ArticlePLoS genetics2010
Rapid assessment of genetic ancestry in populations of unknown origin by genome-wide genotyping of pooled samples.
Article in PLoS genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed.
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- Population structure and breed identification of Chinese indigenous sheep breeds using whole genome SNPs and InDels.Genetics, selection, evolution : GSE · 2024Article
- Definition of metafounders based on population structure analysis.Genetics, selection, evolution : GSE · 2024Article
- A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond.International journal of molecular sciences · 2023Article
- A Novel Insight into the Identification of Potential SNP Markers for the Genomic Characterization of Buffalo Breeds in Pakistan.Animals : an open access journal from MDPI · 2023Article
- Breed identification using breed-informative SNPs and machine learning based on whole genome sequence data and SNP chip data.Journal of animal science and biotechnology · 2023Article
- Variance component estimation and genome-wide association of predicted methane production in crossbred beef steers.Journal of animal science · 2023Article
- Heritability and variance component estimation for feed and water intake behaviors of feedlot cattle.Journal of animal science · 2023Article
- Estimation of dam line composition of 3-way crossbred animals using genomic information.Genetics, selection, evolution : GSE · 2022Article
- Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits-The Hispanic/Latino Anthropometry Consortium.HGG advances · 2022Article
- Unraveling genetic admixture in the Indian crossbred cattle by different approaches using Bovine 50K BeadChip.Tropical animal health and production · 2022Article
- The impact of using different ancestral reference populations in assessing crossbred population admixture and influence on performance.Frontiers in genetics · 2022Article
- Summix: A method for detecting and adjusting for population structure in genetic summary data.American journal of human genetics · 2021Article
- Editorial: Advances in Genomics of Crossbred Farm Animals.Frontiers in genetics · 2021Article
- A low-density SNP genotyping panel for the accurate prediction of cattle breeds.Journal of animal science · 2020Article
- Estimation of Genomic Breed Composition for Purebred and Crossbred Animals Using Sparsely Regularized Admixture Models.Frontiers in genetics · 2020Article
- A Causality Perspective of Genomic Breed Composition for Composite Animals.Frontiers in genetics · 2020Article
- Characterization of water intake and water efficiency in beef cattle1,2.Journal of animal science · 2019Article
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Authors and funding
20 authors.
Funding
Abstract
As we move forward from the current generation of genome-wide association (GWA) studies, additional cohorts of different ancestries will be studied to increase power, fine map association signals, and generalize association results to additional populations. Knowledge of genetic ancestry as well as population substructure will become increasingly important for GWA studies in populations of unknown ancestry. Here we propose genotyping pooled DNA samples using genome-wide SNP arrays as a viable option to efficiently and inexpensively estimate admixture proportion and identify ancestry informative markers (AIMs) in populations of unknown origin. We constructed DNA pools from African American, Native Hawaiian, Latina, and Jamaican samples and genotyped them using the Affymetrix 6.0 array. Aided by individual genotype data from the African American cohort, we established quality control filters to remove poorly performing SNPs and estimated allele frequencies for the remaining SNPs in each panel. We then applied a regression-based method to estimate the proportion of admixture in each cohort using the allele frequencies estimated from pooling and populations from the International HapMap Consortium as reference panels, and identified AIMs unique to each population. In this study, we demonstrated that genotyping pooled DNA samples yields estimates of admixture proportion that are both consistent with our knowledge of population history and similar to those obtained by genotyping known AIMs. Furthermore, through validation by individual genotyping, we demonstrated that pooling is quite effective for identifying SNPs with large allele frequency differences (i.e., AIMs) and that these AIMs are able to differentiate two closely related populations (HapMap JPT and CHB).
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