ArticleGenetic epidemiology2019
A flexible and parallelizable approach to genome-wide polygenic risk scores.
Article in Genetic epidemiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 2 of them syntheses that pooled it.
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Who cites it
24 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Incorporating functional priors improves polygenic prediction accuracy in UK Biobank and 23andMe data sets.Nature communications · 2021Pooled it
- MPGK: A user-friendly tool for Mendelian randomization, polygenic risk score, Geno Ontology, and the Kyoto Encyclopedia of Genes and Genomes analysis.Chinese medical journal · 2026Article
- Integrating common and rare variants improves polygenic risk prediction across diverse populations.Nature communications · 2026Article
- VADEr: Vision Transformer-Inspired Framework for Polygenic Risk Reveals Underlying Genetic Heterogeneity in Prostate Cancer.medRxiv : the preprint server for health sciences · 2025Article
- Polygenic scores and their applications in kidney disease.Nature reviews. Nephrology · 2025Review
- A review of methods and software for polygenic risk score analysis.PeerJ. Computer science · 2025Article
- Advancements and limitations in polygenic risk score methods for genomic prediction: a scoping review.Human genetics · 2024Article
- Pharmacogenomics polygenic risk score: Ready or not for prime time?Clinical and translational science · 2024Review
- Utility of polygenic scores across diverse diseases in a hospital cohort for predictive modeling.Nature communications · 2024Article
- A new method for multiancestry polygenic prediction improves performance across diverse populations.Nature genetics · 2023Article
- Novel Functional Genomics Approaches Bridging Neuroscience and Psychiatry.Biological psychiatry global open science · 2023Review
- Advances and Applications of Polygenic Scores for Coronary Artery Disease.Annual review of medicine · 2023Review
- Challenges and Opportunities for Developing More Generalizable Polygenic Risk Scores.Annual review of biomedical data science · 2022Review
- Construction and Application of Polygenic Risk Scores in Autoimmune Diseases.Frontiers in immunology · 2022Review
- Genetics in parkinson's disease: From better disease understanding to machine learning based precision medicine.Frontiers in molecular medicine · 2022Review
- RápidoPGS: a rapid polygenic score calculator for summary GWAS data without a test dataset.Bioinformatics (Oxford, England) · 2021Article
- A novel transcriptional risk score for risk prediction of complex human diseases.Genetic epidemiology · 2021Article
- Genetic prediction of complex traits with polygenic scores: a statistical review.Trends in genetics : TIG · 2021Review
- Polygenic Risk Scores Contribute to Personalized Medicine of Parkinson's Disease.Journal of personalized medicine · 2021Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The heritability of most complex traits is driven by variants throughout the genome. Consequently, polygenic risk scores, which combine information on multiple variants genome-wide, have demonstrated improved accuracy in genetic risk prediction. We present a new two-step approach to constructing genome-wide polygenic risk scores from meta-GWAS summary statistics. Local linkage disequilibrium (LD) is adjusted for in Step 1, followed by, uniquely, long-range LD in Step 2. Our algorithm is highly parallelizable since block-wise analyses in Step 1 can be distributed across a high-performance computing cluster, and flexible, since sparsity and heritability are estimated within each block. Inference is obtained through a formal Bayesian variable selection framework, meaning final risk predictions are averaged over competing models. We compared our method to two alternative approaches: LDPred and lassosum using all seven traits in the Welcome Trust Case Control Consortium as well as meta-GWAS summaries for type 1 diabetes (T1D), coronary artery disease, and schizophrenia. Performance was generally similar across methods, although our framework provided more accurate predictions for T1D, for which there are multiple heterogeneous signals in regions of both short- and long-range LD. With sufficient compute resources, our method also allows the fastest runtimes.
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Registered trials
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.