ArticleHeredity2016
EigenGWAS: finding loci under selection through genome-wide association studies of eigenvectors in structured populations.
Article in Heredity, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- UK BioCoin: swift trait-specific summary statistics regression for UK Biobank.Nature communications · 2026Article
- Identifying Adaptive Footprints in the Presence of Demographic Uncertainty.Genome biology and evolution · 2026Article
- IPGCA: A Comprehensive Single Cell Atlas of 1 074 127 Porcine Intestinal Cells Revealing Cellular Dynamics, Genetic Regulation, and Cross-Species Conservation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- X-LDR: an atlas of linkage disequilibrium across species.Genome biology · 2025Article
- Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi.Genome biology · 2025Article
- Integrating parental genomes to reduce reference bias and identify intramuscular fat genes in Qinchuan Black pigs.Journal of animal science and biotechnology · 2025Article
- Precise estimation of in-depth relatedness in biobank-scale datasets using deepKin.Cell reports methods · 2025Article
- Deciphering genetic characteristics of South China and North China indigenous pigs through selection signatures.BMC genomics · 2024Article
- Rapid genetic adaptation to a novel ecosystem despite a large founder event.Molecular ecology · 2024Article
- Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm.Scientific reports · 2024Article
- PigBiobank: a valuable resource for understanding genetic and biological mechanisms of diverse complex traits in pigs.Nucleic acids research · 2024Article
- Genomic basis of selective breeding from the closest wild relative of large-fruited tomato.Horticulture research · 2023Article
- Discovering Loci for Breeding Prospective and Phenology in Wheat Mediterranean Landraces by Environmental and eigenGWAS.International journal of molecular sciences · 2023Article
- Genetic networks underlying salinity tolerance in wheat uncovered with genome-wide analyses and selective sweeps.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Genome-wide association study of eigenvectors provides genetic insights into selective breeding for tomato metabolites.BMC biology · 2022Article
- Trends of genetic changes uncovered by Env- and Eigen-GWAS in wheat and barley.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- GWAS Case Studies in Wheat.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Genetic Diversity and Selection Signatures in Synthetic-Derived Wheats and Modern Spring Wheat.Frontiers in plant science · 2022Article
- Inflammation and immunity connect hypertension with adverse COVID-19 outcomes.Frontiers in genetics · 2022Article
- Shared genetic liability between major depressive disorder and osteoarthritis.Bone & joint research · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We develop a novel approach to identify regions of the genome underlying population genetic differentiation in any genetic data where the underlying population structure is unknown, or where the interest is assessing divergence along a gradient. By combining the statistical framework for genome-wide association studies (GWASs) with eigenvector decomposition (EigenGWAS), which is commonly used in population genetics to characterize the structure of genetic data, loci under selection can be identified without a requirement for discrete populations. We show through theory and simulation that our approach can identify regions under selection along gradients of ancestry, and in real data we confirm this by demonstrating LCT to be under selection between HapMap CEU-TSI cohorts, and we then validate this selection signal across European countries in the POPRES samples. HERC2 was also found to be differentiated between both the CEU-TSI cohort and within the POPRES sample, reflecting the likely anthropological differences in skin and hair colour between northern and southern European populations. Controlling for population stratification is of great importance in any quantitative genetic study and our approach also provides a simple, fast and accurate way of predicting principal components in independent samples. With ever increasing sample sizes across many fields, this approach is likely to be greatly utilized to gain individual-level eigenvectors avoiding the computational challenges associated with conducting singular value decomposition in large data sets. We have developed freely available software, Genetic Analysis Repository (GEAR), to facilitate the application of the methods.
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