The Population Reference Sample, POPRES: A Resource for Population, Disease, and Pharmacological Genetics Research
Open accessAbstract
Technological and scientific advances, stemming in large part from the Human Genome and HapMap projects, have made large-scale, genome-wide investigations feasible and cost effective. These advances have the potential to dramatically impact drug discovery and development by identifying genetic factors that contribute to variation in disease risk as well as drug pharmacokinetics, treatment efficacy, and adverse drug reactions. In spite of the technological advancements, successful application in biomedical research would be limited without access to suitable sample collections. To facilitate exploratory genetics research, we have assembled a DNA resource from a large number of subjects participating in multiple studies throughout the world. This growing resource was initially genotyped with a commercially available genome-wide 500,000 single-nucleotide polymorphism panel. This project includes nearly 6,000 subjects of African-American, East Asian, South Asian, Mexican, and European origin. Seven informative axes of variation identified via principal-component analysis (PCA) of these data confirm the overall integrity of the data and highlight important features of the genetic structure of diverse populations. The potential value of such extensively genotyped collections is illustrated by selection of genetically matched population controls in a genome-wide analysis of abacavir-associated hypersensitivity reaction. We find that matching based on country of origin, identity-by-state distance, and multidimensional PCA do similarly well to control the type I error rate. The genotype and demographic data from this reference sample are freely available through the NCBI database of Genotypes and Phenotypes (dbGaP).
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?
Regions of the genome that have structural variation or show strong linkage disequilibrium (LD) have been shown both to confound admixture mapping and to influence the detection of population substructure in studies using Principal Components Analysis (PCA).
“Regions of the genome that have structural variation or show strong linkage disequilibrium (LD) have been shown both to confound admixture mapping and to influence the detection of population substructure in studies using Principal Components Analysis (PCA).27,63,65”
From The genetic ancestry of African Americans, Latinos, and European Americans across the United States (2015) · cites this paper as [63]
Split into 2 atoms — 0 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 1 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredThe use of four-grandparent birth-country has been utilized as a proxy for assessing ancestry.
“The use of four-grandparent birth-country has been utilized as a proxy for assessing ancestry.27,63”
From The genetic ancestry of African Americans, Latinos, and European Americans across the United States (2015) · cites this paper as [63]
The Introduction (page unavailable) says the CoLaus data included grandparental countries of birth, and the Results (page unavailable) lists grandparental birthplaces among the demographic information available for some POPRES subjects. The paper does not say that the birth countries of all four grandparents were used as a proxy to assess ancestry; its reported ancestry analysis uses genotype-based principal components. (LLM, conf=0.78)
Experimental — accuracy not yet measured
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
Part of this paper’s reference list could not be split into single entries.
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
Principal components analysis corrects for stratification in genome-wide association studies
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006) · Nature Genetics · doi:10.1038/ng1847 · Cited by 10,248 · see citing works
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
The Wellcome Trust Case Control Consortium, Management Committee, Burton, P. R., Clayton, D. G., Cardon, L. R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D. P., McCarthy, M. I., et al. (2007) · Nature · doi:10.1038/nature05911 · Cited by 9,442 · see citing works
A haplotype map of the human genome
The International HapMap Consortium (2005) · Nature · doi:10.1038/nature04226 · Cited by 5,858 · see citing works
Population Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280 · see citing works
Yu, J., Pressoir, G., Briggs, W. H., Bi, I. V., Yamasaki, M., Doebley, J., McMullen, M. D., Gaut, B. S., Nielsen, D. M., Holland, J. B., et al. (2005) · Nature Genetics · doi:10.1038/ng1702 · Cited by 4,155 · see citing works
Genetic Dissection of Complex Traits
Lander, E. S., & Schork, N. J. (1994) · Science · doi:10.1126/science.8091226 · Cited by 3,425 · see citing works
Genomic Control for Association Studies
Devlin, B., & Roeder, K. (1999) · Biometrics · doi:10.1111/j.0006-341x.1999.00997.x · Cited by 3,162 · see citing works
Browning, S. R., & Browning, B. L. (2007) · The American Journal of Human Genetics · doi:10.1086/521987 · Cited by 3,138 · see citing works
Genetic Structure of Human Populations
Rosenberg, N. A., Pritchard, J. K., Weber, J. L., Cann, H. M., Kídd, K. K., Анатольевич, Ж. Л., & Feldman, M. W. (2002) · Science · doi:10.1126/science.1078311 · Cited by 2,961 · see citing works
Genome-wide association studies for complex traits: consensus, uncertainty and challenges
McCarthy, M. I., Abecasis, G. R., Cardon, L. R., Goldstein, D. B., Little, J., Ioannidis, J. P. A., & Hirschhorn, J. N. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2344 · Cited by 2,891 · see citing works
A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants
Scott, L. J., Mohlke, K. L., Bonnycastle, L. L., Willer, C. J., Li, Y., Duren, W. L., Erdos, M. R., Stringham, H. M., Chines, P. S., Jackson, A. U., et al. (2007) · Science · doi:10.1126/science.1142382 · Cited by 2,753 · see citing works
The Wellcome Trust Case Control Consortium, U.K.
