Admixed and single-continental genome segments of the same ancestry have distinct linkage disequilibrium patterns Article Swipe
Hanbin Lee
,
Moo Hyuk Lee
,
Kangcheng Hou
,
Bogdan Paşaniuc
,
Buhm Han
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1186/s13059-025-03672-w
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1186/s13059-025-03672-w
Background Admixed populations offer valuable insight into the genetic architecture of complex traits. Many studies have proposed methods for genome-wide association study (GWAS) in admixed populations and various simulation studies have evaluated their performances. In this work, we propose another direction of comparison of recently proposed methods for admixed GWAS from a population genetic viewpoint. Results Our theoretical approach mathematically and directly compares the power of methods given that the causal variant is tested. This is done by deriving the variance formula of the methods from the population genetic admixture model. Our results analytically confirm previous observation that the standard GWAS test is more powerful than alternative tests due to leveraging allele frequency heterogeneity in which alternatives do not. As a by-product, we obtain a simple method to improve the power of multi-degrees-of-freedom tests only using summary statistics. We further investigate the problem when the causal variant is not directly known but is detected by tagging variants in linkage disequilibrium (LD). The analysis shows that a genetic segment from admixed genomes may exhibit distinct LD patterns from the single-continental counterpart of the same ancestry. Conclusions While the classic admixture model is successful in predicting GWAS power, its popular extension in the literature falls short in explaining the LD patterns found in simulations and real data, warranting an improved model for LD in admixed genomes.
Related Topics
Concepts
Linkage disequilibrium
Genome-wide association study
Biology
Genetic association
Genetic architecture
Population
Genetics
Evolutionary biology
Disequilibrium
Linkage (software)
Population genetics
Computational biology
Genome
Allele
Single-nucleotide polymorphism
Quantitative trait locus
Genotype
Gene
Haplotype
Sociology
Medicine
Demography
Ophthalmology
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1186/s13059-025-03672-w
- OA Status
- gold
- References
- 70
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4412195571
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4412195571Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1186/s13059-025-03672-wDigital Object Identifier
- Title
-
Admixed and single-continental genome segments of the same ancestry have distinct linkage disequilibrium patternsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-07-11Full publication date if available
- Authors
-
Hanbin Lee, Moo Hyuk Lee, Kangcheng Hou, Bogdan Paşaniuc, Buhm HanList of authors in order
- Landing page
-
https://doi.org/10.1186/s13059-025-03672-wPublisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.1186/s13059-025-03672-wDirect OA link when available
- Concepts
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Linkage disequilibrium, Genome-wide association study, Biology, Genetic association, Genetic architecture, Population, Genetics, Evolutionary biology, Disequilibrium, Linkage (software), Population genetics, Computational biology, Genome, Allele, Single-nucleotide polymorphism, Quantitative trait locus, Genotype, Gene, Haplotype, Sociology, Medicine, Demography, OphthalmologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
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70Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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