Genome-wide patterns of population structure and admixture among Hispanic/Latino populations
Open accessAbstract
Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped on the Illumina 610-Quad arrays and 112 Mexicans genotyped on Affymetrix 500K platform. Intersecting these data with previously collected high-density SNP data from 4,305 individuals, we use principal component analysis and clustering methods FRAPPE and STRUCTURE to investigate genome-wide patterns of African, European, and Native American population structure within and among Hispanic/Latino populations. Comparing autosomal, X and Y chromosome, and mtDNA variation, we find evidence of a significant sex bias in admixture proportions consistent with disproportionate contribution of European male and Native American female ancestry to present-day populations. We also find that patterns of linkage-disequilibria in admixed Hispanic/Latino populations are largely affected by the admixture dynamics of the populations, with faster decay of LD in populations of higher African ancestry. Finally, using the locus-specific ancestry inference method LAMP , we reconstruct fine-scale chromosomal patterns of admixture. We document moderate power to differentiate among potential subcontinental source populations within the Native American, European, and African segments of the admixed Hispanic/Latino genomes. Our results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Individuals from countries across South America, the Caribbean, and Mexico have different profiles of genetic ancestry molded by each population's unique history and interactions with local Native American populations.
“Individuals from countries across South America, the Caribbean, and Mexico have different profiles of genetic ancestry molded by each population’s unique history and interactions with local Native American populations.1,19–25”
From The genetic ancestry of African Americans, Latinos, and European Americans across the United States (2015) · cites this paper as [24]
Further stratification of individuals by self-reported population affiliation reveals a diversity in genetic ancestry, consistent with previous work studying these populations.
“Further stratification of individuals by their self-reported population affiliation (e.g., “Mexican,” “Puerto Rican,” or “Dominican”) reveals a diversity in genetic ancestry, consistent with previous work studying these populations (see Figure S5 and Table S5).10,20,24,25,68,69”
From The genetic ancestry of African Americans, Latinos, and European Americans across the United States (2015) · cites this paper as [24]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089 · see citing works
Nelson, M. R., Bryc, K., King, K. S., Indap, A., Boyko, A. R., Novembre, J., Briley, L. P., Maruyama, Y., Waterworth, D. M., Waeber, G., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.08.005 · Cited by 293 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations
Martin, A. R., Gignoux, C. R., Walters, R. K., Wojcik, G. L., Neale, B. M., Gravel, S., Daly, M. J., Bustamante, C. D., & Kenny, E. E. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.03.004 · Cited by 1,391 · see citing works
Self-citationRuns of homozygosity: windows into population history and trait architecture
Ceballos, F. C., Joshi, P. K., Clark, D. W., Ramsay, M., & Wilson, J. F. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.109 · Cited by 1,006 · see citing works
The genetic ancestry of African Americans, Latinos, and European Americans across the United States
Bryc, K., Durand, E. Y., Macpherson, J. M., Reich, D., & Mountain, J. L. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.11.010 · Cited by 712 · see citing works
Self-citationRuiz-Linares, A., Adhikari, K., Acuña-Alonzo, V., Quinto-Sanchez, M., Jaramillo, C., Arias, W., Fuentes, M., Pizarro, M., Everardo, P., de Avila, F., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004572 · Cited by 442 · see citing works
Reconstructing the population genetic history of the Caribbean
Moreno-Estrada, A., Gravel, S., Zakharia, F., McCauley, J. L., Byrnes, J. K., Gignoux, C. R., Ortiz-Tello, P. A., Martínez, R. J., Hedges, D. J., Morris, R. W., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003925 · Cited by 327 · see citing works