Mossman, K. (2008) · Scientific American · doi:10.1038/scientificamerican0108-42a · Cited by 2,714 · see citing works
A new multipoint method for genome-wide association studies by imputation of genotypes
Marchini, J., Howie, B., Myers, S., McVean, G., & Donnelly, P. (2007) · Nature Genetics · doi:10.1038/ng2088 · Cited by 2,609 · see citing works
Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation
Li, J. Z., Absher, D. M., Tang, H., Southwick, A. M., Casto, A. M., Ramachandran, S., Cann, H. M., Barsh, G. S., Feldman, M. W., Cavalli-Sforza, L. L., et al. (2008) · Science · doi:10.1126/science.1153717 · Cited by 1,915 · see citing works
Genes mirror geography within Europe
Novembre, J., Johnson, T., Bryc, K., Kutalik, Z., Boyko, A. R., Auton, A., Indap, A., King, K. S., Bergmann, S., Nelson, M. R., et al. (2008) · Nature · doi:10.1038/nature07331 · Cited by 1,479 · see citing works
Self-citationThe NCBI dbGaP database of genotypes and phenotypes
Mailman, M., Feolo, M., Jin, Y., Kimura, M., Tryka, K., Bagoutdinov, R., Hao, L., Kiang, A., Paschall, J., Phan, L., et al. (2007) · Nature Genetics · doi:10.1038/ng1007-1181 · Cited by 1,122 · see citing works
Genotype, haplotype and copy-number variation in worldwide human populations
Jakobsson, M., Scholz, S. W., Scheet, P. A., Gibbs, J. R., Canzoniero, J. V., Fung, H., Szpiech, Z. A., Degnan, J. H., Wang, K., Guerreiro, R. J., et al. (2008) · Nature · doi:10.1038/nature06742 · Cited by 871 · see citing works
Firmann, M., Mayor, V., Marques-Vidal, P. M., Bochud, M., Pécoud, A. R., Hayoz, D., Paccaud, F. M., Preisig, M., Song, K. S., Yuan, X., et al. (2008) · BMC Cardiovascular Disorders · doi:10.1186/1471-2261-8-6 · Cited by 715 · see citing works
Self-citationInterpreting principal component analyses of spatial population genetic variation
Novembre, J., & Stephens, M. (2008) · Nature Genetics · doi:10.1038/ng.139 · Cited by 663 · see citing works
Self-citationAscertainment bias in studies of human genome-wide polymorphismPreprint
Clark, A. G., Hubisz, M. J., Bustamante, C. D., Williamson, S., & Nielsen, R. (2005) · Genome Research · doi:10.1101/gr.4107905 · Cited by 503 · see citing works
Self-citationMethods for High-Density Admixture Mapping of Disease Genes
Patterson, N. J., Hattangadi, N., Lane, B., Lohmueller, K. E., Hafler, D. A., Oksenberg, J. R., Hauser, S. L., Smith, M. W., O’Brien, S. J., Altshuler, D., et al. (2004) · The American Journal of Human Genetics · doi:10.1086/420871 · Cited by 472 · see citing works
Self-citationProportionally more deleterious genetic variation in European than in African populations
Lohmueller, K. E., Indap, A. R., Schmidt, S., Boyko, A. R., Hernandez, R. D., Hubisz, M. J., Sninsky, J. J., White, T. J., Sunyaev, S. R., Nielsen, R., et al. (2008) · Nature · doi:10.1038/nature06611 · Cited by 363 · see citing works
Self-citationTrends in the globalization of clinical trials
Thiers, F. A., Sinskey, A. J., & Berndt, E. R. (2007) · Nature Reviews Drug Discovery · doi:10.1038/nrd2441 · Cited by 363 · see citing works
Mapping Multiple Sclerosis Susceptibility to the HLA-DR Locus in African Americans
Oksenberg, J. R., Barcellos, L. F., Cree, B., Baranzini, S. E., Bugawan, T. L., Khan, O. A., Lincoln, R., Swerdlin, A., Mignot, E. J.-M., Lin, L., et al. (2004) · The American Journal of Human Genetics · doi:10.1086/380997 · Cited by 334 · see citing works
Self-citationGenome-wide scan identifies variation in MLXIPL associated with plasma triglycerides
Kooner, J. S., Chambers, J. C., Aguilar-Salinas, C. A., Hinds, D. A., Hyde, C. L., Warnes, G. R., Pérez, F. J. G., Frazer, K. A., Elliott, P., Scott, J., et al. (2008) · Nature Genetics · doi:10.1038/ng.2007.61 · Cited by 329 · see citing works
Self-citationManolio, T. A., Rodriguez, L. L., Brooks, L., Guttmacher, A. E., Harris, E. L., Collins, F. S., Abecasis, G. R., Ballinger, D. G., Frazer, K. A., Daly, M. J., et al. (2007) · Nature Genetics · doi:10.1038/ng2127 · Cited by 316 · see citing works
Analysis and application of European genetic substructure using 300 K SNP information
Tian, C., Plenge, R. M., Ransom, M., Lee, A., Villoslada, P., Selmi, C., Klareskog, L., Pulver, A. E., Qi, L., Gregersen, P. K., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.0040004 · Cited by 247 · see citing works
Chen, J., Iannone, M. A., Li, M.-S., Taylor, J. D., Rivers, P., Nelsen, A. J., Slentz‐Kesler, K., Roses, A. D., & Weiner, M. P. (2000) · Genome Research · doi:10.1101/gr.10.4.549 · Cited by 211 · see citing works
Self-citationMeasuring European Population Stratification with Microarray Genotype Data
