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

https://doi.org/10.1101/375337
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Polygenic scores via penalized regression on summary statistics
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Multiethnic polygenic risk scores improve risk prediction in diverse populations
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A flexible and parallelizable approach to genome‐wide polygenic risk scores
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Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits
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Joint Analysis of Psychiatric Disorders Increases Accuracy of Risk Prediction for Schizophrenia, Bipolar Disorder, and Major Depressive Disorder
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Leveraging Functional-Annotation Data in Trans-ethnic Fine-Mapping Studies
inferredcites →https://doi.org/10.1016/j.ajhg.2015.09.001openalex-snapshot
Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores
inferredcites →https://doi.org/10.1016/j.ajhg.2015.10.002openalex-snapshot
Two-Variance-Component Model Improves Genetic Prediction in Family Datasets
inferredcites →https://doi.org/10.1016/j.ajhg.2015.12.022openalex-snapshot
Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia
inferredcites →https://doi.org/10.1016/j.ajhg.2016.09.014openalex-snapshot
Population Structure of UK Biobank and Ancient Eurasians Reveals Adaptation at Genes Influencing Blood Pressure
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Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression
inferredcites →https://doi.org/10.1016/j.ajhg.2018.03.026openalex-snapshot
FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications
inferredcites →https://doi.org/10.1016/j.ajhg.2020.05.004openalex-snapshot
Non-parametric Polygenic Risk Prediction via Partitioned GWAS Summary Statistics
inferredcites →https://doi.org/10.1038/nature08185openalex-snapshot
Common polygenic variation contributes to risk of schizophrenia and bipolar disorder
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Integrating common and rare genetic variation in diverse human populations
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Genetic and epigenetic fine mapping of causal autoimmune disease variants
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Integrative analysis of 111 reference human epigenomes
inferredcites →https://doi.org/10.1038/nature14962openalex-snapshot
The UK10K project identifies rare variants in health and disease
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A global reference for human genetic variation
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Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits
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Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis
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Chromatin marks identify critical cell types for fine mapping complex trait variants
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Partitioning heritability by functional annotation using genome-wide association summary statistics
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Reevaluation of SNP heritability in complex human traits
inferredcites →https://doi.org/10.1038/ng.3954openalex-snapshot
Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection
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Estimating the causal tissues for complex traits and diseases
inferredcites →https://doi.org/10.1038/nrg.2016.142openalex-snapshot
Dissecting the genetics of complex traits using summary association statistics
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Pitfalls of predicting complex traits from SNPs
inferredcites →https://doi.org/10.1038/s41467-017-02769-6openalex-snapshot
Improving genetic prediction by leveraging genetic correlations among human diseases and traits
inferredcites →https://doi.org/10.1038/s41467-019-08424-6openalex-snapshot
Quantification of frequency-dependent genetic architectures in 25 UK Biobank traits reveals action of negative selection
inferredcites →https://doi.org/10.1038/s41467-019-09718-5openalex-snapshot
Polygenic prediction via Bayesian regression and continuous shrinkage priors
inferredcites →https://doi.org/10.1038/s41467-019-11112-0openalex-snapshot
Analysis of polygenic risk score usage and performance in diverse human populations
inferredcites →https://doi.org/10.1038/s41467-019-12653-0openalex-snapshot
Improved polygenic prediction by Bayesian multiple regression on summary statistics
inferredcites →https://doi.org/10.1038/s41467-020-17719-yopenalex-snapshot
Theoretical and empirical quantification of the accuracy of polygenic scores in ancestry divergent populations
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Genomics of disease risk in globally diverse populations
inferredcites →https://doi.org/10.1038/s41586-018-0579-zopenalex-snapshot
The UK Biobank resource with deep phenotyping and genomic data
inferredcites →https://doi.org/10.1038/s41588-018-0047-6openalex-snapshot
Genetic analysis of quantitative traits in the Japanese population links cell types to complex human diseases
inferredcites →https://doi.org/10.1038/s41588-018-0081-4openalex-snapshot
Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types
inferredcites →https://doi.org/10.1038/s41588-018-0101-4openalex-snapshot
Signatures of negative selection in the genetic architecture of human complex traits
inferredcites →https://doi.org/10.1038/s41588-018-0144-6openalex-snapshot
Mixed-model association for biobank-scale datasets
inferredcites →https://doi.org/10.1038/s41588-018-0147-3openalex-snapshot
Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals
inferredcites →https://doi.org/10.1038/s41588-018-0231-8openalex-snapshot
Functional architecture of low-frequency variants highlights strength of negative selection across coding and non-coding annotations
inferredcites →https://doi.org/10.1038/s41588-018-0279-5openalex-snapshot
SumHer better estimates the SNP heritability of complex traits from summary statistics
inferredcites →https://doi.org/10.1038/s41588-019-0379-xopenalex-snapshot
Clinical use of current polygenic risk scores may exacerbate health disparities
inferredcites →https://doi.org/10.1038/s41588-019-0464-1openalex-snapshot
Reconciling S-LDSC and LDAK functional enrichment estimates
inferredcites →https://doi.org/10.1093/gigascience/giz082openalex-snapshot
PRSice-2: Polygenic Risk Score software for biobank-scale data
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Ancestry Composition: A Novel, Efficient Pipeline for Ancestry Deconvolution
inferredcites →https://doi.org/10.1101/375337openalex-snapshot
LDpred-funct: incorporating functional priors improves polygenic prediction accuracy in UK Biobank and 23andMe data sets
inferredcites →https://doi.org/10.1101/gr.169375.113openalex-snapshot
MultiBLUP: improved SNP-based prediction for complex traits
inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
inferredcites →https://doi.org/10.1214/17-aoas1046openalex-snapshot
Bayesian large-scale multiple regression with summary statistics from genome-wide association studies
inferredcites →https://doi.org/10.1371/journal.pcbi.1005589openalex-snapshot
Leveraging functional annotations in genetic risk prediction for human complex diseases
inferredcites →https://doi.org/10.1371/journal.pgen.1004969openalex-snapshot
Simultaneous Discovery, Estimation and Prediction Analysis of Complex Traits Using a Bayesian Mixture Model
inferredcites →https://doi.org/10.1371/journal.pgen.1006493openalex-snapshot
Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data
inferredcites →https://doi.org/10.1371/journal.pgen.1006711openalex-snapshot
Phenome-wide heritability analysis of the UK Biobank
inferredcites →https://doi.org/10.1371/journal.pmed.1001779openalex-snapshot
UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age
inferredcites →https://doi.org/10.2307/2529430openalex-snapshot
Best Linear Unbiased Estimation and Prediction under a Selection Model
inferredcites →https://doi.org/10.48550/arxiv.1209.1341openalex-snapshot
Polygenic Modeling with Bayesian Sparse Linear Mixed Models

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Novel strategy for disease risk prediction incorporating predicted gene expression and DNA methylation data: a multi‐phased study of prostate cancer
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Disease Heritability Enrichment of Regulatory Elements Is Concentrated in Elements with Ancient Sequence Age and Conserved Function across Species
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Polygenic prediction via Bayesian regression and continuous shrinkage priors
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Widespread signatures of natural selection across human complex traits and functional genomic categories
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Incorporating functional priors improves polygenic prediction accuracy in UK Biobank and 23andMe data sets
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Functionally informed fine-mapping and polygenic localization of complex trait heritability
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Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability
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In silico integration of thousands of epigenetic datasets into 707 cell type regulatory annotations improves the trans-ethnic portability of polygenic risk scores
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Polygenic Risk Score Improves the Accuracy of a Clinical Risk Score for Coronary Artery Disease
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Reconciling S-LDSC and LDAK models and functional enrichment estimates
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Genomic Prediction of Complex Disease Risk
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Bayesian analysis of GWAS summary data reveals differential signatures of natural selection across human complex traits and functional genomic categories
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Challenges of Adjusting Single-Nucleotide Polymorphism Effect Sizes for Linkage Disequilibrium
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Integrated Polygenic Tool Substantially Enhances Coronary Artery Disease Prediction
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Predictive Accuracy of a Clinical and Genetic Risk Model for Atrial Fibrillation
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