ArticleBioinformatics (Oxford, England)2011
Adjustment for local ancestry in genetic association analysis of admixed populations.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers, 1 of them a synthesis 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
54 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genome-wide association study of white blood cell count in 16,388 African Americans: the continental origins and genetic epidemiology network (COGENT).PLoS genetics · 2011Pooled it
- Genome- and exome-wide association study of serum lipoprotein (a) in the Jackson Heart Study.Journal of human genetics · 2015Trial
- Local ancestry-informed rare variant burden testing improves gene discovery in admixed populations.medRxiv : the preprint server for health sciences · 2026Article
- From individuals to ancestries: Towards attributing trait variation to haplotypes.PLoS genetics · 2025Article
- Admixed and single-continental genome segments of the same ancestry have distinct linkage disequilibrium patterns.Genome biology · 2025Article
- SURFBAT: a surrogate family based association test building on large imputation reference panels.G3 (Bethesda, Md.) · 2025Article
- Opportunities and challenges of local ancestry in genetic association analyses.American journal of human genetics · 2025Review
- Characterizing substructure via mixture modeling in large-scale genetic summary statistics.American journal of human genetics · 2025Article
- Gene expression and splicing QTL analysis of blood cells in African American participants from the Jackson Heart Study.Genetics · 2024Article
- Characterizing substructure via mixture modeling in large-scale genetic summary statistics.bioRxiv : the preprint server for biology · 2024Article
- Strategies for the Genomic Analysis of Admixed Populations.Annual review of biomedical data science · 2023Review
- Impact of cross-ancestry genetic architecture on GWASs in admixed populations.American journal of human genetics · 2023Article
- The immunogenetics of tuberculosis (TB) susceptibility.Immunogenetics · 2023Review
- Impact of cross-ancestry genetic architecture on GWAS in admixed populations.bioRxiv : the preprint server for biology · 2023Article
- Incorporating local ancestry improves identification of ancestry-associated methylation signatures and meQTLs in African Americans.Communications biology · 2022Article
- Article
- Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases.International journal of molecular sciences · 2021Review
- locStra: Fast analysis of regional/global stratification in whole-genome sequencing studies.Genetic epidemiology · 2021Article
- An Overview of Strategies for Detecting Genotype-Phenotype Associations Across Ancestrally Diverse Populations.Frontiers in genetics · 2021Review
- Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx.Genome biology · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationAdmixed populations offer a unique opportunity for mapping diseases that have large disease allele frequency differences between ancestral populations. However, association analysis in such populations is challenging because population stratification may lead to association with loci unlinked to the disease locus. METHODS AND
resultsWe show that local ancestry at a test single nucleotide polymorphism (SNP) may confound with the association signal and ignoring it can lead to spurious association. We demonstrate theoretically that adjustment for local ancestry at the test SNP is sufficient to remove the spurious association regardless of the mechanism of population stratification, whether due to local or global ancestry differences among study subjects; however, global ancestry adjustment procedures may not be effective. We further develop two novel association tests that adjust for local ancestry. Our first test is based on a conditional likelihood framework which models the distribution of the test SNP given disease status and flanking marker genotypes. A key advantage of this test lies in its ability to incorporate different directions of association in the ancestral populations. Our second test, which is computationally simpler, is based on logistic regression, with adjustment for local ancestry proportion. We conducted extensive simulations and found that the Type I error rates of our tests are under control; however, the global adjustment procedures yielded inflated Type I error rates when stratification is due to local ancestry difference.
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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.