Bauchet, M., McEvoy, B., Pearson, L. N., Quillen, E. E., Sarkisian, T., Hovhannesyan, K., Deka, R., Bradley, D. G., & Shriver, M. D. (2007) · The American Journal of Human Genetics · doi:10.1086/513477 · Cited by 163 · see citing works
Luca, D., Ringquist, S., Klei, L., Lee, A. B., Gieger, C., Wichmann, H.-E., Schreiber, S., Krawczak, M., Lu, Y., Styche, A., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.11.003 · Cited by 128 · see citing works
Genome-wide approaches to identify pharmacogenetic contributions to adverse drug reactions
Nelson, M. R., Bacanu, S., Mosteller, M., Li, L.-L., Bowman, C. E., Roses, A. D., Lai, E., & Ehm, M. G. (2008) · The Pharmacogenomics Journal · doi:10.1038/tpj.2008.4 · Cited by 108 · see citing works
Self-citationMatching Strategies for Genetic Association Studies in Structured Populations
Hinds, D. A., Stokowski, R. P., Patil, N., Konvicka, K., Kershenobich, D., Cox, D., & Ballinger, D. G. (2004) · The American Journal of Human Genetics · doi:10.1086/381716 · Cited by 99 · see citing works
Genes mirror geography within Europe
Novembre, J., Johnson, T., Bryc, K., Kutalik, Z., Boyko, A. R., Auton, A., Indap, A. R., King, K. S., Bergmann, S., Nelson, M. R., et al. (2008) · Nature · doi:10.1038/nature07566 · Cited by 41 · see citing works
Self-citation
Flagged first, then by citations
1 of the 36 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- [11]11. International Conference on Harmonization E15 Definitions for genomic biomarkers, pharmacogenomics, pharmacogenetics, genomic data and sample coding categories Federal Register. 2008; 78:19074-19076 Google Scholar
Cited by
Sorted by citations
STING is an endoplasmic reticulum adaptor that facilitates innate immune signalling
Ishikawa, H., & Barber, G. N. (2008) · Nature · doi:10.1038/nature07317 · Cited by 3,576 · see citing works
Ancient Admixture in Human History
Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T., & Reich, D. (2012) · Genetics · doi:10.1534/genetics.112.145037 · Cited by 2,848 · see citing works
Genes mirror geography within Europe
Novembre, J., Johnson, T., Bryc, K., Kutalik, Z., Boyko, A. R., Auton, A., Indap, A., King, K. S., Bergmann, S., Nelson, M. R., et al. (2008) · Nature · doi:10.1038/nature07331 · Cited by 1,479 · see citing works
Self-citationAncient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357 · see citing works
HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin
study, F. T. D., Daly, A. K., Donaldson, P. T., Bhatnagar, P., Shen, Y., Pe’er, I., Floratos, A., Daly, M. J., Goldstein, D. B., John, S., et al. (2009) · Nature Genetics · doi:10.1038/ng.379 · Cited by 1,041 · see citing works
Self-citationRFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference
Maples, B. K., Gravel, S., Kenny, E. E., & Bustamante, C. D. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.06.020 · Cited by 900 · see citing works
Self-citationPopulation differentiation as a test for selective sweepsPreprint
Chen, H., Patterson, N. J., & Reich, D. (2010) · Genome Research · doi:10.1101/gr.100545.109 · Cited by 888 · 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-citationAn abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people
Nelson, M. R., Wegmann, D., Ehm, M. G., Kessner, D., St. Jean, P., Verzilli, C., Shen, J., Tang, Z., Bacanu, S.-A., Fraser, D., et al. (2012) · Science · doi:10.1126/science.1217876 · Cited by 647 · see citing works
Self-citationVisualizing spatial population structure with estimated effective migration surfaces
Petkova, D., Novembre, J., & Stephens, M. (2015) · Nature Genetics · doi:10.1038/ng.3464 · Cited by 624 · see citing works
Self-citationOrigins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe
Skoglund, P., Malmström, H., Raghavan, M., Storå, J., Hall, P. N., Willerslev, E., Gilbert, M. T. P., Götherström, A., & Jakobsson, M. (2012) · Science · doi:10.1126/science.1216304 · Cited by 593 · see citing works
The genetics of Mexico recapitulates Native American substructure and affects biomedical traits
Moreno-Estrada, A., Gignoux, C. R., Fernández-López, J. C., Zakharia, F., Sikora, M., Contreras, A. V., Acuña-Alonzo, V., Sandoval, K., Eng, C., Romero-Hidalgo, S., et al. (2014) · Science · doi:10.1126/science.1251688 · Cited by 478 · see citing works
Self-citationLucena, M. I., Molokhia, M., Shen, Y., Urban, T. J., Aithal, G. P., Andrade, R. J., Day, C. P., Ruiz‐Cabello, F., Donaldson, P. T., Stephens, C. M., et al. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.04.001 · Cited by 474 · see citing works
Self-citationNew insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing
Keller, A., Graefen, A., Ball, M., Matzas, M., Boisguerin, V., Maixner, F., Leidinger, P., Backes, C., Khairat, R., Forster, M., et al. (2012) · Nature Communications · doi:10.1038/ncomms1701 · Cited by 437 · see citing works
