polygenic risk

Standing covariation between genomic and epigenomic patterns as source for natural selection in wild strawberry plants

This study shows that SNPs and DMCs in wild strawberries covary under drought stress, suggesting genomic redundancy and polygenic adaptation.

The Polygenic Score Catalog: an open database for reproducibility and systematic evaluation

PGS Catalog standardizes 192 curated polygenic scores and metadata (86 traits); reapplied in UK Biobank, eight of nine colorectal cancer scores predicted disease in European-ancestry participants.

Improving reporting standards for polygenic scores in risk prediction studies

ClinGen and the PGS Catalog expand the GRIPS guideline into a 22-item Polygenic Risk Score Reporting Statement covering study populations, model construction, evaluation, and clinical interpretation.

A smoothed version of the Lassosum penalty for fitting integrated risk models

This paper introduces a smoothed version of the Lassosum penalty to improve integrated risk models, showing increased accuracy in predicting Alzheimer's and COPD risks compared to the original Lassosum and LDpred2.

Population-specific causal disease effect sizes in functionally important regions impacted by selection

The paper develops a method to identify population-specific causal effect sizes in functionally important regions using trans-ethnic genetic correlations.

Imputed Gene Expression Risk Scores: A Functionally Informed Component of Polygenic Risk

This study evaluates gene expression risk scores (GeRS) for predicting neuropsychiatric and anthropometric traits, finding they improve prediction when combined with polygenic risk scores (PRS).

GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background

This study performs GWAS on three molecular traits, identifying core genes and pathways while highlighting a polygenic background contributing to trait variance.

Polygenic Prediction of Type 2 Diabetes in Continental Africa

This study evaluates if African American or multi-ethnic polygenic risk scores improve type 2 diabetes prediction in continental Africans, finding that African American-derived scores are more predictive.

Extreme Phenotypic Diversity in Operant Responding for an Intravenous Cocaine or Saline Infusion in the Hybrid Mouse Diversity Panel

The paper investigates genetic influences on cocaine IVSA in the HMDP, finding substantial heritability and unique genetic variants for cocaine versus saline responding.

Low generalizability of polygenic scores in African populations due to genetic and environmental diversity

This study evaluates the generalizability of polygenic scores in African populations, finding that PRS accuracy varies significantly across African ancestries and is improved by using ancestrally diverse genetic studies.

Additional SNPs improve the performance of a polygenic hazard score for prostate cancer

This study improves a polygenic hazard score for prostate cancer by adding 120 SNPs, enhancing hazard ratios but not positive predictive value of PSA testing.

Using genomic prediction to detect microevolutionary change of a quantitative trait

This study uses genomic prediction to detect microevolutionary changes in adult body weight of Soay sheep over 35 years, finding an increase in the genetic component despite a decrease in average body weight.

Investigating the Genetic Architecture of Non-Cognitive Skills Using GWAS-by-Subtraction

This study identifies 157 genome-wide significant loci associated with non-cognitive contributions to educational attainment, explaining 57% of genetic variance.

LDpred2: better, faster, stronger

LDpred2 reworks LDpred with a 3 cM LD window plus sparse and auto options, reaching mean AUC 65.1% over 8 real traits versus 63.8% for lassosum.

Inclusion of Variants Discovered from Diverse Populations Improves Polygenic Risk Score Transferability

This study shows that including variants from African ancestry populations improves the accuracy and fairness of polygenic risk scores across diverse populations.

Large uncertainty in individual PRS estimation impacts PRS-based risk stratification

The paper shows that individual PRS estimates have large uncertainty, impacting risk stratification, and introduces a method to quantify this uncertainty using Bayesian approaches.

Polygenic Prediction of Complex Traits with Iterative Screen Regression Models

This study introduces the iterative screen regression model (ISR) for polygenic prediction of complex traits and shows it outperforms existing methods in simulations and across multiple species.

Pharmacogenetics at scale: An analysis of the UK Biobank

The paper analyzes pharmacogenetics in the UK Biobank, finding that most individuals may have atypical drug responses and non-European populations have more deleterious variants.

Bivariate genomic prediction of phenotypes by selecting epistatic interactions across years

This paper compares bivariate genomic prediction models for plant traits across two growing seasons, finding that models incorporating epistasis improve prediction accuracy.

Functionally-informed fine-mapping and polygenic localization of complex trait heritability

This paper introduces PolyFun, a method that improves fine-mapping accuracy by integrating genome-wide functional data, leading to more causal variant identifications and polygenic localization of trait heritability.

Exons as units of phenotypic impact for truncating mutations in autism

The paper shows that truncating mutations affecting the same exon in autism lead to similar intellectual phenotypes, suggesting exons, not genes, are units of phenotypic impact.

Gamete simulation improves polygenic transmission disequilibrium analysis

ORIGAMI simulates offspring genomes from parental data to improve polygenic transmission disequilibrium analysis, revealing significant within-family risk variation for complex traits.

Genome-Wide Polygenic Risk Score Identifies Individuals at Elevated Parkinson's Disease Risk

This paper computes a genome-wide polygenic risk score for Parkinson's Disease using 6.2 million variants and finds it strongly associates with increased disease risk and earlier onset.

Genome-wide association study of suicide death and polygenic prediction of clinical antecedents

This paper conducts a genome-wide association study of suicide death and shows polygenic scores predict suicide case-control status and related psychiatric traits.

Greater Effect of Polygenic Risk Score for Alzheimer's Disease Among Younger Cases Who are Apolipoprotein E-ϵ4 Carriers

The paper examines how polygenic risk scores for Alzheimer's disease affect younger APOE4 carriers, finding earlier disease onset associated with higher PRS.

Cancer PRSweb - an Online Repository with Polygenic Risk Scores (PRS) for Major Cancer Traits and Their Phenome-wide Exploration in Two Independent Biobanks

The paper introduces Cancer-PRSweb, an online repository of polygenic risk scores for cancer traits, evaluated in two biobanks with predictive performance metrics and phenome-wide association studies.

Allele frequency differentiation at height-associated SNPs among continental human populations

The paper examines allele frequency differentiation at height-associated SNPs across continental populations and finds significant FST differences, suggesting polygenic adaptation, while polygenic scores show less consistent results.

More Research Needed: There is a Robust Causal vs. Confounding Problem for Intelligence-associated Polygenic Scores in Context to Admixed American Populations.

The paper investigates whether correlations between polygenic scores for intelligence, genetic ancestry, and cognitive ability in admixed American populations are causal or due to confounding.

African-specific improvement of a polygenic hazard score for age at diagnosis of prostate cancer

The paper improves a polygenic hazard score for prostate cancer age at diagnosis by adding SNPs specific to African ancestry, enhancing performance in this population.

Sleep Deficits and Cannabis Use Behaviors: An Analysis of Shared Genetics Using Linkage Disequilibrium Score Regression and Polygenic Risk Prediction

This study finds genetic links between cannabis use and sleep deficits, including eveningness chronotype and insomnia, using LDSC and polygenic risk scores.