ArticleNature communications2022
Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- The landscape of the methodology in drug repurposing using human genomic data: a systematic review.Briefings in bioinformatics · 2024Pooled it
- Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus.Nature communications · 2023Pooled it
- Multi-ancestry transcriptome prediction with functionally informed variants in TOPMed MESA improves performance of transcriptome-wide association studies.American journal of human genetics · 2026Article
- Sex-specific effects ofVeterinary world · 2026Article
- Review
- Review
- GENEasso: a curated resource of credible disease-gene associations across complex diseases from GWAS summary statistics.Nucleic acids research · 2026Article
- Integrating axis quantitative trait loci looks beyond cell types and offers insights into brain-related traits.Nature communications · 2025Article
- A Transcriptome-Wide Association Study Identifies Candidate Susceptibility Loci and Genes for Lung Cancer Risk.Cancer medicine · 2025Article
- DeepWheat: predicting the effects of genomic variants on gene expression and regulatory activities across tissues and varieties in wheat using deep learning.Genome biology · 2025Article
- TransferTWAS: A transfer learning framework for cross-tissue transcriptome-wide association study.American journal of human genetics · 2025Article
- Update on the genetics of allergic diseases.The Journal of allergy and clinical immunology · 2025Review
- FarmGTEx TWAS-server: An Interactive Web Server for Customized TWAS Analysis.Genomics, proteomics & bioinformatics · 2025Article
- An atlas of single-cell eQTLs dissects autoimmune disease genes and identifies novel drug classes for treatment.Cell genomics · 2025Article
- MAAT: a new nonparametric Bayesian framework for incorporating multiple functional annotations in transcriptome-wide association studies.Genome biology · 2025Article
- Multi-INTACT: integrative analysis of the genome, transcriptome, and proteome identifies causal mechanisms of complex traits.Genome biology · 2025Article
- Enhancing disease risk gene discovery by integrating transcription factor-linked trans-variants into transcriptome-wide association analyses.Nucleic acids research · 2025Article
- Transferability of Single- and Cross-Tissue Transcriptome Imputation Models Across Ancestry Groups.Genetic epidemiology · 2025Article
- Epigenetics of Hypertensive Nephropathy.Biomedicines · 2024Review
- Sex-Stratified Genome-Wide Association Study in the Spanish Population Identifies a Novel Locus for Lacunar Stroke.Stroke · 2024Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Transcriptome-wide association studies (TWAS) are popular approaches to test for association between imputed gene expression levels and traits of interest. Here, we propose an integrative method PUMICE (Prediction Using Models Informed by Chromatin conformations and Epigenomics) to integrate 3D genomic and epigenomic data with expression quantitative trait loci (eQTL) to more accurately predict gene expressions. PUMICE helps define and prioritize regions that harbor cis-regulatory variants, which outperforms competing methods. We further describe an extension to our method PUMICE +, which jointly combines TWAS results from single- and multi-tissue models. Across 79 traits, PUMICE + identifies 22% more independent novel genes and increases median chi-square statistics values at known loci by 35% compared to the second-best method, as well as achieves the narrowest credible interval size. Lastly, we perform computational drug repurposing and confirm that PUMICE + outperforms other TWAS methods.
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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.