Self-citationGenome-wide patterns of population structure and admixture in West Africans and African Americans
Bryc, K., Auton, A., Nelson, M. R., Oksenberg, J. R., Hauser, S. L., Williams, S., Froment, A., Bodo, J.-M., Wambebe, C., Tishkoff, S. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909559107 · Cited by 455 · see citing works
Self-citationDerived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European
Olalde, I., Allentoft, M. E., Sánchez-Quinto, F., Santpere, G., Chiang, C. W. K., DeGiorgio, M., Prado-Martinez, J., Rodríguez, J. A., Rasmussen, S., Quilez, J., et al. (2014) · Nature · doi:10.1038/nature12960 · Cited by 360 · see citing works
Self-citationThe Geography of Recent Genetic Ancestry across Europe
Ralph, P. L., & Coop, G. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001555 · Cited by 374 · see citing works
Genome-wide patterns of population structure and admixture among Hispanic/Latino populations
Bryc, K., Velez, C., Karafet, T., Moreno-Estrada, A., Reynolds, A., Auton, A., Hammer, M., Bustamante, C. D., & Ostrer, H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914618107 · Cited by 442 · see citing works
Self-citationSidore, C., Busonero, F., Maschio, A., Porcu, E., Naitza, S., Żołędziewska, M., Mulas, A., Pistis, G., Steri, M., Danjou, F., et al. (2015) · Nature Genetics · doi:10.1038/ng.3368 · Cited by 376 · see citing works
Self-citationFast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia
Galinsky, K. J., Bhatia, G., Loh, P., Georgiev, S., Mukherjee, S., Patterson, N. J., & Price, A. L. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.12.022 · Cited by 357 · see citing works
Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr
Privé, F., Aschard, H., Ziyatdinov, A., & Blum, M. G. B. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty185 · Cited by 371 · see citing works
Sohail, M., Maier, R. M., Ganna, A., Bloemendal, A., Martin, A. R., Turchin, M. C., Chiang, C. W., Hirschhorn, J., Daly, M. J., Patterson, N., et al. (2019) · eLife · doi:10.7554/elife.39702 · Cited by 359 · see citing works
Ascertainment Biases in SNP Chips Affect Measures of Population Divergence
Albrechtsen, A., Nielsen, F. C., & Nielsen, R. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq148 · Cited by 345 · see citing works
Privé, F., Aschard, H., Carmi, S., Folkersen, L., Hoggart, C. J., O’Reilly, P. F., & Vilhjálmsson, B. J. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.11.008 · Cited by 337 · see citing works
Evidence of widespread selection on standing variation in Europe at height-associated SNPs
Turchin, M. C., Chiang, C. W., Palmer, C. D., Sankararaman, S., Reich, D., Genetic Investigation of ANthropometric Traits (GIANT) Consortium, & Hirschhorn, J. N. (2012) · Nature Genetics · doi:10.1038/ng.2368 · Cited by 329 · 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-citationThe Pediatric Imaging, Neurocognition, and Genetics (PING) Data Repository
Jernigan, T. L., Brown, T. T., Hagler, D. J., Akshoomoff, N. A., Bartsch, H., Newman, E. R., Thompson, W. K., Bloss, C. S., Murray, S. S., Schork, N. J., et al. (2015) · NeuroImage · doi:10.1016/j.neuroimage.2015.04.057 · Cited by 281 · see citing works
Kehdy, F. S. G., Gouveia, M. H., Machado, M., Magalhães, W. C. S., Horimoto, A. R. V. R., Horta, B. L., MOREIRA, R. G., Leal, T. P., Scliar, M. O., Soares‐Souza, G. B., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1504447112 · Cited by 274 · see citing works
Atzmon, G., Hao, L., Pe'er, I., Velez, C., Pearlman, A., Palamara, P. F., Morrow, B., Friedman, E., Oddoux, C., Burns, E., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.04.015 · Cited by 260 · see citing works
Genomic Insights into the Ancestry and Demographic History of South America
Homburger, J. R., Moreno‐Estrada, A., Gignoux, C. R., Nelson, D., Sánchez, E., Ortiz-Tello, P. A., Pons‐Estel, B. A., Acevedo‐Vásquez, E. M., Miranda, P., Langefeld, C. D., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005602 · Cited by 258 · see citing works
Self-citationThe History of African Gene Flow into Southern Europeans, Levantines, and Jews
Moorjani, P., Patterson, N. J., Hirschhorn, J. N., Keinan, A., Hao, L., Atzmon, G., Burns, E. R., D, H. O. M., Price, A. L., & Reich, D. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001373 · Cited by 240 · see citing works
UMAP reveals cryptic population structure and phenotype heterogeneity in large genomic cohorts
Diaz-Papkovich, A., Anderson-Trocmé, L., Ben-Eghan, C., & Gravel, S. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008432 · Cited by 231 · see citing works
