ArticleNature genetics2024
Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries.
Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers, 9 of them syntheses that pooled it.
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Who cites it
125 citing papers in PubMed, 9 syntheses or guidelines pooled it.
- Genome-Wide Association Study of Corneal Dystrophy Uncovers Novel Risk Loci and Enables Improved Polygenic Prediction of Fuchs Endothelial Corneal Dystrophy.Investigative ophthalmology & visual science · 2026Pooled it
- Genome-wide meta-analysis of quantitatively measured generalized anxiety symptoms in individuals of European ancestry.Nature human behaviour · 2026Pooled it
- Multi-ancestry genome-wide association analyses of refractive error augment genetic discovery and polygenic prediction.Nature genetics · 2026Pooled it
- Genetic landscape and functional exploration of kidney cancer predisposition in cross-ancestral populations.Nature communications · 2026Pooled it
- A large-scale genome-wide association meta-analysis for nevus count provides direct insights into the genetics of melanoma.Nature communications · 2026Pooled it
- A genome- and phenome-wide association study of plasma procalcitonin concentrations in individuals of European ancestry.EBioMedicine · 2026Pooled it
- GWAS for primary angle-closure glaucoma identifies loci related to ocular biometry and morphology.Nature communications · 2025Pooled it
- Pooled it
- A genome-wide association meta-analysis implicates Hedgehog and Notch signaling in Dupuytren's disease.Nature communications · 2024Pooled it
- SPLENDID incorporates continuous genetic ancestry in biobank-scale data to improve polygenic risk prediction across diverse populations.Nature methods · 2026Article
- Genetics of Educational Attainment and Childhood Problem Behavior: Direct Genetic Effects, Cognitive Pathways, and Sex Differences.Behavior genetics · 2026Article
- Article
- Protein Biomarkers in Risk and Prognosis of Amyotrophic Lateral Sclerosis.European journal of neurology · 2026Article
- Rare variant effect estimation and polygenic risk prediction.Nature genetics · 2026Article
- Post-genome-wide association study variant-to-function challenges in asthma research.The Journal of allergy and clinical immunology · 2026Review
- Partitioned blood pressure polygenic risk reveals differential genetic effects of tissue-specific enhancers and their interactions on cardiovascular disease.Research square · 2026Article
- Neurodevelopmental traits as mechanisms linking genetic predispositions to bullying involvement.European child & adolescent psychiatry · 2026Article
- Psychosis Polyrisk Score and Polygenic Risk Score to Improve Detection and Prognosis in Individuals at Clinical High Risk for Psychosis: Model Development and Internal Validation.Schizophrenia bulletin · 2026Article
- Integrated Analysis of SNPs and Structural Variations via High-depth Whole-genome Sequencing Reveals the Genetic Architecture and Optimizes Genomic Prediction in Chickens.Poultry science · 2026Article
- Artificial Intelligence-Driven Multimodal Prediction of 10-Year Incident Glaucoma Integrating Genetic and Deep Learning-Derived Imaging Features.Ophthalmology science · 2026Article
65 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
Abstract
We develop a method, SBayesRC, that integrates genome-wide association study (GWAS) summary statistics with functional genomic annotations to improve polygenic prediction of complex traits. Our method is scalable to whole-genome variant analysis and refines signals from functional annotations by allowing them to affect both causal variant probability and causal effect distribution. We analyze 50 complex traits and diseases using ∼7 million common single-nucleotide polymorphisms (SNPs) and 96 annotations. SBayesRC improves prediction accuracy by 14% in European ancestry and up to 34% in cross-ancestry prediction compared to the baseline method SBayesR, which does not use annotations, and outperforms other methods, including LDpred2, LDpred-funct, MegaPRS, PolyPred-S and PRS-CSx. Investigation of factors affecting prediction accuracy identifies a significant interaction between SNP density and annotation information, suggesting whole-genome sequence variants with annotations may further improve prediction. Functional partitioning analysis highlights a major contribution of evolutionary constrained regions to prediction accuracy and the largest per-SNP contribution from nonsynonymous SNPs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.