

Polygenic Risk Score for Gastric Cancer

The paper develops a polygenic risk score model for gastric cancer using GWAS data and machine learning, achieving 0.93 accuracy with 100 SNPs.

Polygenic modelling of treatment effect heterogeneity

The paper develops a polygenic response score to identify subgroups with different treatment effects by testing gene-gene interactions using pharmacomimetic genetic variants.

Within-Family Validation of Polygenic Risk Scores and Complex Trait Prediction

The paper validates polygenic risk scores by comparing disease risk and trait prediction accuracy between genetic siblings and non-siblings.

Theoretical and empirical quantification of the accuracy of polygenic scores in ancestry divergent populations

This paper quantifies the accuracy loss of polygenic scores in non-European populations by modeling linkage disequilibrium, allele frequencies, and effect size correlations.

A guide to performing Polygenic Risk Score analyses

Best-practice guidance for polygenic risk score (PRS) analysis: PRS-specific quality control, shrinkage and linkage disequilibrium handling, liability-scale R^2, overfitting control, and UK Biobank power examples.

Genetic Architecture of Complex Traits and Disease Risk Predictors

The paper analyzes genetic variants used in disease risk predictors and finds that most SNPs are outside coding regions, suggesting exome data alone cannot capture heritability for complex traits.

Non-additive polygenic models improve predictions of fitness traits in three eukaryote model species

The paper develops a non-additive polygenic model to predict fitness traits in three eukaryote species and finds non-additive models better explain fitness in some cases.

Assessment of Polygenic Architecture and Risk Prediction based on Common Variants Across Fourteen Cancers

This study assesses polygenicity and risk prediction using common variants across 14 cancers, finding varying numbers of susceptibility variants and risk score effectiveness.

Family Analysis with Mendelian Imputations

The paper introduces mendelian imputation to disentangle genotype-phenotype associations by leveraging family data, showing improved predictive power for educational attainment.

Impute.me: an open source, non-profit tool for using data from DTC genetic testing to calculate and interpret polygenic risk scores.

Impute.me provides an open-source tool for calculating and interpreting polygenic risk scores from consumer genetic data to better communicate genetic risk for complex diseases.

Discovery of 318 novel loci for type-2 diabetes and related micro- and macrovascular outcomes among 1.4 million participants in a multi-ethnic meta-analysis.

Multi-ethnic type 2 diabetes (T2D) meta-analysis of 228,499 cases and 1,178,783 controls finds 318 previously unreported loci, 804 expression-colocalized genes, and 13 SNP-by-T2D vascular-outcome interactions.

Large-Scale Sparse Regression for Multiple Responses with Applications to UK Biobank

The paper develops a scalable sparse reduced-rank regression method for high-dimensional multitask learning, applied to UK Biobank data to generate polygenic risk scores.

Non-parametric polygenic risk prediction using partitioned GWAS summary statistics

This paper introduces a non-parametric polygenic risk prediction method using GWAS summary statistics, improving prediction accuracy for several diseases.

Low additive genetic variation in a trait under selection in domesticated rice

The paper estimates additive genetic variation in rice root growth under selection and finds low marker heritability and no associated loci in a tropical japonica population.

Genotype Concordance and Polygenic Risk Score Estimation across Consumer Genetic Testing Data

This study examines genotype concordance and polygenic risk score differences across three consumer genetic testing services, finding significant discrepancies in Alzheimer's disease risk estimates.

Quantifying genetic effects on disease mediated by assayed gene expression levels

The paper introduces MESC to estimate disease heritability mediated by gene expression, finding that only a small proportion of heritability is explained by cis-genetic expression levels.

LDpred-funct: incorporating functional priors improves polygenic prediction accuracy in UK Biobank and 23andMe data sets

LDpred-funct adds baseline-LD functional priors to polygenic scores: average prediction R2 0.144 across 21 UK Biobank traits, a 4.6% relative gain over SBayesR.

High complexity and degree of genetic variation in Brettanomyces bruxellensis population

The paper sequenced 53 Brettanomyces bruxellensis genomes to study genetic variation and its relationship with ploidy level and gene content.

Chromosomal scale length variation of germline DNA can predict individual cancer risk

This paper shows that chromosomal-scale length variation in germline DNA can predict cancer risk better than SNP-based methods in two datasets.