Maier, R., Moser, G., Chen, G., Ripke, S., Absher, D., Agartz, I., Akil, H., D, F. A. M., Andreassen, O. A., Anjorin, A., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.12.006 · Cited by 227 · see citing works
Nicoletti, P., Aithal, G. P., Bjornsson, E. S., Andrade, R. J., Sawle, A., Arrese, M. A., Barnhart, H. X., Bondon‐Guitton, E., Hayashi, P. H., Bessone, F., et al. (2016) · Gastroenterology · doi:10.1053/j.gastro.2016.12.016 · Cited by 227 · see citing works
Self-citationLocal PCA Shows How the Effect of Population Structure Differs Along the Genome
Li, H., & Ralph, P. L. (2018) · Genetics · doi:10.1534/genetics.118.301747 · Cited by 210 · see citing works
Gene flow from North Africa contributes to differential human genetic diversity in southern Europe
Botigué, L. R., Henn, B. M., Gravel, S., Maples, B. K., Gignoux, C. R., Corona, E., Atzmon, G., Burns, E., Ostrer, H., Flores, C., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1306223110 · Cited by 199 · see citing works
Self-citationThe NIH Toolbox Cognition Battery: Results from a Large Normative Developmental Sample (PING)
Akshoomoff, N., Newman, E., Thompson, W., McCabe, C. J., Bloss, C., Chang, L., Amaral, D., Casey, B. J., Ernst, T., Frazier, J., et al. (2013) · Neuropsychology · doi:10.1037/neu0000001 · Cited by 206 · see citing works
Understanding 6th-century barbarian social organization and migration through paleogenomics
Amorim, C. E. G., Vai, S., Posth, C., Modi, A., Koncz, I., Hakenbeck, S. E., Rocca, M. C. L., Mende, B. G., Bobo, D., Pohl, W., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06024-4 · Cited by 195 · see citing works
Spatial patterns of variation due to natural selection in humans
Novembre, J., & Di Rienzo, A. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2632 · Cited by 205 · see citing works
Self-citationGenomic and geographic distribution of SNP-defined runs of homozygosity in Europeans
出口, 保., Lu, T. T., Kayser, M., & Krawczak, M. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq198 · Cited by 188 · see citing works
Duforet-Frebourg, N., Luu, K., Laval, G., Bazin, É., & Blum, M. G. B. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv334 · Cited by 182 · see citing works
Kidd, J. R., Friedlaender, F. R., Speed, W. C., PAKSTIS, A. J., Vega, F. M. D. L., & Kídd, K. K. (2011) · Investigative Genetics · doi:10.1186/2041-2223-2-1 · Cited by 184 · see citing works
Slavov, G. T., DiFazio, S. P., Martin, J., Schackwitz, W., Muchero, W., Rodgers‐Melnick, E., Lipphardt, M. F., Pennacchio, C., Hellsten, U., Pennacchio, L. A., et al. (2012) · New Phytologist · doi:10.1111/j.1469-8137.2012.04258.x · Cited by 175 · see citing works
A female Viking warrior confirmed by genomics
Hedenstierna‐Jonson, C., Kjellström, A., Zachrisson, T., Krzewińska, M., Sobrado, V., Price, N. S., Günther, T., Jakobsson, M., Götherström, A., & Storå, J. (2017) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23308 · Cited by 164 · see citing works
Auton, A., Bryc, K., Boyko, A. R., Lohmueller, K. E., Novembre, J., Reynolds, A., Indap, A. R., Wright, M. H., Degenhardt, J. D., Gutenkunst, R. N., et al. (2009) · Genome Research · doi:10.1101/gr.088898.108 · Cited by 164 · see citing works
Self-citationGenome-Wide Association Study Link Novel Loci to Endometriosis
Albertsen, H. M., Chettier, R., Farrington, P., & Ward, K. (2013) · PLoS ONE · doi:10.1371/journal.pone.0058257 · Cited by 161 · see citing works
Engelhardt, B. E., & Stephens, M. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001117 · Cited by 160 · see citing works
Elhaik, E., Tatarinova, T. V., Chebotarov, D., Piras, I. S., Calò, C. M., Montis, A. D., Atzori, M., Marini, M., Tofanelli, S., Francalacci, P., et al. (2014) · Nature Communications · doi:10.1038/ncomms4513 · Cited by 147 · see citing works
Evolutionary Patterns and Processes: Lessons from Ancient DNA
Leonardi, M., Librado, P., Sarkissian, C. S. I. D., Schubert, M., Alfarhan, A., Alquraishi, S. A., Al‐Rasheid, K. A. S., Gamba, C., Willerslev, E., & Orlando, L. (2016) · Systematic Biology · doi:10.1093/sysbio/syw059 · Cited by 151 · see citing works
A model-based approach for analysis of spatial structure in genetic data
Yang, W.-Y., Novembre, J., Eskin, E., & Halperin, E. (2012) · Nature Genetics · doi:10.1038/ng.2285 · Cited by 148 · see citing works
Self-citationHeterogeneity in Genetic Admixture across Different Regions of Argentina
Avena, S. A., Vía, M., Ziv, E., Pérez‐Stable, E. J., Gignoux, C. R., Dejean, C. B., Huntsman, S., Torres-Mejı́a, G., Dutil, J., Matta, J. L., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034695 · Cited by 145 · see citing works
