ArticleGenome biology2020
Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers, 2 of them syntheses that pooled it.
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Who cites it
73 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Multi-ancestry meta-analysis and fine-mapping in Alzheimer's disease.Molecular psychiatry · 2023Pooled it
- Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals.Nature genetics · 2023Pooled it
- Reporting and representation of population descriptors in public RNA-seq databases.Cell genomics · 2026Article
- Tissue-resident immune cells drive genetic risk in autoimmune and lung diseases.Nature immunology · 2026Article
- Integrative genetic analysis identifies shared regulation of DNA methylation and gene expression in migraine risk.The journal of headache and pain · 2026Article
- From GWAS Signals to Molecular Mechanisms: Explainable AI for Causal Gene Prioritization and Biomolecular Target Interpretation.Biomolecules · 2026Review
- Evaluating sequence-to-function deep learning models for ancestry-stratified regulatory variant effect prediction using multi-ancestry blood eQTLs.bioRxiv : the preprint server for biology · 2026Article
- The tissue-specific effects of glucose-lowering drug targets on aging mediated through DNA methylation: a multi-omics genetic study.BMC medicine · 2026Article
- Integrative genomics establishes GNL3 as a pleiotropic hub and causal gene for osteoarthritis.Human genomics · 2026Article
- OmiGA for ultra-efficient molecular quantitative trait loci mapping.Nature communications · 2026Article
- Association between genetically predicted expression of TPMT and azathioprine adverse events.BMC pharmacology & toxicology · 2026Article
- Strategies in Global Ancestry and Local Ancestry Inference.Current protocols · 2026Article
- The Genetic Landscape of Androgenetic Alopecia: Current Knowledge and Future Perspectives.Biology · 2026Review
- A Functional Variant ofJournal of asthma and allergy · 2026Article
- Genetic regulation of the plasma proteome and its link to cardiometabolic disease in Greenlandic Inuit.American journal of human genetics · 2025Article
- Article
- Local ancestry-informed GWAS of warfarin dose requirement in African Americans identifies a CYP2C19 splicing QTL.American journal of human genetics · 2025Article
- Methodological opportunities in genomic data analysis to advance health equity.Nature reviews. Genetics · 2025Review
- [Multi-omics analysis of the relationship between oxidative stress-related gene and prostate cancer].Beijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences · 2025Article
- Admixed and single-continental genome segments of the same ancestry have distinct linkage disequilibrium patterns.Genome biology · 2025Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
20 authors.
Funding
Abstract
backgroundPopulation structure among study subjects may confound genetic association studies, and lack of proper correction can lead to spurious findings. The Genotype-Tissue Expression (GTEx) project largely contains individuals of European ancestry, but the v8 release also includes up to 15% of individuals of non-European ancestry. Assessing ancestry-based adjustments in GTEx improves portability of this research across populations and further characterizes the impact of population structure on GWAS colocalization.
resultsHere, we identify a subset of 117 individuals in GTEx (v8) with a high degree of population admixture and estimate genome-wide local ancestry. We perform genome-wide cis-eQTL mapping using admixed samples in seven tissues, adjusted by either global or local ancestry. Consistent with previous work, we observe improved power with local ancestry adjustment. At loci where the two adjustments produce different lead variants, we observe 31 loci (0.02%) where a significant colocalization is called only with one eQTL ancestry adjustment method. Notably, both adjustments produce similar numbers of significant colocalizations within each of two different colocalization methods, COLOC and FINEMAP. Finally, we identify a small subset of eQTL-associated variants highly correlated with local ancestry, providing a resource to enhance functional follow-up.
conclusionsWe provide a local ancestry map for admixed individuals in the GTEx v8 release and describe the impact of ancestry and admixture on gene expression, eQTLs, and GWAS colocalization. While the majority of the results are concordant between local and global ancestry-based adjustments, we identify distinct advantages and disadvantages to each approach.
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