SynthesisNature communications2022
GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies.
Synthesis in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Robust Inference With Ghostknockoffs in Genome-Wide Association Studies With Sample Relatedness.Genetic epidemiology · 2026Article
- CIT-Lasso: a scalable approach beyond guilty by association for identifying causal variants from genome-wide summary statistics.Genome biology · 2026Article
- Implications of autolysosome- astrocyte-associated signature in the pathogenesis of Alzheimer's disease: evidence from artificial intelligence and multi-omics and clinical validation.Frontiers in neuroscience · 2026Article
- Identification and validation of circadian rhythm and astrocyte-associated diagnostic and therapeutic model for cirrhosis encephalopathy patients via integrative bioinformatic pipelines andFrontiers in neuroscience · 2026Article
- Reflection knockoffs via householder reflection: applications in proteomics and genetic fine mapping.Genetics · 2025Article
- Fast Probabilistic Whitening Transformation for Ultra-High Dimensional Genetic Data.bioRxiv : the preprint server for biology · 2025Article
- Quantifying interventional causality by knockoff operation.Science advances · 2025Article
- Knockoff procedure improves susceptibility gene identifications in conditional transcriptome-wide association studies.American journal of human genetics · 2025Article
- Distilling Direct Effects via Conditional Differential Gene Expression Analysis.bioRxiv : the preprint server for biology · 2025Article
- It's a wrap: deriving distinct discoveries with FDR control after a GWAS pipeline.bioRxiv : the preprint server for biology · 2025Article
- A statistical view of column subset selection.Journal of the Royal Statistical Society. Series B, Statistical methodology · 2025Article
- Alzheimer's Disease Sequencing Project release 4 whole genome sequencing dataset.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Alzheimer's Disease Sequencing Project Release 4 Whole Genome Sequencing Dataset.medRxiv : the preprint server for health sciences · 2024Article
- Local genetic correlation via knockoffs reduces confounding due to cross-trait assortative mating.American journal of human genetics · 2024Article
- Second-order group knockoffs with applications to genome-wide association studies.Bioinformatics (Oxford, England) · 2024Article
- TWAS-GKF: a novel method for causal gene identification in transcriptome-wide association studies with knockoff inference.Bioinformatics (Oxford, England) · 2024Article
- KnockoffHybrid: A knockoff framework for hybrid analysis of trio and population designs in genome-wide association studies.American journal of human genetics · 2024Article
- Article
- Article
- Improving fine-mapping by modeling infinitesimal effects.Nature genetics · 2024Article
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Authors and funding
15 authors.
Funding
Abstract
Recent advances in genome sequencing and imputation technologies provide an exciting opportunity to comprehensively study the contribution of genetic variants to complex phenotypes. However, our ability to translate genetic discoveries into mechanistic insights remains limited at this point. In this paper, we propose an efficient knockoff-based method, GhostKnockoff, for genome-wide association studies (GWAS) that leads to improved power and ability to prioritize putative causal variants relative to conventional GWAS approaches. The method requires only Z-scores from conventional GWAS and hence can be easily applied to enhance existing and future studies. The method can also be applied to meta-analysis of multiple GWAS allowing for arbitrary sample overlap. We demonstrate its performance using empirical simulations and two applications: (1) a meta-analysis for Alzheimer's disease comprising nine overlapping large-scale GWAS, whole-exome and whole-genome sequencing studies and (2) analysis of 1403 binary phenotypes from the UK Biobank data in 408,961 samples of European ancestry. Our results demonstrate that GhostKnockoff can identify putatively functional variants with weaker statistical effects that are missed by conventional association tests.
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