Veeramah, K. R., Rott, A., Groß, M., van Dorp, L., López, S., Kirsanow, K., Sell, C., Blöcher, J., Wegmann, D., Link, V., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1719880115 · Cited by 141 · see citing works
Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence
Dewey, F. E., Chen, R., Cordero, S. P., Ormond, K. E., Caleshu, C. A., Karczewski, K. J., Whirl‐Carrillo, M., Wheeler, M. T., Dudley, J. T., Byrnes, J., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002280 · Cited by 140 · see citing works
Self-citationAncestry estimation and control of population stratification for sequence-based association studies
Study, T. F., Wang, C., Zhan, X., Bragg‐Gresham, J. L., Kang, H. M., Stambolian, D. E., Chew, E. Y., Branham, K. E. H., Heckenlively, J. R., Fulton, R. S., et al. (2014) · Nature Genetics · doi:10.1038/ng.2924 · Cited by 133 · see citing works
Population Genetic Structure of the People of Qatar
Hunter-Zinck, H., Musharoff, S. A., Salit, J., Alali, K., Chouchane, L., Gohar, A., Matthews, R., Butler, M. W., Fuller, J. A., Hackett, N. R., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.05.018 · Cited by 127 · see citing works
Wang, C., Zöllner, S. K., & Rosenberg, N. A. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002886 · Cited by 122 · see citing works
Limited contribution of common genetic variants to risk for liver injury due to a variety of drugs
Urban, T. J., Shen, Y., Stolz, A., Chalasani, N., Fontana, R. J., Rochon, J., Ge, D., Shianna, K. V., Daly, A. K., Lucena, M. I., et al. (2012) · Pharmacogenetics and Genomics · doi:10.1097/fpc.0b013e3283589a76 · Cited by 117 · see citing works
Self-citationDiscovering genetic ancestry using spectral graph theory
Lee, A. B., Luca, D., Klei, L., Devlin, B., & Roeder, K. (2010) · Genetic Epidemiology · doi:10.1002/gepi.20434 · Cited by 108 · see citing works
“We conclude with a presentation of the new algorithm, which is illustrated via an analysis of the POPRES data [Nelson et al., 2008].”
BackgroundMethodInfluentialGenomewide Pharmacogenetics of Bisphosphonate-Induced Osteonecrosis of the Jaw: The Role of RBMS3
Nicoletti, P., Cartsos, V. M., Palaska, P. K., Shen, Y., Floratos, A., & Zavras, A. I. (2012) · The Oncologist · doi:10.1634/theoncologist.2011-0202 · Cited by 111 · see citing works
Estimating recent migration and population-size surfaces
Al-Asadi, H., Petkova, D., Stephens, M., & Novembre, J. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1007908 · Cited by 105 · see citing works
Self-citationBycroft, C., Fernández–Rozadilla, C., Ruíz-Ponte, C., Quintela, I., Carracedo, Á., Donnelly, P., & Myers, S. (2019) · Nature Communications · doi:10.1038/s41467-018-08272-w · Cited by 97 · see citing works
Veeramah, K. R., Tönjes, A., Kovacs, P. L., Gross, A., Wegmann, D., Geary, P. J., Gašperíková, D., Klimeś, I., Scholz, M. R., Novembre, J., et al. (2011) · European Journal of Human Genetics · doi:10.1038/ejhg.2011.65 · Cited by 100 · see citing works
Self-citationFine-scaled human genetic structure revealed by SNP microarraysPreprint
Xing, J., Watkins, W. S., Witherspoon, D. J., Zhang, Y., Guthery, S. L., THARA, R., Mowry, B. J., Bulayeva, K., Weiss, R. B., & Jorde, L. B. (2009) · Genome Research · doi:10.1101/gr.085589.108 · Cited by 93 · see citing works
Corona, E., Chen, R., Sikora, M., Morgan, A. A., Patel, C. J., Ramesh, A., Bustamante, C. D., & Butte, A. J. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003447 · Cited by 92 · see citing works
Self-citationAncestry informative markers for fine-scale individual assignment to worldwide populations
Paschou, P., Lewis, J., Javed, A., & Petros Drineas, B. (2010) · Journal of Medical Genetics · doi:10.1136/jmg.2010.078212 · Cited by 93 · see citing works
Dietary adaptation of FADS genes in Europe varied across time and geography
Ye, K., Gao, F., Wang, D., Bar‐Yosef, O., & Keinan, A. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0167 · Cited by 87 · see citing works
Perspectives on Human Population Structure at the Cusp of the Sequencing Era
Novembre, J., & Ramachandran, S. (2011) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090810-183123 · Cited by 86 · see citing works
Self-citationLowering industry firewalls: pre-competitive informatics initiatives in drug discovery
Barnes, M. R., Harland, L., Foord, S. M., Hall, M. D., Dix, I., Thomas, S., Williams-Jones, B. I., & Brouwer, C. (2009) · Nature Reviews Drug Discovery · doi:10.1038/nrd2944 · Cited by 84 · see citing works
Neutral genomic regions refine models of recent rapid human population growth
Gazave, É., Ma, L., Chang, D., Coventry, A., Gao, F., Muzny, D. M., Boerwinkle, E., Gibbs, R. A., Sing, C. F., Clark, A. G., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1310398110 · Cited by 79 · see citing works
Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland
Furtwängler, A., Rohrlach, A. B., Lamnidis, T. C., Papac, L., Neumann, G. U., Siebke, I., Reiter, E., Steuri, N., Hald, J., Denaire, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15560-x · Cited by 80 · see citing works
Nicoletti, P., Werk, A. N., Sawle, A., Shen, Y., Urban, T. J., Coulthard, S. A., Bjornsson, E. S., Cascorbi, I., Floratos, A., Stammschulte, T., et al. (2016) · Pharmacogenetics and Genomics · doi:10.1097/fpc.0000000000000209 · Cited by 79 · see citing works
Self-citationAgrawal, A., Ali, A., & Boyd, S. (2021) · Foundations and Trends® in Machine Learning · doi:10.1561/2200000090 · Cited by 78 · see citing works
Chen, G., Lee, S., Zhu, Z.-X., Benyamin, B., & Robinson, M. R. (2016) · Heredity · doi:10.1038/hdy.2016.25 · Cited by 75 · see citing works
Schaid, D. J., Spraggs, C. F., McDonnell, S. K., Parham, L. R., Cox, C. J., Ejlertsen, B., Finkelstein, D. M., Rappold, E., Curran, J., Cardon, L. R., et al. (2014) · Journal of Clinical Oncology · doi:10.1200/jco.2013.52.9867 · Cited by 74 · see citing works
Twenty years of the Human Genome Diversity Project
Aneli, S., Birolo, G., & Matullo, G. (2022) · Green Energy and Sustainability · doi:10.47248/hpgg2202040005 · Cited by 72 · see citing works
Facial recognition from DNA using face-to-DNA classifiers
Sero, D., Zaidi, A. A., Li, J., White, J. D., Zarzar, T. G., Marazita, M. L., Weinberg, S. M., Suetens, P., Vandermeulen, D., Wagner, J. K., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10617-y · Cited by 72 · see citing works
Reconstructing Roma History from Genome-Wide Data
Moorjani, P., Patterson, N. J., Loh, P., Lipson, M., Kisfali, P., Melegh, B., von Bonin, M., Kádaši, Ľ., Rieß, O., Berger, B., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0058633 · Cited by 69 · see citing works
Shared Genetic Risk Factors Across Carbamazepine‐Induced Hypersensitivity Reactions
Nicoletti, P., Barrett, S., McEvoy, L., Daly, A. K., Aithal, G. P., Lucena, M. I., Andrade, R. J., Wadelius, M., Hallberg, P., Stephens, C. M., et al. (2019) · Clinical Pharmacology & Therapeutics · doi:10.1002/cpt.1493 · Cited by 69 · see citing works
Self-citationBansal, V., & Libiger, O. (2015) · BMC Bioinformatics · doi:10.1186/s12859-014-0418-7 · Cited by 64 · see citing works
Behr, E. R., Ritchie, M. D., Tanaka, T., Kääb, S., Crawford, D. C., Nicoletti, P., Floratos, A., Sinner, M. F., Kannankeril, P. J., Wilde, A. A. M., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078511 · Cited by 66 · see citing works
Reconstructing human population history from dental phenotypes
Rathmann, H., Reyes‐Centeno, H., Ghirotto, S., Creanza, N., Hanihara, T., & Harvati, K. (2017) · Scientific Reports · doi:10.1038/s41598-017-12621-y · Cited by 67 · see citing works
Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks
Ringbauer, H., Coop, G., & Barton, N. (2017) · Genetics · doi:10.1534/genetics.116.196220 · Cited by 66 · see citing works
Dai, C. L., Vazifeh, M. M., Yeang, C., Combes, R. T. D., Wells, R. S., Vilar, M. G., Daly, M. J., Ratti, C., & Martin, A. R. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.02.002 · Cited by 59 · see citing works
Assessing and managing risk when sharing aggregate genetic variant data
Craig, D. W., Goor, R. M., Wang, Z., Paschall, J. E., Ostell, J., Feolo, M., Sherry, S. T., & Manolio, T. A. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3067 · Cited by 56 · see citing works
Indian Siddis: African Descendants with Indian Admixture
Shah, A. M., Tamang, R., Moorjani, P., Rani, D. S., Govindaraj, P., Kulkarni, G. D., Bhattacharya, T., Mustak, M. S., Bhaskar, L. V., Reddy, A. G., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.05.030 · Cited by 59 · see citing works
Effects of Sample Selection Bias on the Accuracy of Population Structure and Ancestry Inference
Shringarpure, S., & Xing, E. P. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.007633 · Cited by 58 · see citing works
Fast admixture analysis and population tree estimation for SNP and NGS data
Cheng, J. Y., Mailund, T., & Nielsen, R. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx098 · Cited by 58 · see citing works
Genetic Landscapes Reveal How Human Genetic Diversity Aligns with Geography
Peter, B. M., Petkova, D., & Novembre, J. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz280 · Cited by 61 · see citing works
Self-citationNationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity
