ArticleGenome research2014
MultiBLUP: improved SNP-based prediction for complex traits.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 164 papers, 3 of them syntheses that pooled it.
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Who cites it
164 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Incorporating functional priors improves polygenic prediction accuracy in UK Biobank and 23andMe data sets.Nature communications · 2021Pooled it
- Validation of Polygenic Scores for QT Interval in Clinical Populations.Circulation. Cardiovascular genetics · 2017Pooled it
- JAM: A Scalable Bayesian Framework for Joint Analysis of Marginal SNP Effects.Genetic epidemiology · 2016Pooled it
- Improving genomic prediction accuracy of complex traits by integrating massive types of functional annotation information.Nature communications · 2026Article
- Integrating network annotation from multiple correlated traits to improve polygenic risk scores based on GWAS summary statistics.Research square · 2026Article
- Estimating the heritability of longitudinal rate-of-change: genetic insights into PSA velocity in prostate cancer-free individuals.Biostatistics (Oxford, England) · 2026Article
- FSBLUP: a novel strategy of fusion similarity matrix construction via optimally integrating intermediate omics data to enhance genomic prediction.Genome biology · 2026Article
- Allelic variation in CYP3A4 and PLB1 drives feed efficiency and immunometabolic resilience in beef cattle.BMC genomics · 2025Article
- Genome Selection for Fleece Traits in Inner Mongolia Cashmere Goats Based on GWAS Prior Marker Information.Animals : an open access journal from MDPI · 2025Article
- MIXED MODELING APPROACH FOR CHARACTERIZING THE GENETIC EFFECTS IN A LONGITUDINAL PHENOTYPE.The annals of applied statistics · 2025Article
- Impact of Selection Signature on Genomic Prediction and Heritability Estimation in Livestock.Animals : an open access journal from MDPI · 2025Article
- Mammary gland multi-omics data reveals new genetic insights into milk production traits in dairy cattle.PLoS genetics · 2025Article
- Evaluation of genomic selection models using whole genome sequence data and functional annotation in Belgian Blue cattle.Genetics, selection, evolution : GSE · 2025Article
- Massively parallel variant-to-function mapping determines functional regulatory variants of non-small cell lung cancer.Nature communications · 2025Article
- Integrating Significant SNPs Identified by GWAS for Genomic Prediction of the Number of Ribs and Carcass Length in Suhuai Pigs.Animals : an open access journal from MDPI · 2025Article
- DeepAnnotation: A novel interpretable deep learning-based genomic selection model that integrates comprehensive functional annotations.GigaScience · 2025Article
- Leveraging haplotype information in heritability estimation and polygenic prediction.Nature communications · 2025Article
- Genetic risk predictions using deep learning models with summary data.Frontiers in bioinformatics · 2025Article
- Optimizing and benchmarking polygenic risk scores with GWAS summary statistics.Genome biology · 2024Article
- Construction and evaluation of a polygenic hazard score for prognostic assessment in localized gastric cancer.Fundamental research · 2024Article
104 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
BLUP (best linear unbiased prediction) is widely used to predict complex traits in plant and animal breeding, and increasingly in human genetics. The BLUP mathematical model, which consists of a single random effect term, was adequate when kinships were measured from pedigrees. However, when genome-wide SNPs are used to measure kinships, the BLUP model implicitly assumes that all SNPs have the same effect-size distribution, which is a severe and unnecessary limitation. We propose MultiBLUP, which extends the BLUP model to include multiple random effects, allowing greatly improved prediction when the random effects correspond to classes of SNPs with distinct effect-size variances. The SNP classes can be specified in advance, for example, based on SNP functional annotations, and we also provide an adaptive procedure for determining a suitable partition of SNPs. We apply MultiBLUP to genome-wide association data from the Wellcome Trust Case Control Consortium (seven diseases), and from much larger studies of celiac disease and inflammatory bowel disease, finding that it consistently provides better prediction than alternative methods. Moreover, MultiBLUP is computationally very efficient; for the largest data set, which includes 12,678 individuals and 1.5 M SNPs, the total analysis can be run on a single desktop PC in less than a day and can be parallelized to run even faster. Tools to perform MultiBLUP are freely available in our software LDAK.
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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.