ArticleProceedings of the National Academy of Sciences of the United States of America2021
Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genome-wide analysis of common and rare variants via multiple knockoffs at biobank scale, with an application to Alzheimer disease genetics.American journal of human genetics · 2021Pooled it
- Hi-C informed kernel association test for integrating 3D genome structure into variant-set analysis.Briefings in bioinformatics · 2026Article
- An empirical Bayes framework for burden and dispersion association tests helps prioritize rare variants associated with Alzheimer's disease.medRxiv : the preprint server for health sciences · 2026Article
- Article
- Integrative Analysis of Vitamin D-Associated Genetic Variants Reveals Cis-Regulatory Architecture and Multigenic Mechanisms Underlying Chronic Disease-Relevant Pathways.Human mutation · 2026Article
- Hi-C informed kernel association test: integrating 3-dimensional genome structure into variant-set association for whole-genome sequencing data.bioRxiv : the preprint server for biology · 2025Article
- Leveraging functional annotations to map rare variants associated with Alzheimer disease with gruyere.American journal of human genetics · 2025Article
- RetroFun-RVS: A Retrospective Family-Based Framework for Rare Variant Analysis Incorporating Functional Annotations.Genetic epidemiology · 2025Article
- Genome-wide association neural networks identify genes linked to family history of Alzheimer's disease.Briefings in bioinformatics · 2024Article
- KnockoffHybrid: A knockoff framework for hybrid analysis of trio and population designs in genome-wide association studies.American journal of human genetics · 2024Article
- A Large-Scale Candidate-Gene Association Mapping for Drought Tolerance and Agronomic Traits in Sugarcane.International journal of molecular sciences · 2023Article
- BIGKnock: fine-mapping gene-based associations via knockoff analysis of biobank-scale data.Genome biology · 2023Article
- Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
Gene-based tests are valuable techniques for identifying genetic factors in complex traits. Here, we propose a gene-based testing framework that incorporates data on long-range chromatin interactions, several recent technical advances for region-based tests, and leverages the knockoff framework for synthetic genotype generation for improved gene discovery. Through simulations and applications to genome-wide association studies (GWAS) and whole-genome sequencing data for multiple diseases and traits, we show that the proposed test increases the power over state-of-the-art gene-based tests in the literature, identifies genes that replicate in larger studies, and can provide a more narrow focus on the possible causal genes at a locus by reducing the confounding effect of linkage disequilibrium. Furthermore, our results show that incorporating genetic variation in distal regulatory elements tends to improve power over conventional tests. Results for UK Biobank and BioBank Japan traits are also available in a publicly accessible database that allows researchers to query gene-based results in an easy fashion.
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Registered trials
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