polygenic risk

Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies

The paper introduces LD graphical models (LDGMs) for efficient linkage disequilibrium representation in diverse ancestry studies, showing significant runtime improvements and better polygenic prediction.

Gene expression and RNA splicing explain large proportions of the heritability for complex traits in cattle

The paper quantifies how gene expression and splicing QTL explain heritability in cattle traits using Bayesian methods across 16 tissues.

Genetic and brain similarity independently predict childhood anthropometrics and socioeconomic markers

The paper examines how genetic and brain similarities predict childhood anthropometric and socioeconomic traits using a mixed model framework in the ABCD cohort.

Predicting risk of Alzheimer's disease using polygenic risk scores developed for Parkinson's disease

This study evaluates the predictive power of polygenic risk scores for Alzheimer's disease and Parkinson's disease, finding that filtered scores for both diseases are strongly predictive, with AD scores better predicting PD than vice versa.

T2T-YAO: a Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese

The paper presents T2T-YAO, a telomere-to-telomere diploid reference genome for a Han Chinese male, offering improved haplotype resolution and genetic diversity compared to T2T-CHM13.

Mapping pQTLs of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and novel therapeutic targets

The paper identifies pQTLs for 91 plasma proteins, finds novel associations, and uses MR to uncover causal roles in immune-mediated diseases, suggesting new therapeutic targets.

Trans-ancestry polygenic models for the prediction of LDL blood levels: An analysis of the UK Biobank and Taiwan Biobank

This paper compares ancestry-specific and multi-ancestry polygenic risk scores for LDL prediction in East Asian populations using UK Biobank and Taiwan Biobank data, finding that multi-ancestry models are more generalizable.

Biobank-scale methods and projections for sparse polygenic prediction from machine learning

The paper evaluates sparse machine learning algorithms for polygenic prediction, showing LASSO performs well and provides projections for new biobanks.

A Polygenic Quincunx

The paper models polygenic risk as a branching tree where each SNP adds a random walk step, showing that more SNPs increase risk dispersion and potential clinical benefit.

Polygenic architecture of flowering time and its relationship with local environments in the grass Brachypodium distachyon.

This study investigates the polygenic architecture of flowering time in Brachypodium distachyon, linking genetic variation to environmental factors and vernalization requirements.

Testing a polygenic risk score for morphological microglial activation in Alzheimer's disease and aging

The paper tests a polygenic risk score for microglial activation in Alzheimer's disease and aging, finding no significant improvement in predictive power for AD diagnosis or cognitive performance.

Estimation of indirect genetic effects and heritability under assortative mating

The paper develops a method to estimate indirect genetic effects and heritability under assortative mating, showing biases in existing methods and providing corrected estimates for height and educational attainment.

Optimal strategies for learning multi-ancestry polygenic scores vary across traits

This study shows that optimal polygenic score strategies vary by trait and ancestry, with smaller African-ancestry training sets outperforming larger European-ancestry sets for some traits.

Malaria resistance-related biological adaptation and complex evolutionary footprints of Tai-Kadai people inferred from 796 genomes

This study analyzes 796 Tai-Kadai genomes to uncover genetic adaptations and evolutionary history, revealing Malaria resistance and population structure in TK-speaking groups.

PA-FGRS is a novel estimator of pedigree-based genetic liability that complements genotype-based inferences into the genetic architecture of major depressive disorder

The paper introduces PA-FGRS, a method to estimate genetic liability from family records, and shows it improves MDD classification and GWAS power when combined with genotypes.

Flexibly encoded genome-wide association study identifies novel nonadditive genetic risk variants for cardiometabolic traits

This paper introduces EDGE, a method to detect nonadditive genetic effects in GWAS, finding nonadditive patterns in over 52% of significant loci for coronary artery disease and body mass index.

Rare penetrant mutations confer severe risk of common diseases

The paper identifies rare variant polygenic risk scores as more effective than common variant polygenic risk scores in identifying individuals with outlier phenotypes in common human diseases and complex traits.

A comprehensive workflow for target adaptive sampling long-read sequencing applied to hereditary cancer patient genomes

This study develops a computational workflow for target adaptive sampling long-read sequencing and applies it to hereditary cancer genomes to identify genetic variants and epigenetic changes.

Selection, optimization, and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse populations

The paper selects and validates ten polygenic risk scores for clinical use in diverse populations, focusing on chronic diseases and addressing disparities in predictive performance.

Deep integrative models for large-scale human genomics

The paper introduces a deep learning framework for polygenic risk score prediction, showing improved performance over traditional methods for various diseases.

Assortative mating and parental genetic relatedness drive the pathogenicity of variably expressive variants

The paper examines how assortative mating and parental genetic relatedness influence the pathogenicity of variably expressive variants in neurodevelopmental disorders.

Multi-ancestry meta-analysis and fine-mapping in Alzheimer's Disease

This study conducts a multi-ancestry GWAS meta-analysis of Alzheimer's disease, identifies two novel loci, and assesses polygenic risk score generalizability across populations.

Contraception ends the genetic maintenance of human same-sex sexual behavior

The paper shows that genetic maintenance of same-sex sexual behavior has declined due to contraception reducing the reproductive impact of having more sexual partners.

Go west: population genomics reveals unexpected population fluctuations and little gene flow in Western Hemisphere populations of the predatory lady beetle, Hippodamia convergens

This study uses ddRADseq to analyze population genetics of Hippodamia convergens, finding significant differentiation and no recent admixture despite population augmentation.

Imputed Gene Expression versus Single Nucleotide Polymorphism in Predicting Gray Matter Phenotypes

The paper compares imputed gene expression (gPRS) and SNP-based polygenic risk scores (sPRS) in predicting gray matter phenotypes using UK Biobank data, finding gPRS provides better prediction accuracy.

GARSA: An integrative pipeline for genome wide association studies and polygenic risk score inference in admixed human populations

GARSA is a pipeline for GWAS and PRS analysis in admixed populations, incorporating bias correction and multiple analytical methods.

Functional archaic DNA regulates molecular variation and is associated with disease risk across global populations

This study identifies functional archaic DNA from Neanderthals and Denisovans that regulates gene expression and disease risk in European and East Asian populations.

Multi-organ imaging-derived polygenic indexes for brain and body health

The paper uses genetic data to predict imaging-derived phenotypes from the UK Biobank, creating polygenic scores that identify disease risk in external cohorts.

PGSbuilder: An end-to-end platform for human genome association analysis and polygenic risk score predictions

PGSbuilder provides a web platform for GWAS and PRS analysis, enabling medical professionals to assess genetic risk using variant annotations and multiple PRS methods.

Fast and Accurate Bayesian Polygenic Risk Modeling with Variational Inference

VIPRS improves polygenic risk prediction using variational inference, achieving high accuracy and efficiency in both simulated and real datasets.