ArticleAmerican journal of human genetics2022
Analyzing and reconciling colocalization and transcriptome-wide association studies from the perspective of inferential reproducibility.
Article in American journal of human genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 4 of them syntheses that pooled it.
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Who cites it
39 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- A contextual genomic perspective on physical activity and its relationship to health, well being and illness.Nature genetics · 2025Pooled it
- Large-scale genome-wide analyses of stuttering.Nature genetics · 2025Pooled it
- Validation of human telomere length multi-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as human telomere length regulation genes.Nature communications · 2024Pooled it
- Transcriptomic risk scores for attention deficit/hyperactivity disorder.Molecular psychiatry · 2023Pooled it
- Post-genome-wide association study variant-to-function challenges in asthma research.The Journal of allergy and clinical immunology · 2026Review
- Multidimensional dissection of shared genetic susceptibility in ulcerative colitis and colorectal cancer: novel insights from integrative single-cell and multi-omics analysis.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Article
- Multivariable genome-wide analysis elucidates the shared genetic architecture, immunosenescence features, and gut-origin therapeutic targets of ulcerative colitis-associated multisystem inflammation.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Article
- Functionally informed cis and trans proteome-wide association studies prioritize disease-critical genes.Research square · 2026Article
- Functionally informed cis and trans proteome-wide association studies prioritize disease-critical genes.medRxiv : the preprint server for health sciences · 2026Article
- Genomics of drug target prioritization for complex diseases.Nature reviews. Genetics · 2026Review
- Farm animal evolution demonstrates hidden molecular basis of human traits.bioRxiv : the preprint server for biology · 2026Article
- Trans-ancestry genome-wide analyses of bipolar disorder in East Asian and European populations improve genetic discovery.Nature neuroscience · 2026Article
- Bridging scales: integrated multi-omics and deep phenotyping for climate resilience in crop plants.Frontiers in plant science · 2026Review
- Challenges and Opportunities in Characterizing the Genetics of Stuttering: From Sample Acquisition to Functional Interpretation of the Genome.Journal of speech, language, and hearing research : JSLHR · 2025Review
- Mitigating inconsistencies in GWAS follow-up analyses with LocusCompare2.Nature genetics · 2025Article
- Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle.Genomics, proteomics & bioinformatics · 2025Article
- Single-cell transcriptome-wide Mendelian randomization and colocalization analyses uncover cell-specific mechanisms in atherosclerotic cardiovascular disease.American journal of human genetics · 2025Article
- Article
- Genetic regulation of gene expression across multiple tissues in chickens.Nature genetics · 2025Article
- Large-scale transcriptomic analyses of major depressive disorder reveal convergent dysregulation of synaptic pathways in excitatory neurons.Nature communications · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Transcriptome-wide association studies and colocalization analysis are popular computational approaches for integrating genetic-association data from molecular and complex traits. They show the unique ability to go beyond variant-level genetic-association evidence and implicate critical functional units, e.g., genes, in disease etiology. However, in practice, when the two approaches are applied to the same molecular and complex-trait data, the inference results can be markedly different. This paper systematically investigates the inferential reproducibility between the two approaches through theoretical derivation, numerical experiments, and analyses of four complex trait GWAS and GTEx eQTL data. We identify two classes of inconsistent inference results. We find that the first class of inconsistent results (i.e., genes with strong colocalization but weak transcriptome-wide association study [TWAS] signals) might suggest an interesting biological phenomenon, i.e., horizontal pleiotropy; thus, the two approaches are truly complementary. The inconsistency in the second class (i.e., genes with weak colocalization but strong TWAS signals) can be understood and effectively reconciled. To this end, we propose a computational approach for locus-level colocalization analysis. We demonstrate that the joint TWAS and locus-level colocalization analysis improves specificity and sensitivity for implicating biologically relevant genes.
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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.