ArticleBMC genetics2015
Leveraging local ancestry to detect gene-gene interactions in genome-wide data.
Article in BMC genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 25 citations in OpenAlex.
- Hidden structure in polygenic scores and the challenge of disentangling ancestry interactions in admixed populations.Genetics · 2025Article
- CADET: Enhanced transcriptome-wide association analyses in admixed samples using eQTL summary data.American journal of human genetics · 2025Article
- SURFBAT: a surrogate family based association test building on large imputation reference panels.G3 (Bethesda, Md.) · 2025Article
- Characterizing features affecting local ancestry inference performance in admixed populations.American journal of human genetics · 2025Article
- Haplotype analysis incorporating ancestral origins identified novel genetic loci associated with chicken body weight using an advanced intercross line.Genetics, selection, evolution : GSE · 2024Article
- Characterizing features affecting local ancestry inference performance in admixed populations.bioRxiv : the preprint server for biology · 2024Article
- Identifying QTLs involved in hybrid performance and heterotic group complementarity: new GWAS models applied to factorial and admixed diallel maize hybrid panels.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Strategies for the Genomic Analysis of Admixed Populations.Annual review of biomedical data science · 2023Review
- Tractor uses local ancestry to enable the inclusion of admixed individuals in GWAS and to boost power.Nature genetics · 2021Article
- Admixed Populations Improve Power for Variant Discovery and Portability in Genome-Wide Association Studies.Frontiers in genetics · 2021Article
- Mixed-model admixture mapping identifies smoking-dependent loci of lung function in African Americans.European journal of human genetics : EJHG · 2020Article
- A comprehensive survey of models for dissecting local ancestry deconvolution in human genome.Briefings in bioinformatics · 2019Article
- The clinical imperative for inclusivity: Race, ethnicity, and ancestry (REA) in genomics.Human mutation · 2018Article
- An ancestry-based approach for detecting interactions.Genetic epidemiology · 2018Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundAlthough genome-wide association studies have successfully identified thousands of variants associated to complex traits, these variants only explain a small amount of the entire heritability of the trait. Gene-gene interactions have been proposed as a source to explain a significant percentage of the missing heritability. However, detecting gene-gene interactions has proven to be very difficult due to computational and statistical challenges. The vast number of possible interactions that can be tested induces very stringent multiple hypotheses corrections that limit the power of detection. These issues have been mostly highlighted for the identification of pairwise effects and are even more challenging when addressing higher order interaction effects. In this work we explore the use of local ancestry in recently admixed individuals to find signals of gene-gene interaction on human traits and diseases.
resultsWe introduce statistical methods that leverage the correlation between local ancestry and the hidden unknown causal variants to find distant gene-gene interactions. We show that the power of this test increases with the number of causal variants per locus and the degree of differentiation of these variants between the ancestral populations. Overall, our simulations confirm that local ancestry can be used to detect gene-gene interactions, solving the computational bottleneck. When compared to a single nucleotide polymorphism (SNP)-based interaction screening of the same sample size, the power of our test was lower on all settings we considered. However, accounting for the dramatic increase in sample size that can be achieve when genotyping only a set of ancestry informative markers instead of the whole genome, we observe substantial gain in power in several scenarios.
conclusionLocal ancestry-based interaction tests offer a new path to the detection of gene-gene interaction effects. It would be particularly useful in scenarios where multiple differentiated variants at the interacting loci act in a synergistic manner.
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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.