The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Fast and Efficient Estimation of Individual Ancestry Coefficients
Open accessAbstract
Inference of individual ancestry coefficients, which is important for population genetic and association studies, is commonly performed using computer-intensive likelihood algorithms. With the availability of large population genomic data sets, fast versions of likelihood algorithms have attracted considerable attention. Reducing the computational burden of estimation algorithms remains, however, a major challenge. Here, we present a fast and efficient method for estimating individual ancestry coefficients based on sparse nonnegative matrix factorization algorithms. We implemented our method in the computer program sNMF and applied it to human and plant data sets. The performances of sNMF were then compared to the likelihood algorithm implemented in the computer program ADMIXTURE. Without loss of accuracy, sNMF computed estimates of ancestry coefficients with runtimes ∼10–30 times shorter than those of ADMIXTURE.
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Citations
Cites
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
Population Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280
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
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
Atwell, S., Huang, Y. S., Vilhjálmsson, B. J., Willems, G., Horton, M., Li, Y., Meng, D., Platt, A., Tarone, A. M., Hu, T. T., et al. (2010) · Nature · doi:10.1038/nature08800 · Cited by 1,780
Inference of Population Structure using Dense Haplotype Data
Lawson, D. J., Hellenthal, G., Myers, S., & Falush, D. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002453 · Cited by 1,188
The effects of human population structure on large genetic association studies
Marchini, J., Cardon, L. R., Phillips, M. S., & Donnelly, P. (2004) · Nature Genetics · doi:10.1038/ng1337 · Cited by 869
Cited by
Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data
Meisner, J., & Albrechtsen, A. (2018) · Genetics · doi:10.1534/genetics.118.301336 · Cited by 673
A genomic history of Aboriginal Australia
Malaspinas, A.-S., Westaway, M. C., Muller, C., Sousa, V. C., Lao, O., Alves, I., Bergström, A., Athanasiadis, G., Cheng, J. Y., Crawford, J. E., et al. (2016) · Nature · doi:10.1038/nature18299 · Cited by 650
Privé, F., Aschard, H., Carmi, S., Folkersen, L., Hoggart, C., O’Reilly, P. F., & Vilhjálmsson, B. J. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.11.008 · Cited by 375
Convergent genomic signatures of domestication in sheep and goats
Alberto, F. J., Boyer, F., Orozco-terWengel, P., Streeter, I., Servin, B., de Villemereuil, P., Benjelloun, B., Librado, P., Biscarini, F., Colli, L., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03206-y · Cited by 339
The rise and fall of African rice cultivation revealed by analysis of 246 new genomes
Cubry, P., Tranchant-Dubreuil, C., Thuillet, A.-C., Monat, C., Ndjiondjop, M.-N., Labadie, K., Cruaud, C., Engelen, S., Scarcelli, N., Rhoné, B., et al. (2018) · Current Biology · doi:10.1016/j.cub.2018.05.066 · Cited by 142
Self-citationSystematics and conservation of an endemic radiation of Accipiter hawks in the Caribbean islands
Catanach, T. A., Halley, M. R., Allen, J. M., Johnson, J. A., Thorstrom, R., Palhano, S., Poor Thunder, C., Gallardo, J. C., & Weckstein, J. D. (2021) · Ornithology · doi:10.1093/ornithology/ukab041 · Cited by 12
Metadata
- Authors
- Frichot, E., Mathieu, F., Trouillon, T., Bouchard, G., & François, O.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-04-01
- Volume
- 196
- Issue
- 4
- Pages
- 973-983
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2032456334
- Cited by
- 931
- References
- 6
- FWCI
- 13.47
- Type
- journal article
- Language
- en
- Open access
- green
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