Athanasiadis, G. I., Cheng, J. Y., Vilhjálmsson, B. J., Jørgensen, F. G., Als, T. D., Hellard, S. L., Espeseth, T., Sullivan, P. F., Hultman, C. M., Kjærgaard, P. C., et al. (2016) · Genetics · doi:10.1534/genetics.116.189241 · Cited by 52 · see citing works
Galinsky, K. J., Loh, P., Mallick, S., Patterson, N. J., & Price, A. L. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.09.014 · Cited by 51 · see citing works
Li, Q. S., Cheng, P. Y., Favis, R., Wickenden, A., Romano, G. J., & Wang, H. (2015) · Clinical Journal of Pain · doi:10.1097/ajp.0000000000000205 · Cited by 54 · see citing works
Choudhury, A., Hazelhurst, S., Meintjes, A., Oduaran, O. H., Aron, S., Gamieldien, J., Dashti, M. J. S., Mulder, N., Tiffin, N., & Ramsay, M. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-437 · Cited by 55 · see citing works
Genome-wide Insights into the Patterns and Determinants of Fine-Scale Population Structure in Humans
Biswas, S., Scheinfeldt, L., & Akey, J. M. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.04.015 · Cited by 52 · see citing works
Mine, Yours, Ours? Sharing Data on Human Genetic Variation
Milia, N., Congiu, A., Anagnostou, P., Montinaro, F., Capocasa, M., Sanna, E., & Destro‐Bisol, G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037552 · Cited by 48 · see citing works
Luisi, P., García, A., Berros, J. M., Motti, J. M. B., Demarchi, D. A., Alfaro, E., Aquilano, E., Argüelles, C. F., Avena, S. A., Bailliet, G., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0233808 · Cited by 55 · see citing works
Influence of Admixture and Paleolithic Range Contractions on Current European Diversity Gradients
Arenas, M., François, O., Currat, M., Ray, N., & Excoffier, L. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mss203 · Cited by 50 · see citing works
Across language families: Genome diversity mirrors linguistic variation within E urope
Longobardi, G., Ghirotto, S., Guardiano, C., Tassi, F., Benazzo, A., Ceolin, A., & Barbujani, G. (2015) · American Journal of Physical Anthropology · doi:10.1002/ajpa.22758 · Cited by 50 · see citing works
Principals about principal components in statistical genetics
Abegaz, F., Chaichoompu, K., Génin, E., Fardo, D. W., König, I. R., John, J. M., & Steen, K. V. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby081 · Cited by 50 · see citing works
Convex Clustering: An Attractive Alternative to Hierarchical Clustering
Chen, G. K., Chi, E. C., Rañola, J. M. O., & Lange, K. L. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004228 · Cited by 48 · see citing works
ArunKumar, G., Soria‐Hernanz, D. F., Kavitha, V. J., Arun, V. S., Syama, A., Ashokan, K. S., Gandhirajan, K. T., Vijayakumar, K., Narayanan, M., Jayalakshmi, M., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0050269 · Cited by 48 · see citing works
- Authors
- 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., Vollenweider, P., Oksenberg, J. R., Hauser, S. L., Stirnadel, H. A., Kooner, J. S., Chambers, J. C., Jones, B., Mooser, V., Bustamante, C. D., Roses, A. D., Burns, D. K., Ehm, M. G., & Lai, E. H.
- Affiliations
- GlaxoSmithKline (United States) (US)
- Cornell University (US)
- University of California, Los Angeles (US)
- Centre Hospitalier Universitaire Vaudois (CH)
- University of California, San Francisco (US)
- Imperial College London (GB)
- Corresponding author
- Nelson, Matthew R.
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2008-09
- Volume
- 83
- Issue
- 3
- Pages
- 347-358
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC2556436
- OpenAlex
- W1981638214
- Cited by
- 293
- References
- 36
- Citations by year
- 2026: 3 · 2025: 8 · 2024: 6 · 2023: 17 · 2022: 7 · 2021: 2 · 2020: 10 · 2019: 13 · 2018: 47 · 2017: 13 · 2016: 17 · 2015: 25 · 2014: 21 · 2013: 22 · 2012: 27
- FWCI
- 10.47
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- IRIS (submittedVersion)
- SERVAL (Université de Lausanne) (submittedVersion)
- Funders
- GlaxoSmithKline
- Tri-Service General Hospital
- National Institutes of Health
- University of California, San Francisco
- National Institute of General Medical Sciences (R01GM083606)
- National Institute of Neurological Disorders and Stroke (R01NS046297)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Race, Genetics, and Society
- Keywords
- single nucleotide polymorphisms, genetic ancestry, population structure, genetic matching, abacavir hypersensitivity, pharmacogenetics, disease genetics, dbGaP
- MeSH terms
- Abacavir, Drug Hypersensitivity, Female, Genetics, Population, Genotype, Humans, Male, Pharmacogenetics, Dideoxynucleosides, Genome, Human, Case-Control Studies, Polymorphism, Single Nucleotide, Databases, Genetic, Population Groups, White People
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