Self-citationNative American gene flow into Polynesia predating Easter Island settlement
Ioannidis, A. G., Blanco-Portillo, J., Sandoval, K., Hagelberg, E., Miquel-Poblete, J. F., Moreno-Mayar, J. V., Rodríguez-Rodríguez, J. E., Quinto-Cortés, C. D., Auckland, K., Parks, T., et al. (2020) · Nature · doi:10.1038/s41586-020-2487-2 · Cited by 196 · see citing works
Self-citationOrigins and genetic legacies of the Caribbean Taino
Schroeder, H., Sikora, M., Gopalakrishnan, S., Cassidy, L. M., Maisano Delser, P., Sandoval Velasco, M., Schraiber, J. G., Rasmussen, S., Homburger, J. R., Ávila-Arcos, M. C., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1716839115 · Cited by 126 · see citing works
Self-citationAncestral components of admixed genomes in a Mexican cohort
Johnson, N. A., Coram, M. A., Shriver, M. D., Romieu, I., Barsh, G. S., London, S. J., & Tang, H. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002410 · Cited by 114 · see citing works
History Shaped the Geographic Distribution of Genomic Admixture on the Island of Puerto Rico
Via, M., Gignoux, C. R., Roth, L. A., Fejerman, L., Galanter, J., Choudhry, S., Toro-Labrador, G., Viera-Vera, J., Oleksyk, T. K., Beckman, K., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016513 · Cited by 105 · see citing works
<i>ABCA7</i> frameshift deletion associated with Alzheimer disease in African Americans
Cukier, H. N., Kunkle, B. W., Vardarajan, B. N., Rolati, S., Hamilton-Nelson, K. L., Kohli, M. A., Whitehead, P. L., Dombroski, B. A., Van Booven, D., Lang, R., et al. (2016) · Neurology Genetics · doi:10.1212/nxg.0000000000000079 · Cited by 100 · see citing works
Vardarajan, B. N., Faber, K. M., Bird, T. D., Bennett, D. A., Rosenberg, R., Boeve, B. F., Graff-Radford, N. R., Goate, A. M., Farlow, M., Sweet, R. A., et al. (2014) · JAMA Neurology · doi:10.1001/jamaneurol.2013.5570 · Cited by 73 · see citing works
A call for clinical trial globalization in Alzheimer's disease and related dementia
Llibre‐Guerra, J. J., Heavener, A., Brucki, S. M. D., Marante, J. P. D., Pintado‐Caipa, M., Chen, Y., Behrens, M. I., Hardi, A., Admirall‐Sanchez, A., Akinyemi, R., et al. (2023) · Alzheimer's & Dementia · doi:10.1002/alz.12995 · Cited by 37 · see citing works
Population Genetic Structure and Origins of Native Hawaiians in the Multiethnic Cohort Study
Kim, S. K., Gignoux, C. R., Wall, J. D., Lum-Jones, A., Wang, H., Haiman, C. A., Chen, G. K., Henderson, B. E., Kolonel, L. N., Le Marchand, L., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047881 · Cited by 23 · see citing works
- Authors
- Bryc, K., Velez, C., Karafet, T., Moreno-Estrada, A., Reynolds, A., Auton, A., Hammer, M., Bustamante, C. D., & Ostrer, H.
- Affiliations
- Cornell University (US)
- Human Genetics Program, Department of Pediatrics, New York University School of Medicine, New York, NY 10016;
- University of Arizona (US)
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850;
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2010-05-05
- Volume
- 107
- Issue
- supplement_2
- Pages
- 8954-8961
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC3024022
- OpenAlex
- W2016716898
- Cited by
- 442
- References
- 2
- Citations by year
- 2026: 13 · 2025: 16 · 2024: 22 · 2023: 38 · 2022: 35 · 2021: 24 · 2020: 24 · 2019: 35 · 2018: 28 · 2017: 31 · 2016: 25 · 2015: 35 · 2014: 30 · 2013: 28 · 2012: 31
- FWCI
- 14.96
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM083606)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Race, Genetics, and Society
- Keywords
- Hispanic/Latino populations, admixture, population structure, Native American ancestry, European ancestry, African ancestry, sex-biased admixture, linkage disequilibrium, admixture mapping, genetic ancestry, genome-wide association study, Ecuador, Colombia, Puerto Rico, Dominican Republic
- MeSH terms
- Bayes Theorem, Chromosome Mapping, DNA, Mitochondrial, Female, Genetics, Population, Hispanic or Latino, Humans, Male, Sex Factors, United States, Genome, Human, Cluster Analysis, Computational Biology, Principal Component Analysis, Genome-Wide Association Study
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
